Automated Quantitative Analysis Research Articles

Abstract 3623: Quantifying pharmacodynamic markers of radioligand therapies in tumor by multiplex immunofluorescence and automated quantitative analysis (AQUA) algorithms

Abstract Purpose: Due to profound clinical successes observed with radioligand therapies (RLT) across multiple cancers coupled with advances in drug handling and delivery logistics recently, clinical trials investigating RLTs are on the rise. Ionizing radiation produced by radioisotopes linked to antibodies causes double-stranded breaks either directly or via generation of reactive oxygen species. This type of DNA damage is associated with an increase in proteins mediating cell cycle arrest (e.g., p21/CIP1) and repairing damaged DNA (e.g., CHK2 and γH2Ax). Additionally, proliferating cells (identifiable by Ki67) are most susceptible to ionizing radiation as DNA is exposed during the mitotic phase of the cell cycle. We incorporated these biologically verified markers into a multiplexed fluorescence immunohistochemistry (mFIHC) assay for robust quantitation of the pharmacodynamic activity of RLTs and gain insights into the DNA damage response in on-treatment tumor core biopsies. Study Design: We designed a novel mFIHC assay incorporating antibodies to p21, pCHK2, γH2Ax, Ki67, CK to quantitatively characterize DNA damage across five tumor indications of commercially available ovarian cancer, colorectal cancer, gastric cancer, endometrial (uterine) cancer, and breast cancer formalin-fixed paraffin-embedded (FFPE) tissue blocks. We successfully validated this mFIHC assay using automated staining (Bond RX), imaging (PhenoImager HT), and combined with hypothesis-driven spatial profiling algorithms (e.g., AQUA Technology). Results: Sensitivity and specificity were confirmed on known positive and negative controls. Reproducibility and precision were observed across instruments, operators, and independent experiments for all markers The frequency of p21 ranged from 5% - 8%, pCHK2 from 3% - 36%, pH2Ax from 0% - 8%, Ki67 from 4% - 61%, and CK cells ranged from 25% to 87%. Over 56 unique parameters were evaluated. The prevalence of p21, pCHK2, and γH2Ax ranged from 0% to >30% across five tumor indications tested and were highly concordant. Conclusion: The validated mFIHC assay examines the expression of proteins mediating cell cycle arrest and DNA damage in tumor and stromal cells. This panel may be used to further understand the complexity of DNA damage response pathways in tumor and non-tumor areas in the context of RLT clinical trials. Citation Format: James Santos, Virginia Nyanchama, Vincent Romanet, Ernesta Dammassa, Lisa Kattenhorn, Ying Huang, Jimmie Lim, Xun Li, James Deeds, Lori Iaconis, Emmanuel Pacia, Margaret McLaughlin, Naveen Dakappagari, Jennifer Bordeaux. Quantifying pharmacodynamic markers of radioligand therapies in tumor by multiplex immunofluorescence and automated quantitative analysis (AQUA) algorithms [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3623.

Subsets of interferon signaling and response to immune checkpoint blockade.

9522 Background: Interferon (IFN) signaling in tumors is critical for both response and resistance to immune checkpoint inhibitors (ICI). While PD-L1 is an approved biomarker for ICI response in some cancers, most have no approved biomarkers for ICI response. Further, there are no clinical strategies to predict IFN sensitive vs resistant states. We hypothesized that distinct patterns of IFN signaling in melanoma, including STAT1 (precursor to IFN signaling), phosphorylated STAT1 (pSTAT1, marker of active IFN signaling), and PD-L1 (canonical inhibitory output), are associated with response or resistance to ICI. Methods: Samples from 2 tissue microarrays of 97 patients total with metastatic melanoma who received ICI from 2011-2017 were randomized into discovery [D] or validation [V] cohorts. Multiplexed immunofluorescent microscopy was used to assess STAT1, pSTAT1, and PD-L1. 54 tumors were assessed for CD3. Signals were quantified via AQUA (Automated Quantitative Analysis). High vs low signals were defined around the discovery cohort median AQUA scores. Treatment response was assessed using RECIST, and 3-year survival was analyzed. For in vitro studies, 4 human melanoma cell lines were stimulated with IFNγ/β, and Western blots were performed for STAT1, pSTAT1, and PD-L1. Results: Median follow up time was 20.2 mos (range 0.9-95.4 mos). Higher overall histospot, tumor, and nuclear STAT1 were in responders (CR/PR/SD > 6 mos) compared to non-responders (SD < 6 mos/PD, histospot p = 0.029 [D] and 0.040 [V]) and were associated with improved survival (histospot HR 0.25 [95% CI 0.08-0.76] p = 0.015 [D]; HR 0.32 [95% CI 0.12-0.84] p = 0.021 [V]). PD-L1 and pSTAT1 did not validate as associated with ICI response/survival. While many tumors had concordant high/low STAT1, pSTAT1, and PD-L1, many also had a discordant STAT1 or PD-L1 predominance. To assess the basis of this discordance, we performed IFN stimulation and Western blots of melanoma cell lines. IFNβ upregulated STAT1 greater than PD-L1 in both acute and chronic settings (p < 0.001 and < 0.001), while chronic IFNγ upregulated PD-L1 compared to the acute setting (p = 0.039) but not STAT1 (p = 0.105). Therefore, we hypothesized patients with discordant STAT1 and PD-L1 expression may have differential responses to ICI. In the overall cohort, STAT1highPD-L1high tumors (IFN engaged) were associated with improved survival compared to STAT1lowPD-L1low tumors (IFN low, HR 0.28 [95% CI 0.11-0.70] p = 0.007). Interestingly, STAT1highPD-L1low tumors were associated with improved survival compared to STAT1lowPD-L1high tumors (HR 0.28 [95% CI 0.08-0.94] p = 0.04). Accordingly, STAT1highPD-L1high and STAT1highPD-L1low tumors had greater CD3 AQUA scores compared to STAT1lowPD-L1low tumors (p < 0.001 and p = 0.018 respectively). Conclusions: Combined STAT1 and PD-L1 expression patterns may better predict melanoma response to ICI and provide insight into IFN sensitive versus resistant states.

Abstract 3445: Immune cells infiltration and activation are higher in breast cancers resistant to antiestrogen therapy

Abstract We investigated the tumor microenvironment (TME) in estrogen receptor positive (ER+) primary breast cancers from stage I-III patients treated with estrogen deprivation (ED, induced with letrozole) for 10-21 days. We used primary breast cancer biopsies, collected from 198 patients, to assess tumor-infiltrating lymphocytes (TILs), transcriptomic profiles, and TME composition. Diagnostic biopsy and surgical on-treatment tumor specimens were collected; Ki67, ERα, PR, and HER2 expression were measured using automated quantitative analysis (AQUA). Tumors were categorized as estrogen deprivation-sensitive (ED-S) or -resistant (ED-R) based on the natural log (ln) of the Ki67 score (ln ≤1.0 or ≤2.7% Ki67+ cells vs. ln ≥2.0 or ≥7.4%, respectively) in the on-treatment (surgical) biopsy. Scoring of stromal (s)TILs, using hematoxylin and eosin staining of on-treatment specimens, revealed that sTILs were elevated in ED-R compared to ED-S tumors (p<0.0001). We next constructed tissue microarrays (TMAs) of on-treatment tumor sections and performed cyclic immunofluorescence (CyCIF) with 38 antibodies, including markers of hormone receptors, immune cells, signaling pathways, proliferation, DAPI (nuclei), and others. We then segmented single cells from each tumor core and designated them as immune, cancer, or stromal cells based on expression of a set of markers. Briefly, cells that stained strongly for CD45 (leukocyte marker), and/or CD4 (T lymphocyte marker), or CD68 (macrophage marker) were considered immune cells. CD45/CD4/CD68-negative cells were categorized as tumor, if E-cadherin and/or cytokeratin-positive, or stromal cells, if -negative. To investigate the TME composition, we next assessed cell specific spatial enrichment by quantifying the expression of immune markers in the area immediately adjacent to each tumor cell. Relative to ED-S, ED-R samples exhibited higher CD45+ cells (p<0.0001) and higher CD8+ T cells (p=0.0329), while CD4+ T cells showed no difference. Conversely, immune-suppressive T-reg (CD4+FOXP3+) cells were enriched in the ED-S samples (p=0.0004). In addition, PD1, a marker for T cell exhaustion, was higher in the ED-S group (p=0.0004), as were CD68+ cells (p<0.0001). To confirm and expand upon these findings, RNA-sequencing was performed on the on-treatment tumor sections. Gene set enrichment analysis of hallmark gene signatures revealed that immune-related gene sets, such as “IFNα response”, “IFNɣ response”, “allograft rejection”, and “inflammatory response” were enriched in ED-R vs. ED-S tumors. In summary, our study shows that activated anti-tumor immune cells are enriched in the TME of ER+ breast tumors resistant to estrogen deprivation, whereas ED-sensitive tumors show a more immunosuppressed or immune cold milieu. These data suggest a potential causal link between antiestrogen treatment and modulation of antitumor immunity in ER+ breast cancers. Citation Format: Fabiana Napolitano, Dhivya R. Sudhan, Yunguan Wang, Paula I. González-Ericsson, Luigi Formisano, Kyung-Min Lee, Chang-Ching Lin, María Rosario Chica-Parrado, Hongli Ma, Nathaniel Evans, Alberto Servetto, Saurabh Mendiratta, Spencer Barnes, Yisheng V. Fang, Justin M. Balko, Gordon B. Mills, Marilyne Labrie, Ariella B. Hanker, Carlos L. Arteaga. Immune cells infiltration and activation are higher in breast cancers resistant to antiestrogen therapy [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 3445.

Abstract 1725: Tissue-based biomarker analysis of DLBCL using multiplex immunofluorescence AQUA (Automated Quantitative Analysis) algorithms

Abstract Purpose: Deeper understanding of immune landscape of DLBCL tumor microenvironment is critical for exploration and development of next generation immunotherapies. Although conventional immunohistochemical (IHC) analysis can provide information on the immune landscape or target expression, it is generally limited to single marker analysis. Advantages of multiplex fluorescence IHC (mFIHC) include the ability to assess different cell types, their spatial relationship as well as variable antigen expression on tumor cells. As such, we developed quantitative mFIHC panels using AQUA® (Automated Quantitative Analysis) technology to evaluate T and B cell populations and their functional status to generate detailed spatial information of immune checkpoint (IC) markers. mFIHC combined with hypothesis driven spatial profiling algorithms (e.g., AQUA Technology) were found to provide the most powerful predictors of immunotherapies in a systematic meta-analyses of over 8000 patients treated with PD1/L1 pathway blockers (Lu et al., JAMA Oncol 2019). Implementation of mFIHC coupled with robust image analysis may provide great insight into DLBCL immune surveillance, mechanism of resistance and patient stratification. Study Design: We designed two novel mFIHC assays to (1) characterize various B cell populations (CD19, CD20, CD22, PAX5, CD3, TIM3), and (2) evaluate T cell functional status (CD8, Granzyme B, PD1, PDL1, TIM3, Tumor). We successfully validated clinical grade mFIHC assays using automated staining (Leica Bond RX), imaging (Vectra Polaris) and analyses (AQUA Technology) workflow. Results: Sensitivity, accuracy and specificity were confirmed for all mFIHC assays on known positive and negative controls. Excellent reproducibility (less than 35% CV) and precision were observed across instruments, operators and independent experiments for all markers. Between these two panels, over 200 unique parameters were evaluated. The prevalence of CD19, CD20, CD22, and PAX5 ranged from 30% to >90% positive for the DLBCL samples tested and were overall highly concordant with each other. Conclusion: The validated mFIHC assays examine B cell antigen expression in DLBCL and their interaction with CD3+ T cells and further characterize CD8+ T cells and immune checkpoint expression. These panels may be used to further understand the complex immune cell and tumor cell spatial biology in the context of clinical trials. Citation Format: James Paul Santos, Jacob Levy, Kristen Ruma, David Yang, Steve Woolfenden, Jimmie Lim, Xun Li, Ariana Valencia, James Deeds, Ramu Thiruvamoor, Xin Li, Emmanuel Pacia, Margaret McLaughlin, Thai Tran, Sarah Choi, Jennifer Bordeaux. Tissue-based biomarker analysis of DLBCL using multiplex immunofluorescence AQUA (Automated Quantitative Analysis) algorithms [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1725.

Clinical Significance of PD-1 and PD-L1 Expression and Ongoing Interaction in the Tumor Microenvironment in Diffuse Large B Cell Lymphoma (DLBCL) Treated with R-CHOP

Background: PD-1 blockade has demonstrated antitumor activity in diffuse large B-cell lymphoma (DLBCL). In order to select patients who are more likely to respond to PD-1 blockade, predictive biomarkers are being intensively pursued. PD-1 and PD-L1 expression in DLBCL treated with R-CHOP as standard-of-care has been examined in several studies. However, only overall PD-1+ cells but not T-cell specific PD-1 expression have been quantitated, and results of the prognostic significance of PD-L1 expression have been inconsistent in DLBCL patients. Whether ongoing PD-1/PD-L1 interaction in tumors contributes to the adverse prognostic effect of PD-1 and PD-L1 expression is unknown.Patients and Methods: Tissue microarray (TMA) sections ofdiagnostic samples from 414 patients with de novo DLBCL treated with R-CHOP were fluorescently stained with CD3 (T cell marker), PD-1, and PD-L1. Positive cells and PD-1/PD-L1 interaction were quantitatively assessed by the Automated Quantitative Analysis (AQUA) algorithms. To characterize PD-1/PD-L1 expression in each sample, CD3+, PD-1+, PD-L1+, and PD-1+CD3+ (double positive, i.e., PD-1+ T) cell numbers were divided by total nucleated cells (DAPI+) in the representative tumor areas. Ongoing PD-1/PD-L1 interactions were evaluated by the proximity of PD-1+ T cells to the PD-L1+ compartments and proportion of PD-1+ T cells co-localized with PD-L1, generating an interaction score for each sample. Biomarker expression and interaction scores were correlated with patient survival.Results: CD3+, PD-1+, PD-L1+, and PD-1+CD3+ cells were identified in 90%, 30%, 53%, and 18% of the cohort, respectively. The mean percentages of CD3+, PD-1+, PD-L1+, and PD-1+CD3+ cells in DLBCL tissues were 12.1%, 0.44%, 3.6%, and 0.19%, respectively. Activated B-cell-like DLBCL had a significantly higher mean percentage of PD-L1+ cells, but not PD-1+CD3+ cells, compared to germinal center B-cell-like DLBCL (p=0.0012). Three prognostic tiers were identified. Firstly, absence to very low percentage (0-3.5%) of tumor-infiltrating CD3+ T cells in the tissues was associated with poorer overall survival (OS) of DLBCL patients (p=0.028). CD3high DLBCL (>3.5% of all cells were CD3+) was associated with significantly higher percentages of PD-L1+ and PD-1+ cells (p<0.0001 and p=0.005, respectively). Secondly, in CD3high DLBCL, presence of PD-1+ T cells correlated with significantly poorer OS and progression-free survival (PFS) of patients (p=0.028 and p=0.0099, respectively). In contrast, presence/absence of PD-1+ non-T cells was not prognostic. Presence of PD-1+ T cells in CD3high DLBCL was associated with a higher mean percentage of PD-L1+ cells (p=0.019). However, PD-1/PD-L1 interaction scores did not add to the prognostic effect. This may suggest that phenotype of PD-1/PD-L1 interaction is not a biomarker to specify the immunosuppressive role of the PD-1/PD-L1 axis. Lastly, in CD3high DLBCL cases with PD-1−negative T cells, PD-L1 positivity correlated with significantly poorer OS and PFS of patients (p=0.0034 and p=0.0059, respectively), although PD-L1+ was not associated with non-T PD-1 expression either, suggesting PD-1−independent function of PD-L1. In the overall cohort, presence of PD-1+ T cells was associated with a trend of poorer PFS (p=0.079), whereas PD-L1 expression was not prognostic.Conclusions: PD-1 expression in T cells and lack of tumor-infiltrating CD3+ T cells are associated with significantly poorer survival of DLBCL patients. In addition, our data suggest that PD-1 can be a prognostic marker independent of PD-1/PD-L1 co-localization, and that PD-L1 has other PD-1-independent inhibitory functions. These results demonstrate the importance of both T-cell influx and antitumor function in prolonging the survival of DLBCL patients, and provide rationales for PD-1 blockade and immunotherapies activating T cell-mediated immune responses in DLBCL. DisclosuresTran:Genoptix, Inc: Employment. Adams:Navigate BioPhama Services, Inc: Employment. Roscoe:Navigate BioPhama Services, Inc: Employment. Hsi:Seattle Genetics: Consultancy, Honoraria, Speakers Bureau; Abbvie: Research Funding; Eli Lilly and Co.: Research Funding; Cellerant Therapeutics: Research Funding. Piris:Kura Oncology: Research Funding. Winter:Glaxo-Smith-Kline: Research Funding; Merck: Research Funding. Vaupel:Genoptix Laboratory: Employment. Dakappagari:Genoptix, Inc: Employment.

Impact of a randomized weight loss trial on breast tissue markers in breast cancer survivors.

e12501 Background: Weight loss interventions are effective approaches to reduce body weight and alter serum biomarkers in breast cancer survivors, however the impact on breast tissue biomarkers is unknown. The Lifestyle, Exercise and Nutrition (LEAN) study was a randomized trial designed to test the effect of a weight loss intervention on body composition and breast tissue and serum biomarkers. Methods: Fifity-one women with a BMI ³ 25.0 kg/m2 diagnosed with breast cancer, who had completed chemotherapy and/or radiation therapy were randomized to weight loss intervention or usual care. Breast tissue biopsies from the unaffected breast, fasting serum samples, and body composition were measured at baseline and 6-months. Ki67, insulin receptor (IR), CD68 and CD163 were measured by Automated Quantitative Analysis (AQUA) method. Mean baseline to 6-month changes were compared using ANCOVA adjusting for baseline values. Results: Pre- and post-intervention biopsies were conducted in 49 and 42 women respectively, with both pre- and post- epithelial tissue available from 25 women; epithelial tissue was unavailable in the remaining 66 women. Women were 56.8 ± 8.9 years old, diagnosed 3.3 + 3.8 years prior, primarily Stage I breast cancer (54%), with a BMI of 32.8 ± 6.0 kg/m2. At baseline, breast tissue levels of IR were inversely associated with both percent body fat (r = -0.47, p = .03) and serum insulin levels (r = -0.45, p = .04); serum insulin levels were inversely associated with CD68 (r = -0.47, p = .03). Significant between-group biomarker changes are presented in Table 1. At month 6, loss in percent body fat was associated with increased IR (r = -0.42, p = .05). Increased CD68 breast tissue expression was associated with reductions in serum levels of CRP (r = -0.49, p=0.02). There was no significant effect of the intervention on IR expression or Ki67 (p&gt;0.10). Conclusions: Breast tissue biopsies are feasible to collect in a clinical research setting among breast cancer survivors. A 6-month weight loss intervention led to decreased levels of CD163 in breast tissue and serum levels of leptin, and increased serum levels of adiponectin among breast cancer survivors. At baseline and month 6, changes in breast tissue biomarkers were favorably associated with serum biomarkers and body composition. Future confirmation is required to confirm the added benefit of tissue biomarkers beyond serum as an endpoint for lifestyle interventions among breast cancer survivors. Clinical trial information: NCT02110641. [Table: see text]

Quantitative analysis of tumor-specific BCL2 expression in DLBCL: refinement of prognostic relevance of BCL2

BCL2 overexpression has been reported to be associated with poor prognosis in patients with diffuse large B-cell lymphoma (DLBCL). However, currently there is no consensus on the evaluation of BCL2 expression and only the proportion of BCL2 positive cells are evaluated for the determination of BCL2 positivity. This study aimed to define BCL2 positivity by quantitative analysis integrating both the intensity and proportion of BCL2 expression. BCL2 expression of 332 patients (221 patients for the training set and 111 patients for the validation set) with newly diagnosed DLBCL who received R-CHOP (rituximab, cyclophosphamide, doxorubicin, vincristine, and prednisone) were analyzed using the tumor-specific automated quantitative analysis (AQUA) scoring method based on multiplex immunofluorescence. In the training set, high BCL2 AQUA score (N = 86, 38.9%) was significantly associated with poor prognosis (p = 0.01, HR 2.00; 95% CI [1.15–3.49]) independent of international prognostic index, cell of origin, and MYC expression. The poor prognostic impact of the high BCL2 AQUA score was validated in the validation set. AQUA scoring of BCL2 expression incorporating both the intensity and proportion of BCL2 positive cells was independently associated with survival outcomes of patients with primary DLBCL treated with R-CHOP.

Quantitative Analysis of Tumor-Specific BCL2 Expression in DLBCL: Refinement of Prognostic Relevance of BCL2

Introduction Diffuse large B-cell lymphoma (DLBCL) is the most common subtype of non-Hodgkin lymphoma and a heterogeneous disease with a variety of molecular aberrations and diverse clinical outcomes. BCL2 expression has been implicated for a poor prognosis among patients with DLBCL. However, there is no consensus regarding the interpretation of BCL2 expression in DLBCL. In previous studies, the range of BCL2-positive cases, determined by immunohistochemistry (IHC), was highly variable (24 - 80%) due to subjective and semiquantitative interpretation and the absence of the established cutoff value for BCL2 expression. Consequently, the prognostic impact of BCL2 varies between studies. In addition, only the proportion of BCL2 positive tumor cells are considered in determining the BCL2 positivity. We aimed to define BCL2 positivity by quantitative analysis integrating both the intensity and proportion of BCL2 expression. Methods We retrospectively collected formalin-fixed, paraffin-embedded (FFPE) diagnostic biopsies from 221 patients with de novo DLBCL between January 2007 and December 2012 at our institute. All patients were treated with R-CHOP (rituximab, cyclophosphamide, doxorubicin, vincristine, and prednisone) as first-line treatment. A separate validation set included 111 patients with de novo DLBCL who received first-line R-CHOP at another tertiary hospital in South Korea. BCL2 expression was analyzed using the tumor-specific Automated Quantitative Analysis (AQUA) scoring system based on multiplex immunofluorescence. The tumor-specific quantified intensity information in pixels was converted to protein expression information on a cell basis using the AQUA scoring system. The AQUA scores for BCL2 was calculated as the signal intensities of BCL2 in the target compartment divided by the pixel area of the target compartment. Cell of origin (COO) was determined according to the Hans classification using IHC. Results Ninety-eight patients (44.3%) were &gt; 60 years old of age, 126 patients (57.0%) were male and 81 patients (36.7%) had an International Prognostic Index of 3-5 in the training set. With a median follow-up duration of 59 months, the 5-year event-free survival (EFS) and overall survival (OS) rate were 62.2% and 69.0%, respectively. The BCL2 AQUA score of 41.47 was determined as the optimal cutoff value in the ROC analysis. A total of 86 patients (38.9%) were classified as high BCL2 AQUA score group according to the determined cutoff value. High BCL2 AQUA score was significantly associated with worse OS and EFS (P = 0.00015; OS, P = 0.00012; EFS) (Figure 1A, B). Multivariate analysis revealed that high BCL2 AQUA score was a significant poor prognostic factor for both OS and EFS independent of the IPI, and COO (P = 0.01; OS, P = 0.015; EFS). The high BCL2 AQUA score group in the validation set was also significantly associated with worse OS and EFS (P = 0.0075; OS, P = 0.0049; EFS) (Figure 1C, D). The poor prognostic impact of BCL2 AQUA score was also in good correlation with both OS and EFS in the entire cohort (P &lt; 0.0001; OS, P &lt; 0.0001; EFS) (Figure 1E, F). The adverse impact of high BCL2 AQUA score was identified within both low (IPI 0-2) and high IPI (IPI 3-5) groups (Figure 2A-D). The high BCL2 AQUA score was also associated with poor prognosis within both GCB (P = 0.0077; OS, P = 0.0055; EFS) and non-GCB type DLBCL (P = 0.059; OS, P = 0.04; EFS), although a marginal statistical significance was observed regarding OS in the non-GCB type (Figure 2E-H). Conclusion Our study demonstrated that BCL2 expression analyzed by AQUA scoring system, incorporating both intensity and proportion, is an independent prognostic factor for patients with DLBCL. Given the growing clinical implications of BCL2 and the therapeutic progress in targeting BCL2 in hematologic malignancies, the concrete definition of BCL2 positivity in DLBCL holds great promise for the study of the pathophysiology of DLBCL and could be used to establish new therapeutic strategies. Disclosures No relevant conflicts of interest to declare.

Functional profile and clinical significance of major tumor infiltrating lymphocyte subsets in lung cancer-associated brain metastases.

2066 Background: Despite the biological and clinical implications, the immune composition and functional characteristics of adaptive immune cells in brain metastases (BrM) are poorly understood. Using multiplexed quantitative immunofluorescence (QIF), this study evaluates the level and functional profile of major T-cell subsets in primary lung tumors, BrM, and extracranial metastases (ECM) from lung cancers. Methods: A tissue microarray was constructed from formalin-fixed, paraffin-embedded tumor samples of 94 lung cancer patients treated at Yale Cancer Center between 2002-2013. Multiplexed QIF was used to evaluate the cases with a panel containing phenotype markers for major T-cell subsets (CD3, CD4, CD8 and FOXP3), and cell-localized activation and proliferation (granzyme-B and Ki-67). Signal for each marker was measured in marker-selected tissue compartments using the Automated Quantitative Analysis (AQUA) platform. Associations between markers and major clinicopathologic variables were studied. Results: In total, 40 primary lung tumors, 63 BrM, and 15 ECM were analyzed, including paired samples from 22 patients. Lung cancer histology included adenocarcinoma 62.5%, squamous cell carcinoma 11.5%, small cell 9.4%, and other non-small cell 16.7%. BrM had both significantly lower levels of CD3+ T-cells ( p&lt; 0.0001) and T-cell granzyme B ( p= 0.0188) compared with primary lung tumors. No significant differences were observed in T-cell Ki-67 levels across tissues. FOXP3 measured in CD4+ T-cells were significantly lower in BrM compared with primary malignancies ( p= 0.0002) and ECM ( p= 0.0404). Among patients with BrM, higher levels of CD3+ T-cells in BrM were associated with longer overall survival. Conclusions: Lung cancer-associated BrM have lower T-cell infiltration, cytolytic function, and regulatory T-cells than primary lesions. These results indicate lower adaptive anti-tumor responses in BrM and suggest the presence of a tolerogenic microenvironment in the brain. Overcoming this could be used to design optimal treatment strategies.

Semen AMACR protein as a novel method for detecting prostate cancer

BackgroundAlpha methylacyl A coenzyme racemase (AMACR) has shown to be an excellent immunohistological biomarker for prostate cancer (CaP). Given the connection between prostate and urethra, we hypothesized that semen ejaculate would be an ideal specimen for detection of CaP specific biomarkers, such as AMACR. This study explores the detection of semen AMACR protein in men with and without CaP. MethodsSemen ejaculates from 28 biopsy proven CaP patients prior to radical prostatectomy and 15 age-comparable controls were analyzed. An indirect sandwich ELISA chemiluminescence assay was used to detect semen AMACR, PSA, and Matriptase proteins. Tissue AMACR protein was quantified in 12 corresponding prostatectomy specimens using automated quantitative analysis (AQUA). ResultsSemen AMACR protein was detected in 23 of 28 (82%) CaP patients and 23 of 24 (96%) CaP patients with significant tumor volume (>0.5 cc or 0.3 g). Among the 5 cancer patients with undetectable semen AMACR, 4 patients had small tumor volumes (<1% or 0.3 g). Semen AMACR protein was also detected in 7 of 15 (47%) control noncancer patients. Using 76 ng/ml as a cutoff value, 20 of 28 (71%) patients and 20 of 24 (83%) patients with significant tumor volume were positive for semen AMACR protein, whereas only 5 of 15 (33%) age-comparable controls were positive. AMACR levels degrade with time. ConclusionsThis is the first study to demonstrate that AMACR protein is detectable in semen ejaculate. The higher AMACR levels detected in cancer patients suggests that semen AMACR protein may be useful as a noninvasive test for prostate cancer. Further validation is warranted.

SPOT-004 NEDD9 is crucial for tumour progression in renal cell carcinoma mouse models

IntroductionRenal cell carcinoma (RCC) is characterised by high lethality in advanced stages. Vastly resistant to radio- and chemotherapy, RCCs respond to targeted therapies such as tyrosine kinase inhibitors, mTOR antagonists and immune checkpoint inhibitors. However, limited response rates and emerging resistance mechanisms demand new treatment strategies.Scaffolding protein NEDD9 (neural precursor cell expressed, developmentally down regulated 9) is frequently overexpressed in various cancer types and associated with tumour aggressiveness. In vivo,high NEDD9 expression is associated with adverse clinical outcome and in vitro, NEDD9 promotes aggressiveness in RCC cells. Thus, we systematically characterised the role of NEDD9 in RCC both in vitro and in vivo with the goal to establish basis for new treatment strategies.Material and methodsUsing RNAi, we generated NEDD9-proficient and -deficient syngeneic (RENCA) and xenograft (786-O) tumour models via subcutaneous and orthotopic transplantations as well as tail vein injections. Tumour growth was monitored dynamically using calliper and MRI imaging. Extensive in vitro studies were performed to analyse NEDD9 and its associated oncogenic signalling cascades including Western blot, proliferation, migration and gene expression analyses. Tissue microarrays (TMAs) of 92 RCC patients were stained for NEDD9 and analysed using automated quantitative analysis (AQUA) technology to associate NEDD9 protein expression with clinical outcome.Results and discussionsNEDD9 is highly expressed in RCC cells and NEDD9 depletion significantly impairs migration and proliferation in both human and murine RCC cells. This is accompanied by reduced signalling of oncogenic pathways, particularly activation of ERK1/2. NEDD9 tumour promoting role was confirmed in vivo where NEDD9-deficient murine RCC cells exhibited significantly reduced tumour growth after subcutaneous and orthotopic syngeneic transplantation as well as inhibited lung metastatic seeding capacity after tail vein injection.In human RCC cells, only NEDD9 down-regulation was sufficient to completely abolish tumour growth in subcutaneous, orthotopic and lung seeding xenograft models. In line with our in vitro and in vivo results, we found high NEDD9 expression in human RCC tissue to be significantly associated with shorter overall survival.ConclusionWe show for the first time a crucial role for NEDD9 in RCC tumour progression in vivo, which potentially offers new therapeutic approaches.

MHC-II expression to drive a unique pattern of adaptive resistance to antitumor immunity through receptor checkpoint engagement.

180 Background: Anti-PD-1 therapy is effective in many cancers, but tumor-intrinsic factors governing response and resistance are largely unknown. MHC-II (HLA-DR) expression on tumor cells can predict response to anti-PD-1. Thus, we sought to determine the molecular features of MHC-II+ tumors in the evolution of anti-PD-1 response. Methods: We performed RNA-seq on 58 anti-PD-1 treated melanoma and lung tumors, including a subset of matched specimens prior to treatment and at acquired resistance. We performed immunohistochemistry (IHC) for immunologic markers, including HLA-DR on tumor cells. In triple-negative breast cancers (TNBC; n = 103), we performed IHC and/or quantitative immunofluorescence (QIF) for LAG3, PD-L1, CD4, CD8, Fc-receptor-like 6 (FCRL6), and granzyme B (GZMB). QIF images were assessed by Automated Quantitative Analysis (AQUA). To determine the functional effect of MHC-II on tumor cells, we generated isogenic MHC-II+ mouse tumors and assessed immune responsiveness and efficacy of checkpoint inhibition. Results: We identified unique inflammatory signatures in HLA-DR+ tumors, correlating with enhanced pre-treatment CD4+ and CD8+ tumor-infiltrating lymphocytes (TILs) and response to anti-PD-1. LAG3+ and FCRL6+ TILs were enriched in HLA-DR+ tumors. LAG3 and FCRL6, known inhibitory receptors which bind MHC-II, were elevated at anti-PD-1 resistance. Similarly, in &gt; 100 TNBCs, HLA-DR+ tumor cells associated with increased CD4+ and CD8+ TILs and enhanced LAG3+ and FCRL6+ TILs. Further, presence of MHC-II-suppressing (LAG3+/FCRL6+) TILs associated with decreased GZMB+ CD8+ T cells, suggesting suppressed cytotoxicity. In mice, enforced expression of MHC-II on tumor cells enhanced CD4-enhanced anti-tumor immunity but was thwarted by LAG3+ TIL recruitment. Combined anti-LAG3 and anti-PD-1 therapy was selectively effective in MHC-II+ tumors. Conclusions: MHC-II+ tumors are immunologically active and may circumvent anti-tumor immunity by targeting MHC-II antigen presentation via recruitment of MHC-II-suppressing TILs. MHC-II expression may be useful to stratify patients to anti-PD-1/anti-LAG3 and eventually, anti-PD-1/anti-FCRL6 combinations.

Multiplexed ion beam imaging analysis for quantitation of protein expresssion in cancer tissue sections

Part of developing therapeutics is the need to identify patients who will respond to treatment. For HER2-targeted therapies, such as trastuzumab, the expression level of HER2 is used to identify patients likely to receive benefit from therapy. Currently, chromogenic immunohistochemistry on patient tumor tissue is one of the methodologies used to assess the expression level of HER2 to determine eligibility for trastuzumab. However, chromogenic staining is fraught with serious drawbacks that influence scoring, which is additionally flawed due to the subjective nature of human/pathologist bias. Thus, to advance drug development and precision medicine, there is a need to develop technologies that are more objective and quantitative through the collection and integration of larger data sets. In proof of concept experiments, we show multiplexed ion beam imaging (MIBI), a novel imaging technology, can quantitate HER2 expression on breast carcinoma tissue with known HER2 status and those values correlate with pathologist-determined IHC scores. The same type of quantitative analysis using the mean pixel value of five individual cells and total pixel count of the entire image was extended to a blinded study of breast carcinoma samples of unknown HER2 scores. Here, a strong correlation between quantitation of HER2 by MIBI analysis and pathologist-derived HER2 IHC score was identified. In addition, a comparison between MIBI analysis and immunofluorescence-based automated quantitative analysis (AQUA) technology, an industry-accepted quantitation system, showed strong correlation in the same blind study. Further comparison of the two systems determined MIBI was comparable to AQUA analysis when evaluated against pathologist-determined scores. Using HER2 as a model, these data show MIBI analysis can quantitate protein expression with greater sensitivity and objectivity compared to standard pathologist interpretation, demonstrating its potential as a technology capable of advancing cancer and patient diagnostics.

Quantitative spatial profiling of PD-1/PD-L1 interaction and HLA-DR/IDO1 to predict outcomes to anti-PD-1 in metastatic melanoma (MM).

9517 Background: Although PD-1/L1 axis directed therapies induce durable responses in some mm patients (pts), biomarkers of response remain elusive. We hypothesized that quantifying key immune suppression mechanisms within the tumor microenvironment would provide superior predictors of response to anti-PD-1 compared with single marker assessment. Methods: Pre-treatment tumor biopsies from 124 mm pts treated with anti-PD-1 at 7 academic centers were fluorescently stained with multiple immune markers in discovery (n = 24) and validation (n = 100) cohorts. Selected biomarker signatures, PD-1/PD-L1 interaction score (proportion of PD-1+ cells co-localized with PD-L1) and IDO1/HLA-DR co-expression were evaluated for anti-PD-1 treatment response and survival. Slides were imaged using Vectra; biomarker positive cells and their co-localization were objectively quantified in pathologist-selected regions using novel Automated Quantitative Analysis (AQUA) algorithms. Results: In the discovery cohort, high levels of PD-1/PD-L1 interaction score and/or IDO1/HLA-DR coexpression was strongly positively associated with response to anti-PD-1 (p = 0.0005). In contrast, other individual biomarkers (PD-1, PD-L1, CD8) were not associated with response or survival (p &gt; 0.10). This finding was replicated in the validation cohort: pts with high PD-1/PD-L1 and/or IDO1/HLA-DR were more likely to respond to treatment (p = 0.009). These pts also experienced a three-fold increase in progression free survival (hazards ratio (HR) = 0.33; p = 0.003) and overall survival (HR = 0.34; p = 0.004). Multivariate analyses revealed that these findings were independent of BRAF mutation, stage, LDH and prior therapy. In the combined cohort (n = 124), 80% of responding pts had higher levels of PD-1/PD-L1 interaction scores and/or IDO1/HLA-DR. In contrast, PD-L1 expression alone (≥1% or ≥50%) was not predictive of PFS or OS (p &gt; 0.1). Conclusions: This novel multiplexed method profiling key tumor-immune suppression pathways identified mm pts likely to respond to anti-PD-1 therapy. This method could help stratify patients for PD-1 monotherapy and be useful in guiding future clinical trials.

MPTH-50. AUTOMATED QUANTITATIVE ANALYSIS (AQUA) AS A RELIABLE METHOD TO ASSESS MGMT PROTEIN EXPRESSION IN GLIOBLASTOMAS

MGMT methylation in glioblastomas is associated with better response to temozolomide + radiation therapy (Stupp protocol). While MGMT protein expression cut-off values using traditional immunohistochemistry (T-IHC) were previously reported, fluorescence-based IHC, Automated Quantitative Analysis (AQUA), still lacks standardization to be used as an alternative to assess MGMT protein expression. Our aim was to describe the results of MGMT expression by AQUA analysis and to evaluate for the first time its correlation with methylation and T-IHC results. We evaluated 533 GBMs FFPE samples (primary and recurrent tumors) arranged in 10 tissue microarrays. MGMT nuclear expression in tumor cells was adequately assessed in 501/533 samples. The results were compared with T-IHC (n=493) and methylation (n=227) data both for primary and recurrent tumors. Statistical analyses were performed with SPSS. AQUA values in primary tumors ranged from 12.87 – 815.29 (median=180.56) and appeared to follow a continuous unimodal distribution. Those values were significantly related to MGMT methylation status and loss of expression in T-IHC (p<0.0001 for both) in one-way ANOVA. AQUA values in first recurrence (n=32) were significantly higher (79.35 – 596.49, median= 195.91; p=0.013 on t-test) than in primary tumors. Our results showed that AQUA has excellent correlation with gene methylation and protein expression assessed by T-IHC. The lower cost and availability of semi-quantitative IHC makes it a worldwide accessible and cost-effective method to evaluate MGMT in a general Neuropathology practice. Cutoff values for AQUA to determine loss of expression and relationship with overall survival are to be determined in future studies. R01CA108633, R01CA169368, RC2CA148190, U10CA180850-01 (NCI), Brain Tumor Funders Collaborative Grant, and The Ohio State University CCC (all to AC).

Automated measurement of estrogen receptor in breast cancer: a comparison of fluorescent and chromogenic methods of measurement

Whereas FDA-approved methods of assessment of estrogen receptor (ER) are ‘fit for purpose', they represent a 30-year-old technology. New quantitative methods, both chromogenic and fluorescent, have been developed and studies have shown that these methods increase the accuracy of assessment of ER. Here, we compare three methods of ER detection and assessment on two retrospective tissue microarray (TMA) cohorts of breast cancer patients: estimates of percent nuclei positive by pathologists and by Aperio's nuclear algorithm (standard chromogenic immunostaining), and immunofluorescence as quantified with the automated quantitative analysis (AQUA) method of quantitative immunofluorescence (QIF). Reproducibility was excellent (R2>0.95) between users for both automated analysis methods, and the Aperio and QIF scoring results were also highly correlated, despite the different detection systems. The subjective readings show lower levels of reproducibility and a discontinuous, bimodal distribution of scores not seen by either mechanized method. Kaplan–Meier analysis of 10-year disease-free survival was significant for each method (Pathologist, P=0.0019; Aperio, P=0.0053, AQUA, P=0.0026); however, there were discrepancies in patient classification in 19 out of 233 cases analyzed. Out of these, 11 were visually positive by both chromogenic and fluorescent detection. In 10 cases, the Aperio nuclear algorithm labeled the nuclei as negative; in 1 case, the AQUA score was just under the cutoff for positivity (determined by an Index TMA). In contrast, 8 out of 19 discrepant cases had clear nuclear positivity by fluorescence that was unable to be visualized by chromogenic detection, perhaps because of low positivity masked by the hematoxylin counterstain. These results demonstrate that automated systems enable objective, precise quantification of ER. Furthermore, immunofluorescence detection offers the additional advantage of a signal that cannot be masked by a counterstaining agent. These data support the usage of automated methods for measurement of this and other biomarkers that may be used in companion diagnostic tests.

Abstract 5064: CORO1B amplification and expression status identifies an aggressive subset of chromosome 11q13 amplified HNSCC

Abstract Head and neck squamous cell carcinoma (HNSCC) is highly invasive cancer type that occurs with greater incidence in West Virginia and the rest of Appalachia. The chromosome 11q13 region is amplified in approximately 30% of late stage HNSCC cases and is associated with a poor patient prognosis. The core 11q13 region encodes the well-studied tumor genes CCND1 (cyclin D1) and CTTN (cortactin). The CORO1B (coronin 1B) gene flanks the 11q13 core and is amplified in 9-14% of all HNSCC, but how CORO1B amplification contributes to HNSCC is unknown. Coronin 1B governs cell motility by negatively regulating F-actin stability through displacement of cortactin at actin related protein 2/3 (Arp 2/3) branch points, generating dynamic turnover of Arp2/3-F-actin networks required for productive cell movement. Kaplan-Meier analysis of two independent patient cohorts indicates that HNSCC cases with CORO1B amplification have significantly reduced overall survival. Cox hazard ratios also indicate the CORO1B amplification is strongly associated with increased mortality in both cohorts. Automated quantitative analysis (AQUA) of coronin 1B expression in HNSCC tissue microarrays indicates that coronin 1B overexpression decreases median survival of HNSCC patients from 81 to 29 months. Reduced expression of coronin 1B by RNAi-mediated knockdown in established HNSCC cell lines decreases several actin-mediated invasive processes, including invadopodia formation and extracelluar matrix degradation. Collectively these results suggest that elevated coronin 1B expression levels in HNSCC function to enhance tumor invasion, potentially through accelerated downregulation of cortactin stabilizing activity at Arp2/3-F-actin junctions. Importantly, CORO1B amplification and coronin 1B expression status may serve a role as a precision biomarker for identification of a subset of late-stage HNSCC patients that would benefit from more aggressive forms of initial clinical treatment. Citation Format: Jessica L. Allen, Elyse L. Walk, Kristen L. Rhodes, Colleen J. Beatty, Steven M. Markwell, Brenen W. Papenberg, Erik T. Interval, Hong Wu, Marileila Varella Garcia, James E. Bear, Scott A. Weed. CORO1B amplification and expression status identifies an aggressive subset of chromosome 11q13 amplified HNSCC. [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 5064.

ING3 is associated with increased cell invasion and lethal outcome in ERG-negative prostate cancer patients.

The inhibitor of growth family member 3 (ING3) is a member of the ING tumor suppressor family. Although its expression has been reported in various types of cancers, the role of ING3 and its prognostic value in prostate cancer (PCa) has not been investigated. ING3 expression and prognostic value was assessed in a cohort of PCa patients (n = 312) treated with transurethral resection of prostate using immumoflourescent automated quantitative analysis (AQUA) system. In vitro studies were carried out in conjunction to investigate its expression in various PCa cell lines. ING3 knockdown was also carried out in DU145 cell lines to assess for any changes in invasion and migration. ING3 expression was highest in benign prostate tissues (mean 3.2 ± 0.54) compared to PCa (mean 2.5 ± 0.26) (p = 0.437), advanced prostate cancer (AdvPCa) (mean 1.5 ± 0.32) (p = 0.004), and castration-resistant prostate cancer (CRPC) (mean 2.28 ± 0.32) (p = 0.285). ING3 expression was inversely correlated to Gleason score (p = 0.039) and ETS-related gene (ERG) expression (p = 0.019). Higher ING3 expression was marginally associated with lethal disease (p = 0.052), and this was more pronounced in patients with ERG-negative status (p = 0.018). Inhibition of ING3 in DU145 PCa cells using small interfering RNA (siRNA) was associated with decreased cell invasion (p = 0.0016) and cell migration compared to control cells. ING3 is significantly associated with PCa disease progression and cancer-specific mortality. To our knowledge, this is the first report suggesting an oncogenic function of ING3, previously well known as a tumor suppressor protein. Further studies should investigate potential-related pathways in association to ING3.

First application of the Automated QUantitative Analysis (AQUA) technique to quantify PTEN protein expression in ovarian cancer: A correlative study of NCIC CTG OV.16

BackgroundPlatinum resistance is a dominant cause of poor outcomes in advanced ovarian cancer (OC). A mechanism of platinum resistance is the inhibition of apoptosis through phosphatidylinositol 3 kinase (PI3K) pathway activation. The role of phosphatase and tensin homolog (PTEN), a negative regulator of this pathway, as a tumor biomarker is unclear. Quantitative analysis of PTEN expression as an alternative to immunohistochemistry has not been considered. Patients and methodsIn 238 patient tumors from the NCIC-CTG trial OV.16, PTEN protein expression was quantified by Automated QUantitative Analysis (AQUA). Cox model was used to study the association between PTEN expression and clinical outcomes using a minimum p-value approach in univariate analysis. Multivariate analysis was used to adjust for clinical and pathological parameters. ResultsPTEN scores (range 13.9–192.3) of the 202 samples that passed quality control were analyzed. In univariate analysis, there was a trend suggesting an association between PTEN expression by AQUA as a binary variable (low ≤61 vs high >61) and progression free survival (HR=0.77, p=0.083), and in multivariate analysis, this association approached significance (HR=0.74, p=0.059). The relationship between quantitative PTEN expression and PFS differed (p=0.01 for interaction) by the extent of surgical debulking (residual disease (RD) <1cm or ≥1cm), with a numerically superior PFS in patients with high PTEN (23.5 vs 14.9m) only when RD<1cm (p=0.19). There was no association between PTEN levels and overall survival. ConclusionsAQUA is a novel method to measure PTEN expression. Further study of PTEN as a biomarker in OC is warranted.

Quantitative Multiplexed Immunohistochemistry Assays for Exploring CAR Modified T Cells and Checkpoint Inhibitors in Lymphoma Trials

Although there have been compelling advances in the cancer immunotherapy space recently in the form of chimeric antigen receptor (CAR) modified T-cells and checkpoint inhibitors, advanced tools to explore the therapeutic mechanisms of their combination are not adequately developed or widely available. To address this growing need, we developed a robust quantitative fluorescent immunohistochemistry platform using multiplex AQUA (Automated Quantitative Analysis) technology to evaluate checkpoint inhibitor expression, enumerate CAR T cells and determine the interaction between tumor cells and immune cells via novel co-localization algorithms. We explored utility of this method both in preclinical- and clinical model systems. In an immunodeficient mouse model of B-cell lymphoma, we evaluated homing of CAR T cells to malignant B-cells in primary lymphoid organs. We determined the phenotype and functional status of the CAR T cells via multiplex analyses of CD4, CD8, PD1 and FOXP3 expression. Additionally, to enable combination immunotherapies in Diffuse Large B-Cell Lymphoma (DLBCL) setting, we explored prevalence of adaptive immune resistance mechanisms in the form of PD1 and PD-L1 expression in immune- and tumor cell compartments via landmarks created by cytoplasmic and nuclear stains in both primary and secondary biopsies from DLBCL patients (n = 63). To support patient selection for CAR T trials, we quantified expression and prevalence of relevant tumor antigens that could not be scored reproducibly by traditional methods to yield objective cut points. We anticipate utilization of these quantitative multiplexed IHC methods for optimal selection of patients into upcoming novel combination immunotherapy trials DisclosuresTran:Genoptix: Employment. Scott:Genoptix: Employment. Lee:Genoptix: Employment. Singh:Novartis: Employment. Cogan:Novartis: Employment. Bordeaux:Genoptix: Employment. Jennifer:Genoptix: Employment. Lameh:Genoptix: Employment. Tribouley:Novartis: Employment. Kassim:Novartis: Employment. Tangri:Genoptix Inc., a Novartis company: Employment. Dakappagari:Genoptix Inc., a Novartis company: Employment.