Quantitative Multiplexed Proteomics Could Assist Therapeutic Decision Making in Non-Small Cell Lung Cancer Patients with Ambiguous ALK Test Results

Therapeutic guidance in non-small cell lung cancer (NSCLC) tumors that are positive for anaplastic lymphoma kinase (ALK) fluorescent in situ hybridization (FISH), but negative for ALK immunohistochemistry, is still challenging. Parallel routine screening of 4588 NSCLC cases identified 22 discordant cases. We rechecked these samples using ALK antibodies and selected reaction monitoring (SRM) quantitative multiplexed proteomics screening multiple protein targets, including ALK and MET for the ALK tyrosine kinase inhibitor (TKI), and FR-alpha, hENT1, RRM1, TUBB3, ERCC1, and XRCC1 for chemotherapy. The presence of ALK (31.8%), MET (36.4%), FR-alpha (72.7%), hENT1 (18.2%), RRM1 (31.8%), TUBB3 (72.9%), ERCC1 (4.5%), and a low level of XRCC1 (54.4%) correlated with clinical outcomes. SRM was more sensitive than the ALK D5F3 assay. Among the eight cases receiving ALK TKI, four cases with ALK or MET detected by SRM had complete or partial responses, whereas four cases without ALK or MET showed progression. Twenty-seven treatment outcomes from 20 cases were assessed and cases expressing more than half of the specific predictive proteins were sensitive to matching therapeutic agents and showed longer progression-free survival than the other cases (p < 0.001). SRM showed a potential role in therapeutic decision making in NSCLC patients with ambiguous ALK test results.

Quantitative proteomic analysis of HER2 expression in the selection of gastric cancer patients for trastuzumab treatment

Background

A wide range of response rates have been reported in HER2-positive gastric cancer (GC) patients treated with trastuzumab. Other HER2-targeted therapies for GC have yet to show efficacy in clinical trials. These findings raise question about the ability of standard HER2 diagnostics to accurately distinguish between GC patients who would and would not benefit from anti-HER2 therapies.

Patients and methods

GC patients (n = 237), including a subset from the Trastuzumab in GC (ToGA) trial were divided into three groups based on HER2 status and history of treatment with standard chemotherapy or chemotherapy plus trastuzumab. We applied mass spectrometry-based proteomic analysis to quantify HER2 protein expression in formalin-fixed tumor samples. Using HER2 expression as a continuous variable, we defined a predictive protein level cutoff to identify which patients would benefit from trastuzumab. We compared quantitated protein level with clinical outcome and HER2 status as determined by conventional HER2 diagnostics.

Results

Quantitative proteomics detected a 115-fold range of HER2 protein expression among patients diagnosed as HER2 positive by standard methods. A protein level of 1825 amol/µg was predicted to determine benefit from the addition of trastuzumab to chemotherapy. Trastuzumab treated patients with HER2 protein levels above this cutoff had twice the median overall survival (OS) of their counterparts below the cutoff (35.0 versus 17.5 months, P = 0.011). Conversely, trastuzumab-treated patients with HER2 levels below the cutoff had outcomes similar to HER2-positive patients treated with chemotherapy. (Progression-free survival = 7.0 versus 6.5 months: P = 0.504; OS = 17.5 versus 12.6 months: P = 0.520). HER2 levels were not prognostic for response to chemotherapy.

Conclusions

Proteomic analysis of HER2 expression demonstrated a quantitative cutoff that improves selection of GC patients for trastuzumab as compared with current diagnostic methods.

Mass-spectrometry-based quantitation of Her2 in gastroesophageal tumor tissue: comparison to IHC and FISH

BACKGROUND

Trastuzumab has shown a survival benefit in cases of Her2-positive gastroesophageal cancer (GEC). Immunohistochemistry (IHC) and fluorescence in situ hybridization (FISH) currently determine eligibility for trastuzumab-based therapy. However, these low-throughput assays often produce discordant or equivocal results.

METHODS

We developed a targeted proteomic assay based on selected reaction monitoring mass spectrometry (SRM-MS) and quantified levels (amol/μg) of Her2-SRM protein in cell lines (n = 27) and GEC tissues (n = 139). We compared Her2-SRM protein expression with IHC/FISH, seeking to determine optimal SRM protein expression cutoffs in order to identify HER2 gene amplification.

RESULTS

After demonstrating assay development, precision, and stability, Her2-SRM protein measurement was observed to be highly concordant with the HER2/CEP17 ratio, particularly in a multivariate regression model adjusted for SRM expression of the covariates Met, Egfr, Her3, and HER2 heterogeneity, as well as their interactions (cell lines r (2) = 0.9842; FFPE r (2) = 0.7643). In GEC tissues, Her2-SRM protein was detected at any level in 71.2 % of cases. ROC curves demonstrated that Her2-SRM protein levels have a high specificity (100 %) at an upper-level cutoff of >750 amol/µg and sensitivity of 75 % at a lower-level cutoff of <450 amol/μg for identifying HER2 FISH-amplified tumors. An "equivocal zone" of 450-750 amol/µg of Her2-SRM protein was analogous to IHC2+ but represented fewer cases (9-16 % of cases versus 36-41 %).

CONCLUSIONS

Compared to IHC, targeted SRM-Her2 proteomics provided more objective and quantitative Her2 expression with excellent HER2/CEP17 FISH correlation and fewer equivocal cases. Along with its multiplex capability for other relevant oncoproteins, these results demonstrate a refined HER2 protein expression assay for clinical application.

Abstract 25: Whole genome sequencing and quantitative proteomics reveal HPV integration and HER2 overexpression in a patient with cervical cancer: Comprehensive omics analysis driving clinical treatment decisions

Introduction: Selection of drugs to treat patients with cancer is typically based on the anatomical site in which the tumor is located. Here we report a treatment decision for a patient with relapsed, advanced cervical cancer that was based on a comprehensive omics analysis using whole genome sequencing (WGS) combined with quantitative proteomics.

Methods: The patient was a 44-year-old female whose disease had progressed following surgery and more than 4 lines of chemotherapy. WGS was performed on the patient's formalin-fixed, paraffin-embedded (FFPE) metastatic tumor sample and a matched-normal reference sample. Quantitative proteomics was performed on the FFPE tumor sample by Selected Reaction Monitoring Mass Spectrometry and was quantitated at the atomolar level.

Results: WGS found somatic mutations and rearrangements and reads mapping to human papillomavirus type 18 (HPV 18). Mutations more commonly found in breast cancer (ERBB2, CDH1, and CLTCL1) were noted. The HPV 18 genome was integrated into chromosome 17 in close proximity to a 7-fold amplification of the ERBB2 gene. Proteomic analysis of the FFPE tumor validated and quantitated overexpression of HER2 protein resulting from ERBB2 gene amplification, with 11,322 amol/μg of tissue protein. Clinically observed ranges for breast or gastric cancer are 150-500 amol/μg, with levels above 750 amol/μg correlating with FISH-positive amplification and clinical efficacy of trastuzumab (unpublished observation). Based on these comprehensive omic findings, trastuzumab, a therapy approved for breast and gastric cancer, was administered. The patient experienced a reduction in the size of her tumor (by CT/PET) and stabilization of her disease for 5 months.

Conclusion: WGS and proteomic profiling of this patient's disease identified, confirmed, and quantitated an appropriate target for pharmaceutical intervention. The patient presented with cervical cancer; however, the WGS analysis pointed towards a potentially causative integration of the HPV 18 genome resulting in ERBB2 amplification along with genomic mutations more commonly found in breast cancer. Proteomic analysis further validated and quantitated the HER2 expression resulting from ERBB2 gene amplification, leading to the patient's treatment with trastuzumab. Our findings argue for the use of comprehensive omics analysis to guide decision support for personalized management of cancer care with therapies determined based on a quantitative proteomic signature, independent of anatomical tumor type.

Citation Format: Stephen Benz, J Zackary Sanborn, Nicole S. Hensley, Todd Hembrough, Charles J. Vaske, Jon Burrows, Shahrooz Rabizadeh, Ivor Royston, Patrick Soon-Shiong. Whole genome sequencing and quantitative proteomics reveal HPV integration and HER2 overexpression in a patient with cervical cancer: Comprehensive omics analysis driving clinical treatment decisions. [abstract]. In: Proceedings of the AACR Precision Medicine Series: Integrating Clinical Genomics and Cancer Therapy; Jun 13-16, 2015; Salt Lake City, UT. Philadelphia (PA): AACR; Clin Cancer Res 2016;22(1_Suppl):Abstract nr 25.

High HER2 protein levels correlate with increased survival in breast cancer patients treated with anti-HER2 therapy

INTRODUCTION

Current methods to determine HER2 (human epidermal growth factor receptor 2) status are affected by reproducibility issues and do not reliably predict benefit from anti-HER2 therapy. Quantitative measurement of HER2 may more accurately identify breast cancer (BC) patients who will respond to anti-HER2 treatments.

METHODS

Using selected reaction monitoring mass spectrometry (SRM-MS), we quantified HER2 protein levels in formalin-fixed, paraffin-embedded (FFPE) tissue samples that had been classified as HER2 0, 1+, 2+ or 3+ by immunohistochemistry (IHC). Receiver operator curve (ROC) analysis was conducted to obtain optimal HER2 protein expression thresholds predictive of HER2 status (by standard IHC or in situ hybridization [ISH]) and of survival benefit after anti-HER2 therapy.

RESULTS

Absolute HER2 amol/μg levels were significantly correlated with both HER2 IHC and amplification status by ISH (p < 0.0001). A HER2 threshold of 740 amol/μg showed an agreement rate of 94% with IHC and ISH standard HER2 testing (p < 0.0001). Discordant cases (SRM-MS-negative/ISH-positive) showed a characteristic amplification pattern known as double minutes. HER2 levels >2200 amol/μg were significantly associated with longer disease-free survival (DFS) and overall survival (OS) in an adjuvant setting and with longer OS in a metastatic setting.

CONCLUSION

Quantitative HER2 measurement by SRM-MS is superior to IHC and ISH in predicting outcome after treatment with anti-HER2 therapy.

Quantification of Anaplastic Lymphoma Kinase Protein Expression in Non-Small Cell Lung Cancer Tissues from Patients Treated with Crizotinib

BACKGROUND

Crizotinib has antitumor activity in ALK (anaplastic lymphoma receptor tyrosine kinase)-rearranged non-small cell lung cancer (NSCLC). The current diagnostic test for ALK rearrangement is breakapart fluorescence in situ hybridization (FISH), but FISH has low throughput and is not always reflective of protein concentrations. The emergence of multiple clinically relevant biomarkers in NSCLC necessitates efficient testing of scarce tissue samples. We developed an anaplastic lymphoma kinase (ALK) protein assay that uses multiplexed selected reaction monitoring (SRM) to quantify absolute amounts of ALK in formalin-fixed paraffin-embedded (FFPE) tumor tissue.

METHODS

After validation in formalin-fixed cell lines, the SRM assay was used to quantify concentrations of ALK in 18 FFPE NSCLC samples that had been tested for ALK by FISH and immunohistochemistry. Results were correlated with patient response to crizotinib.

RESULTS

We detected ALK in 11 of 14 NSCLC samples with known ALK rearrangements by FISH. Absolute ALK concentrations correlated with clinical response in 5 of 8 patients treated with crizotinib. The SRM assay did not detect ALK in 3 FISH-positive patients who had not responded to crizotinib. In 1 of these cases, DNA sequencing revealed a point mutation that predicts a nonfunctional ALK fusion protein. The SRM assay did not detect ALK in any tumor tissue with a negative ALK status by FISH or immunohistochemistry.

CONCLUSIONS

ALK concentrations measured by SRM correlate with crizotinib response in NSCLC patients. The ALK SRM proteomic assay, which may be multiplexed with other clinically relevant proteins, allows for rapid identification of patients potentially eligible for targeted therapies.

Abstract 4255: Development and clinical validation of a quantitative mass spectrometric assay for immuno-oncology targets in FFPE samples

BackgroundImmune check point proteins play a pivotal role in immune evasion by the tumor. Recent trials involving inhibitors of the immune checkpoint protein pairs, PD-1 and PD-L1 have demonstrated anti-tumor activity. Measuring the levels of immune check point proteins and other members of the immunological synapse will help clinicians personalize therapy. Currently, immunohistochemistry (IHC) is the preferred diagnostic to assess PD-L1 status; however, PD-L1 positivity varies based on the antibody that is used. Additionally, PD-L1 negative patients by IHC have responded to anti-PD-L1 therapy implicating disconnect between PD-L1 diagnostics and response. We have developed and clinically validated a quantitative mass spectrometric technique that not only quantitates PD-L1 in formalin fixed paraffin embedded (FFPE) tissue but can concurrently quantitate other members (B7H3, B7.1, B7.2, OX40L) of the immunological synapse using the same tissue section.

MethodRecombinant PD-L1 protein was used to identify optimal quantitative peptides for PD-L1 assay. Standard curves were generated using labeled and unlabeled peptides. The PD-L1 assay was pre-clinically validated on 14 cell lines with known expression levels of PD-L1. The assay was then run on archived FFPE sections from in 9 normal tissues, 21 early staged (stage 1 and 2) and 4 advanced staged (stage 3) NSCLC patients. In addition PD-L1 was also assayed in bladder, breast and gastric cancer.

Results

PD-L1 protein expression was detected in 7 out of 14 cell lines The regression analysis between SRM and mRNA analysis demonstrated moderate correlation (R2 = 0.8894). Normal lung tissue did not express PD-L1; ∼24% of early stage (5/21) and 50% of advanced stage NSCLC (2/4) expressed measurable PD-L1 protein. PD-L1 was detected more frequently in squamous cell carcinoma than adenocarcinoma. We are currently assessing the levels of PD-L1 and other targets of the immunological synapse using multiplex mass spectrometry and comparing it with IHC in 100 cholangiocarcinoma and possible inclusion of PD-L1diagnostics in clinical trials.

DiscussionThe need to characterize expression levels of druggable targets in small biopsies is becoming ever more critical as new drug targets and biomarkers are identified. Initial PD-L1 screening using clinical NSCLC samples suggests that more advanced NSCLC patients are more likely to be PD-L1 positive compared to early stage NSCLC patients. Laser microdissection (LMD) can be used to specifically microdissect the immunological synapse. Additional quantitative assays for both lymphocyte (CD8, CD68) and immunotargets (B7-H3,B.1, B7.2 etc) have been developed for assessing the ‘immune profile’ in tumor associated stroma via LMD. This immuno-proteomic assay of the key immunological synapse members within tumor and/or stroma may lead to improved personalized immunotherapy.

Citation Format: Sheeno P. Thyparambil, Fabiola Cecchi, Eunkyung An, Wei-Li Liao, Jon Burrows, Todd Hembrough, Daniel Catenacci. Development and clinical validation of a quantitative mass spectrometric assay for immuno-oncology targets in FFPE samples. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 4255. doi:10.1158/1538-7445.AM2015-4255

Abstract 3395: Clinical Survey of 19 actionable proteins in multiple indications using multiplex mass spectrometry

Many available oncology therapies are targeted to specific proteins, the most notable examples being therapies targeted to EGFR and Her2. For targeted therapies to have maximal efficacy, it is necessary to identify patients whose tumors express the target protein. As more pathways and proteins are identified as tumor drivers and therapies are developed that target those proteins, and more patient screening tools are needed to efficiently direct patients to correct therapeutic regimens.

While chemotherapy regimens are not often considered targeted therapies, protein biomarkers for chemotherapy efficacy have been identified; for example amplification of TOPO2A is known to improve response to anthracycline-based therapy combinations. Though many chemotherapy biomarkers have been identified, screening is not routine, and chemotherapy regimens are not being adjusted for individual tumor biology.

To address the growing need for efficient patient screening using minimal tissue, OncoPlex Diagnostics has built a comprehensive protein quantification panel that allows for the simultaneous quantitation of multiple actionable proteins from formalin-fixed, paraffin-embedded patient biopsies using multiplex mass spectrometry. This panel currently quantifies nine proteins that are markers of targeted therapy (including ALK, AR, EGFR, HER2, HER3, MET, MSLN, and PD-L1) and includes the ChemoPlex panel, which quantifies chemotherapy biomarkers (ERCC1, FRalpha, hENT1, RRM1, SPARC, TOPO1, TOPO2A). Since 2013, over 270 biopsies from multiple indications have been analyzed for protein expression in the OncoPlex Diagnostics CAP-qualified, CLIA-certified laboratory, revealing large ranges of expression for many drug targets that are not routinely assayed.

Because of the importance of TOPO2A in anthracycline-based therapies, which are commonly prescribed in breast cancer patients, sixty-two breast cancer biopsies were retrospectively reviewed. Of the 62 samples, 41 were positive for TOPO2A expression; ranging from 233-1750amol/ug. Of the primary biopsies, 80% of them expressed TOPO2A; however only two of seven liver metastases were positive for TOPO2A. These data suggest that anthracycline-based therapy might not be as efficacious in metastatic sites due to the lack of TOPO2A.

Also of interest, quantification of FRalpha, a biomarker for folate-targeted therapies, showed a 50-fold range of expression in NSCLC cases, and TOPO1, the target of irinotecan and topotecan, showed a 10-fold range of expression in various indications, with 4% of biopsies having no detectable TOPO1.

These wide expression ranges of known biomarkers suggest that certain therapies might have vastly different response rates based on biomarker expression. To derive the best therapeutic response to both targeted and chemotherapy regimens, it is necessary to understand each patient tumor biology individually.

Citation Format: Fabiola Cecchi, Adele Blackler, Heather Jordan, Marlene Darfler, Todd Hembrough, Michael Stocum, Jon Burrows. Clinical Survey of 19 actionable proteins in multiple indications using multiplex mass spectrometry. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 3395. doi:10.1158/1538-7445.AM2015-3395

Abstract 3398: Development of a mass spectrometry based antibody-drug conjugate biomarker panel

Background: Antibody-Drug Conjugates (ADCs) are poised to become an extremely important class of therapeutics in oncology. By conjugating cytotoxic payloads to antibodies that target proteins found primarily on cancer cells, ADCs represent a novel mechanism for directing extremely toxic small molecules specifically to tumor cells. Due to the unique mechanism of ADCs, patient selection should involve screening not only for the presence of the antibody target, but also screening for the presence of any markers of resistance or response to the payload. Several proteins, such as multi-drug effluxers and tubulin-beta 3, have been implicated in resistance to small molecule cytotoxins and microtubule inhibitor drugs. OncoPlex Diagnostics has built a multiplexed ADC biomarker panel that simultaneously quantifies the levels of the antibody target and putative resistance markers for several known payloads, such as maytansinoids, auristatins and taxanes, as well as response markers for the topoisomerase inhibitor payloads SN-38 and doxorubicin.

Methods: Liquid Tissue-Selected Reaction Monitoring (LT-SRM) is a multiplexed, quantitative method that uses mass spectrometry to quantify proteins based on a unique sequence of amino acids, and thus does not have the same limitations as traditional antibody-based, semi-quantitative protein detection methods, such as immunohistochemistry. We developed a LT-SRM assay to quantify protein levels of EGFR, FRalpha, Her2, CD30 and Mesothelin (antibody targets) and MCL1, MDR, MRP1, tubulin-beta3, Topo1 and Topo2a (payload response and resistance markers) simultaneously from FFPE biopsies. Calibration curves for all the proteins in the ADC panel are linear over 5-orders of magnitude, with limits of detection for each analyte between 25 and 400 amol/ug of tissue.

Results: Analysis of FFPE tumor tissues show a broad range of expression for the ADC proteins, with some tissues showing no detectable levels of some payload markers. Clinical analysis of FRalpha showed a range of expression from &lt;LOD to 13500 amol/ug. An examination of Her2 positive tissue showed a wide range of Her2 expression (over 20-orders of magnitude), as well as a wide range of expression for the payload markers. The differences seen in the payload markers suggest differing responses to Her2-targeted ADCs, independent of Her2 levels, and indicate that different patient populations might respond better to different payloads, depending on tumor biology.

Conclusions: The OncoPlexDx ADC panel can determine of a cutoff for expression levels of the antibody-target protein necessary for ADC response as well as identify markers of payload response or resistance to further understand how these markers affect therapeutic efficacy. This panel can be used to predict which patients will derive the most benefit from ADC therapy based on the specific biology of their tumor.

Citation Format: Adele Blackler, Wei-Li Liao, Sheeno Thyparambil, Eunkyung An, Fabiola Cecchi, Marlene Darfler, Todd Hembrough, Jon Burrows. Development of a mass spectrometry based antibody-drug conjugate biomarker panel. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 3398. doi:10.1158/1538-7445.AM2015-3398

Abstract 566: ChemoPlex SRM assay predicts response to specific chemotherapeutic agents in NSCLC

Current cancer treatment regimens rely on the use of chemotherapy agents that inhibit DNA replication and repair machinery. Several proteins are involved in this mechanism and these proteins have been identified as predictive biomarkers of response for many chemotherapy agents. While it has been demonstrated that expression levels of these biomarkers can predict chemotherapy response, chemotherapy in both the adjuvant and metastatic settings for NSCLC are not based on biomarker analysis. We have developed a quantitative, multiplex, mass spectrometry based diagnostic assay that can identify multiple biomarkers associated with chemotherapy benefit.

At the time of abstract submission, the expression levels of each biomarker were surveyed in 23 NSCLC patients, and the biomarker level for each chemotherapy agent (ERCC1 and XRCC1 for Platinum based chemotherapy; FR alpha and GART for pemetrexed; hENT1 and RRM1 for gemcitabine; and TUBB3 for taxane) was evaluated with clinical outcome. We are extending these analyses with a population of 100 NSCLC tumors with associated outcome.

Our pilot study shows a wide range of expression for each biomarker in patient biopsies. Among these biomarkers, FR alpha in NSCLC shows over 4 orders of magnitude in expression range. Also as expected, each biomarker level was found to be correlated with clinical outcome. For example, patients with high level of FR alpha showed improved response to pemetrexed; patients with lower level of TUBB3 showed improved response to taxane and patients with lower level of hENT1 showed poorer response to gemcitabine.

Our preliminary retrospective data analysis suggests that the ChemoPlex SRM assay can help predict response to specific chemotherapeutic agents. This test can be used to characterize individual tumor biology and identify actionable targets that can better inform patient care.

Citation Format: Eunkyung An, Tae-Jung Kim, Manish Monga, Kathleen Bengali, Alexi Drilea, Joseph Reilly, Marlene Darfler, Jon Burrows, Todd Hembrough. ChemoPlex SRM assay predicts response to specific chemotherapeutic agents in NSCLC. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 566. doi:10.1158/1538-7445.AM2015-566

Abstract 3397: A novel clinical tool that provides quantitative and accurate measurement of Met protein

BACKGROUND:

Overexpression of Met tyrosine kinase receptor is associated with poor prognosis. Overexpression, and particularly MET amplification, are predictive of response to Met-specific therapy in preclinical models. Immunohistochemistry (IHC) of formalin-fixed paraffin-embedded (FFPE) tissues is currently used to select for ‘high Met’ expressing tumors for Met inhibitor trials. IHC suffers from antibody non-specificity, lack of quantitative resolution, and, when quantifying multiple proteins, inefficient use of scarce tissue.

METHODS:

After describing the development of the Liquid-Tissue-Selected Reaction Monitoring-mass spectrometry (LT-SRM-MS) Met assay, we evaluated the expression level of Met in 130 FFPE gastroesophageal cancer (GEC) tissues. We assessed the correlation of SRM Met expression to IHC and mean MET gene copy number (GCN)/nucleus or MET/CEP7 ratio by fluorescence in situ hybridization (FISH).

RESULTS:

Proteomic mapping of recombinant Met identified 418TEFTTALQR426 as the optimal SRM peptide. Limits of detection (LOD) and quantitation (LOQ) for this peptide were 150 and 200 amol/μg tumor protein, respectively. The assay demonstrated excellent precision and temporal stability of measurements in serial sections analyzed one year apart. Expression levels of 130 GEC tissues ranged (&lt;150 amol/μg to 4669.5 amol/μg. High correlation was observed between SRM Met expression and both MET GCN and MET/CEP7 ratio as determined by FISH (n = 30; R2 = 0.898). IHC did not correlate well with SRM (n = 44; R2 = 0.537) nor FISH GCN (n = 31; R2 = 0.509). A Met SRM level of &gt;1500 amol/μg was 100% sensitive (95% CI 0.69-1) and 100% specific (95% CI 0.92-1) for MET amplification.

CONCLUSIONS:

The Met SRM assay measured the absolute Met levels in clinical tissues with high precision. Compared to IHC, SRM provided a quantitative and linear measurement of Met expression, reliably distinguishing between non-amplified and amplified MET tumors. These results demonstrate a novel clinical tool for efficient tumor expression profiling, potentially leading to better informed therapeutic decisions for patients with GEC.

Citation Format: Fabiola Cecchi, Wei-Li Liao, Sheeno Thyparambil, Marlene Darfler, David Krizman, Todd Hembrough, Jon Burrows, Don Bottaro, Daniel V.T. Catenacci. A novel clinical tool that provides quantitative and accurate measurement of Met protein. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 3397. doi:10.1158/1538-7445.AM2015-3397

Abstract P4-11-29: Quantitative measurement of HER2 levels by multiplexed mass spectrometry from FFPE tissue predicts survival in patients treated with anti-HER2 based therapy

Introduction

Approximately 20% of breast cancer patients overexpress HER2 and are treated with anti-HER2 therapies. However, there is a great deal of disparity of HER2 levels in the patients that are classified as HER2 positive (IHC3+). Techniques like FISH or IHC do not allow for HER2 quantification and a significant proportion of patients are wrongly classified as HER2 positive. Liquid Tissue-Selected reaction monitoring (LT-SRM) is a multiplexed mass spectrometric technique that can objectively quantify levels of Her2 and other targets from formalin fixed paraffin embedded (FFPE) sections. Given the different available anti-HER2 therapies (trastuzumab, TDM1, lapatinib and pertuzumab) with different modes of action, it would be beneficial for a clinician to understand the levels EGFR and HER3 so as to personalize the therapy. In this work, we have used LT-SRM to quantitate HER2, EGFR and HER3 from FFPE samples (one slide) of patients treated with anti-HER2 agents and correlated the levels of these proteins to clinical outcome.

Methods

FFPE sections from 60 HER2 positive (IHC3+) primary breast cancer patients were microdissected and proteins were solubilized and digested by trypsin in Liquid Tissue® buffer. Of the 60 samples, 24 were from metastatic setting and 36 from adjuvant setting. After trypsin digestion, internal standards were added and absolute quantitation for multiple proteins was performed using selected reaction monitoring (SRM) mass spectrometry. In addition to LT-SRM, FISH for HER2 was also conducted.

Results

HER2 quantitation by LT-SRM revealed receptor level ranges from 283 to 14938 amol/µg. ROC analysis was conducted and a cut-off of 2758.75 amol/µg gave the optimal sensitivity and specificity. Survival analysis revealed statistically significant DFS (4.40 years vs 3.38 years; p=0.013) and OS (4.43 years vs 4.03 years; p= 0039) in patients expressing ≥ 2758.75 amol/µg in the adjuvant setting and also statistically significant OS (5.51 years vs 3.37 years; p=0.037) in the metastatic setting. Correlation of HER2 FISH and levels of HER2 is ongoing. Approximately 41% of samples expressed EGFR (range 45 to 2317 amol/µg) and similarly 51% of the samples expressed HER3 (range 84 to 360 amol/µg) with 18% of samples expressing all three targets. Correlation of EGFR/HER3 expression with clinical outcome is ongoing.

Conclusion

We used an objective multiplex non-antibody based method to quantify multiple targets from FFPE tissue. Clinical correlation analysis of HER2 revealed improved OS and DFS in samples with high HER2 protein levels. Currently, we are expanding these studies to a larger set of samples and taking into account also the expression of other markers such as EGFR and HER3. This approach can potentially identify those tumors that are more dependent on these receptors for survival and also those patients that are exquisitely sensitive to anti-HER2 therapy.

Citation Format: Paolo Nuciforo, Sheeno Thyparambil, Claudia Aura, Ana Garrido-Castro, Vicente Peg, Jose Jimenez, William Hoos, Jon Burrows, Todd Hembrough, Jose Perez-Garcia, Javier Cortes, Maurizio Scaltriti. Quantitative measurement of HER2 levels by multiplexed mass spectrometry from FFPE tissue predicts survival in patients treated with anti-HER2 based therapy [abstract]. In: Proceedings of the Thirty-Seventh Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2014 Dec 9-13; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2015;75(9 Suppl):Abstract nr P4-11-29.

Her2 expression in gastroesophageal cancer (GEC) FFPE tissue using mass spectrometry (MS) and correlation with HER2 gene amplification

82

Background: HER2+ GEC derived benefit from trastuzumab. Her2 IHC is semi-quantitative, subjective, and sensitive to antigen instability; HER2 FISH is laborious, expensive, and subjective. False positivity/negativity have been described. Also, these are low throughput assays; there is known molecular heterogeneity, with several putative biomarkers, and only scarce tissue to assess for each. We sought to evaluate the association of Her2 MS expression with HER2 FISH, along with other markers within the ‘GEC-plex’. Methods: We utilized a previously described unique Her2 peptide and quantification method (Hembrough et al J Clin Oncol 32,2014(suppl 3;abstr17)). The assay was run on 27 cell lines, in parallel with HER2:CEP17 FISH. Her2 expression thresholds were established for HER2 amplification using ROC curves. We adjusted for Her3, Egfr, and Met MS expression levels and sample HER2:CEP17 ratio heterogeneity in a multiple linear regression model. The model/cut-offs were then validated prospectively on GEC tissues (n=142). Results: Her2 MS on cell lines revealed concordance with FISH (HER2:CEP17) ratio (R2=0.75), which improved by adjusting for Her3 MS, Egfr MS, Met MS and HER2:CEP17 heterogeneity (R2>0.98), with significant interactions. IHC correlation with HER2:CEP17 ratio was poor (R2=0.12). A wide range of expression was noted within IHC3+ patients (<150-24671amol/ug). Her2 MS expression (>150 amol/ug) was seen in 72.9% (102/142) of tissues (range <150-24671amol/ug); 9.9% (14/142) had Her2 > 750 amol/ug - all were HER2 FISH amplified. 6/142 (4%) cases <500 amol/ug were clinically ‘HER2amplified’. IHC/FISH results for cases with 550-750 amol/ug demonstrated an ‘equivocal’ zone, not unlike ‘IHC 2+’, but less frequent (8/142, 5.6% vs 46/142 32.4%). Conclusions: The MS HER2 assay can be multiplexed with other GEC biomarkers. A robust model was developed that showed strong correlation of Her2 MS with HER2:CEP17 ratio, particularly when adjusting for covariates Egfr MS, Met MS, Her3 MS, and HER2 FISH heterogeneity. Future analysis will assess the established model as a tool for better prediction of therapeutic benefit from anti-Her2 therapy compared to current methods.

EBV & HHV6 reactivation is infrequent and not associated with MS clinical course

BACKGROUND

Among the environmental factors associated with multiple sclerosis (MS) causation, some of the strongest associations are with Epstein-Barr virus (EBV), and to a lesser extent human herpesvirus 6 (HHV6). Associations with clinical course are less conclusive, however.

METHODS

We evaluated serum anti-EBV-EA-R IgG and anti-HHV6 IgM, and EBV and HHV6 viral load (VL) for their associations with relapse, disability, and progression in disability in a prospective cohort of 198 participants with clinically definite MS.

RESULTS

Anti-EBV-EA-R IgG was detected in 81.8% of cases at study entry, and titers remained essentially unchanged during the study. Anti-HHV6 IgM was detected in only one participant, and EBV-VL (29%) and HHV6-VL (1.8%) were detected in a minority of samples, and where detected levels were low. Our previously demonstrated association between anti-HHV6 IgG and relapse hazard was not affected by adjustment for parameters of reactivation. We found no evidence that any of the viral markers were associated with disability or progression in disability. In relation to relapse, only EBV-VL was positively associated, although this was strongly influenced by a single individual.

CONCLUSION

Using a prospective cohort design, we found no convincing evidence that reactivation parameters of EBV or HHV6 were associated with subsequent MS relapse hazard or progression in disability, confirming previous findings, and indicating that herpesvirus reactivation is not an important driver of relapse or disability in this established MS population.

Abstract 918: Clinical validation of a multiplexed ChemoPlex SRM assay in FFPE human tumor tissue

Background: Current cancer treatment regimens rely on the use of chemotherapy agents that inhibit DNA replication and repair machinery. Several proteins are involved in this mechanism, such as TOPO1, TOPO2A, RRM1, FR-alpha and hENT1. The expression levels and activities of these proteins can greatly affect the success of chemotherapy; however current treatment indications are not based on tumor expression levels of these proteins. We have developed a quantitative, multiplexed ChemoPlex SRM method to evaluate these markers in a host of solid tumors from a limited amount of FFPE biopsy tissue using our Liquid Tissue®-SRM (LT-SRM) platform. Use of this method will enable a physician to understand individual tumor molecular machinery and ultimately could lead to individualized treatment decisions leading to better patient care.

Methods: We used trypsin digestion mapping of recombinant proteins to identify optimal quantitative peptides for the ChemoPlex SRM assay. Standard curves were generated to determine the LOD, LOQ, accuracy, precision and linearity of the assay. The assay was pre-clinically validated on 14 cell lines with known expression levels of these Chemo-targets, and the assay was then run on microdissected archived FFPE human tissue samples from lung, gastro-esophageal cancer (GEC), breast, liver, colorectal, and ovarian tumors.

Results: The peptides chosen for the 5 Chemo-Plex targets had LOD values of 150, 50, 300, 200, and 100 amol (CV&lt;20%) for FR alpha, hENT1, TOPO1, TOPO2A, and RRM1, respectively. Fourteen cell lines were assayed for the Chemo-target expressions by LT-SRM, and regression analysis between protein and mRNA analysis for each target demonstrated varying correlations (R2=0.91(FR alpha); 0.78 (hENT1); 0.16 (TOPO1); 0.56 (TOPO2A); 0.59 (RRM1)) suggesting that RT-PCR measurements of mRNA levels would not be representative of cellular protein levels and therefore not useful for biomarker analysis for physicians. Our initial clinical analysis shows that FR alpha was detectable only in certain lung tumors (especially adenocarcinoma) and ovarian tumors; breast cancer tumors were found to have a wide range of hENT1 expression (LOD -1,284 amol/ug) while hENT1 expression in other tissues ranged from 90 to 377 amol/ug. TOPO1 had fairly ubiquitous expression (359 -1,300 amol/ug) except for one GEC and one breast cancer tissue. TOPO2A was identified in all tissue types (227-1,057 amol/ug). All samples except 1 GEC tissue express RRM1 (160 - 958 amol/ug)

Discussion: We describe the development and initial clinical validation of a quantitative proteomic ChemoPlex SRM assay which accurately measures the expression of five chemotherapy targets in FFPE tumor tissue. When multiplexed along with other druggable biomarkers, the ChemoPlex SRM assay will allow more accurate identification of patients that are likely to benefit from the combination of chemotherapy and targeted therapies.

Citation Format: Eunkyung An, Wei-Li Liao, Sheeno Thyparambil, Adele Blackler, Jamar Uzzell, Kathleen Bengali, Marlene Darfler, Jon Burrows, Todd Hembrough. Clinical validation of a multiplexed ChemoPlex SRM assay in FFPE human tumor tissue. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 918. doi:10.1158/1538-7445.AM2014-918

Absolute quantitation of Met using mass spectrometry for clinical application: assay precision, stability, and correlation with MET gene amplification in FFPE tumor tissue

Background

Overexpression of Met tyrosine kinase receptor is associated with poor prognosis. Overexpression, and particularly MET amplification, are predictive of response to Met-specific therapy in preclinical models. Immunohistochemistry (IHC) of formalin-fixed paraffin-embedded (FFPE) tissues is currently used to select for ‘high Met’ expressing tumors for Met inhibitor trials. IHC suffers from antibody non-specificity, lack of quantitative resolution, and, when quantifying multiple proteins, inefficient use of scarce tissue.

Methods

After describing the development of the Liquid-Tissue-Selected Reaction Monitoring-mass spectrometry (LT-SRM-MS) Met assay, we evaluated the expression level of Met in 130 FFPE gastroesophageal cancer (GEC) tissues. We assessed the correlation of SRM Met expression to IHC and mean MET gene copy number (GCN)/nucleus or MET/CEP7 ratio by fluorescence in situ hybridization (FISH).

Results

Proteomic mapping of recombinant Met identified ⁴¹⁸TEFTTALQR⁴²⁶ as the optimal SRM peptide. Limits of detection (LOD) and quantitation (LOQ) for this peptide were 150 and 200 amol/µg tumor protein, respectively. The assay demonstrated excellent precision and temporal stability of measurements in serial sections analyzed one year apart. Expression levels of 130 GEC tissues ranged (<150 amol/µg to 4669.5 amol/µg. High correlation was observed between SRM Met expression and both MET GCN and MET/CEP7 ratio as determined by FISH (n = 30; R² = 0.898). IHC did not correlate well with SRM (n = 44; R² = 0.537) nor FISH GCN (n = 31; R² = 0.509). A Met SRM level of ≥1500 amol/µg was 100% sensitive (95% CI 0.69–1) and 100% specific (95% CI 0.92–1) for MET amplification.

Conclusions

The Met SRM assay measured the absolute Met levels in clinical tissues with high precision. Compared to IHC, SRM provided a quantitative and linear measurement of Met expression, reliably distinguishing between non-amplified and amplified MET tumors. These results demonstrate a novel clinical tool for efficient tumor expression profiling, potentially leading to better informed therapeutic decisions for patients with GEC.

Simulated air quality and pollutant budgets over Europe in 2008

Major gaseous and particulate pollutant levels over Europe in 2008 have been simulated using the offline-coupled WRFCMAQ chemistry and transport modeling system. The simulations are compared with surface observations from the EMEP stations, ozone (O3) soundings, ship-borne O3 and nitrogen dioxide (NO2) observations in the western Mediterranean, tropospheric NO2 vertical column densities from the SCIAMACHY instrument, and aerosol optical depths (AOD) from the AERONET. The results show that on average, surface O3 levels are underestimated by 4 to 7% over the northern European EMEP stations while they are overestimated by 7-10% over the southern European EMEP stations and underestimated in the tropospheric column (by 10-20%). Particulate matter (PM) mass concentrations are underestimated by up to 60%, particularly in southern and eastern Europe, suggesting underestimated PM sources. Larger differences are calculated for individual aerosol components, particularly for organic and elemental carbon than for the total PM mass, indicating uncertainty in the combustion sources. Better agreement has been obtained for aerosol species over urban areas of the eastern Mediterranean, particularly for nss-SO4(2), attributed to the implementation of higher quality emission inventories for that area. Simulated AOD levels are lower than the AERONET observations by 10% on average, with average underestimations of 3% north of 40°N, attributed to the low anthropogenic emissions in the model and 22% south of 40°N, suggesting underestimated natural and resuspended dust emissions. Overall, the results reveal differences in the model performance between northern and southern Europe, suggesting significant differences in the representation of both anthropogenic and natural emissions in these regions. Budget analyses indicate that O3 and peroxyacetyl nitrate (PAN) are transported from the free troposphere (FT) to the planetary boundary layer over Europe, while other species follow the reverse path and are then advected away from the source region.

Quantification of MET expression using mass spectrometry (MS): Assay precision and stability in FFPE tumor tissue

16

Background: Overexpression of MET in gastroesophageal cancer (GEC) is associated with poor prognosis and potentially predictive of anti-MET therapeutic benefit. IHC has been the method chosen to quantify MET expression to date. However, IHC is semi-quantitative, suffers from cross-reactivity, and is low throughput. Moreover, MET IHC is hampered by antigenic instability in FFPE sections, limiting its utility to recently cut FFPE sections. Increasing recognition of the importance of other biomarkers in GEC suggests that ‘economic’ testing of scarce samples will be required. We sought to develop a MET quantitative assay within our ‘GEC-plex’ Liquid-Tissue-selected reaction monitoring (LT-SRM) MS test. Methods: We used trypsin digestion mapping of rMET to identify unique peptides for MS assay development. The assay was pre-clinically validated in 5 cell lines, where electrochemiluminescence (ECL) immunoassay measurement of MET was also performed. To assess the MET MS assay stability from archival FFPE sections, freshly cut FFPE tissue sections were immediately microdissected, processed and analyzed, while adjacent sections were processed and analyzed one year after cutting, to compare temporal quantification from the same FFPE samples (n=33). MET expression was assessed in GEC cases (n=121), and compared to IHC and FISH in select cases. Results: Tryptic digestion mapping of rMET showed that peptide TEFTTALQR was optimal for MET quantification. The LLOD for this peptide was 150 amol with CV<20%. Validation of the MET MS assay on 5 cell lines revealed concordance when compared to ECL (R2=0.99). The MET MS assay demonstrated temporal stability of serial sections cut from 33 samples analyzed one year apart: CVs<20%, R2=0.75. Analysis of 121 GEC FFPE tissues showed a broad range of MET expression levels (<150-4600 amol/ug), with 36/121 (29.7%) having detectable levels, similar to that observed using IHC. MS expression thresholds were determined that reliably identified MET gene amplification; sensitivity and specificity of these thresholds will be presented. Conclusions: ‘GEC-plex’ has a quantitative, sensitive, and specific MET MS assay that can be multiplexed along with other GEC biomarkers.

Quantification of HER2 from gastroesophageal cancer (GEC) FFPE tissue by mass spectrometry (MS)

17

Background: Trastuzumab had a survival benefit in ‘HER2 positive’ GEC, determined by IHC/FISH. These companion diagnostics have limitations. IHC is semi-quantitative, subjective, and sensitive to antigen instability in FFPE; FISH is laborious, expensive, and subjective. Gene amplification may not correlate to protein expression. Moreover these are low throughput assays. There is increased recognition of profound interpatient molecular heterogeneity with several putative biomarkers, and only scarce tissue to assess for each one. We sought to evaluate our MS platform on GEC FFPE tissues for HER2 status compared to IHC/FISH. We also applied the “GEC-plex” of 11 other potentially predictive/prognostic markers for GEC. Methods: We utilized trypsin digestion mapping of rHER2 to identify unique peptides for SRM development. Stable isotope-labeled peptides were synthesized as internal standards, and standard curves were generated in a complex eukaryotic matrix (PC3 cells) to determine LOD, LLOQ, accuracy, precision and linearity of the assays. The assay was run on 17 GEC cell lines, in parallel with FISH/IHC, and expression thresholds were established for HER2+/HER2-; the sensitivity/specificity of the established cutoffs were then tested prospectively in FFPE GEC tissues on 10uM FFPE LCM slides (n=121). HER2 stability from FFPE sections was assessed by assaying 33 freshly cut FFPE samples; the adjacent sections were processed one year later. Results: The HER2 peptide chosen (ELVSEFSR) had a LOD of 100 amol and CV<20%. HER2 MS on GEC cell lines revealed concordance with FISH (HER2:CEP17) ratio (R2=0.96). The analysis suggested HER2 expression > 750 amol/ug was indicative of HER2 amplification. The assay was stable in archival FFPE sections (R2=0.76). For GEC FFPE cases, ‘any’ HER2 expression was seen in 69.4% of cases; 8.2% showed HER2 > 750 amol (10/121) - all were HER2 amplified. No cases <550 amol/ug were HER2 amplified. IHC/FISH results for cases with 550-750 amol/ug demonstrated a heterogeneous ‘equivocal’ zone, not unlike ‘IHC 2+’, which may require FISH confirmatory testing. Conclusions: ‘GEC-plex’ has a quantitative, sensitive, and specific HER2 assay that can be multiplexed along with other GEC biomarkers.

Abstract A24: Development and clinical validation of a quantitative mass spectrometric assay for PD-L1 protein in FFPE NSCLC samples

Background: Binding of PD-L1 expressed on tumor cells to the PD1 on T lymphocytes transduces immuno-inhibitory signals which cripples the T cell's ability to combat the tumor. Several anti-PD-L1 and anti-PD1 agents are in clinical trials and both regimens have reported promising preliminary results in NSCLC patients. (Brahmer et al., 2012 and Inman, 2013).These studies suggest that tumor expression of PD-L1 is associated with a response to either anti-PD-L1 and anti-PD1 treatment. Immunohistochemistry (IHC) is the current method to assess PD-L1 expression in FFPE tissue; however, PD-L1 IHC has yielded mixed results; some studies showed high false positive by IHC while another study showed that 13% of the PD-L1 negative patients responded to treatment. Moreover, IHC is low throughput and assessing multiple druggable targets by IHC is tissue consuming. As such, there is an urgent need to develop quantitative and highly multiplexed tests to assess biomarker expression. We have developed and clinically validated a quantitative mass spectrometric assay to measure PD-L1 protein expression in FFPE tissue biopsies.

Method: We used trypsin digestion mapping of recombinant PD-L1 to identify optimal quantitative peptides. Stable isotope-labeled peptides were synthesized as internal standards, and standard curves were generated in pyrococcus complex matrix to determine LOD, LLOQ, accuracy, precision and linearity of the assay. The PD-L1 assay was pre-clinically validated on 14 cell lines with known expression levels of PD-L1. The assay was then run on archived FFPE sections from in 9 normal tissues, 21 early staged (stage 1 and 2) and 4 advanced staged (stage 3) NSCLC patients. We also used Lung OncoPlex assay to sub-classify NSCLC samples to adenocarcinoma and squamous cell carcinoma. All of the samples were screened in replicates and multiple machines were used to check technical variability.

Results: A 10 point calibration curve using five replicates was used to determine the LOD (75 amol) and LOQ (100 amol) for the PD-L1 assay. Fourteen (14) cell lines were assayed for PD-L1 expression by LT-SRM. PD-L1 protein expression was detected in 7 out of 14 cell lines The regression analysis between SRM and mRNA analysis (Broad Institute) demonstrated excellent correlation (R2=0.8894). The NSCLC cell line HCC827 and breast cancer cell line MDA-MB-231 had the highest levels of PD-L1, 374.78 and 298.27 amol/μg protein, respectively. Our initial clinical analysis of NSCLC tissue shows that while no normal lung tissue expresses detectable levels of PD-L1, ~24 % of early stage NSCLC (5/21) and 50 % of advanced stage NSCLC (2/4) express measurable PD-L1 protein. Interestingly, in this initial cohort, all of the PD-L1 positive early staged NSCLC were squamous cell carcinoma while in a small set of advanced staged NSCLC, PD-L1 expression was seen in both squamous cell carcinoma (1/3) and adenocarcinoma (1/1). Characterization of larger cohorts of NSCLC tissue is currently underway and will be presented.

Discussion: The need to characterize expression levels of druggable targets in small NSCLC biopsies is becoming ever more critical as new drug targets and biomarkers are identified. Here we describe the development and initial clinical validation of a quantitative proteomic PD-L1 assay which accurately measures PD-L1 expression levels in FFPE tumor tissue. Initial PD-L1 screening using clinical NSCLC samples suggests that more advanced NSCLC patients are more likely to be PD-L1 positive compared to early stage NSCLC patients. Additionally, patients with squamous cell carcinoma are very likely to express PD-L1. Interestingly, Soria et al. (2013) has recently shown a high response rate to PD-L1 therapy in smokers with squamous cell carcinoma. We are currently expanding this initial clinical validation to assess PD-L1 expression levels in larger cohorts, including both adeno and squamous carcinoma. Additional quantitative assays for both lymphocyte (CD3, CD8, CD68) and immunotargets (PD1, B7-H3) are under development. This proteomic assay promises to be a critical component of our multiplexed biomarker analysis, and will allow more accurate identification of potential candidates for PD-L1 or PD1 targeted therapies.

Citation Format: Eunkyung An, Wei-Li Liao, Sheeno Thyparambil, Jaime Rodriguez, Ravi Salgia, Ignacio I. Wistuba, Jon Burrows, Todd Hembrough. Development and clinical validation of a quantitative mass spectrometric assay for PD-L1 protein in FFPE NSCLC samples. [abstract]. In: Proceedings of the AACR-IASLC Joint Conference on Molecular Origins of Lung Cancer; 2014 Jan 6-9; San Diego, CA. Philadelphia (PA): AACR; Clin Cancer Res 2014;20(2Suppl):Abstract nr A24.

Abstract B09: Multiplexed mass spectrometry-based assay to quantify translocation markers from non-small cell lung cancer (NSCLC) FFPE tissue

Introduction: Translocations in ALK, ROS1 and RET have been shown to be oncogenic in NSCLC. Lung cancers having ALK or ROS1 rearrangements represent unique subpopulations that are seen in only 2-5% and 1-2% of NSCLC, respectively. ALK fusions lead to constitutive activation of ALK signaling involved in cell proliferation. Crizotinib has significant anti-tumor activity in ALK rearranged NSCLC and break-apart FISH is the approved diagnostic test to determine treatment eligibility. However, FISH is laborious, expensive and low throughput, and thus is not ideal for the detection of oncogenic drivers of low frequencies. In patients with advanced disease, a small tissue biopsy is often the only material available so yielding as much information as possible from a limited sample is necessary. The aim of this study was to develop a multiplexed quantitative Liquid-Tissue-selected reaction monitoring (LT-SRM) assay for assessing ALK, ROS1, and RET expression within our “Lung OncoPlex” MS test. The LT-SRM platform quantitates these translocation markers along with several diagnostic and potentially targetable biomarkers, e.g. TTF1, K7, p63, K5, EGFR, HER2, HER3, MET, KRAS and IGF1R, in NSCLC.

Methods: We used trypsin digestion mapping of recombinant proteins specific for ALK, ROS1, and RET to identify optimal quantitative peptides. Stable isotope-labeled peptides were synthesized as internal standards, and standard curves were generated in Pyrococcus complex matrix to determine LOD, LLOQ, accuracy, precision and linearity of the assays. The ALK assay was pre-clinically validated in an EML4-ALK rearrangement positive cell line-H3122. ALK and ROS1 were screened in 87 archived FFPE sections from NSCLC.

Results: We identified at least two optimal peptides for each target. At least one peptide from each protein had acceptable technical assay performance and was used for assay development. H3122 cell expressed 396 amol ALK/ug cell protein, while 11 ALK translocation positive NSCLC tissues expressed ALK from 107 to 437 amol/ug protein. ALK peptides were not detected in ALK negative control NSCLC tissues or in a single ALK translocation positive case. ROS1 was detected in 2 of 87 NSCLC samples at levels of 659 amol/ug in a case of unknown translocation status and 377 amol/ug in a ROS1 translocation positive case. Finally, the Lung OncoPlex assay successfully subtyped lung adenocarcinoma and quantified the other potentially targetable biomarkers.

Conclusions: The Lung OncoPlex assay was able to detect ALK protein in 11/12 ALK rearranged samples. In the one proteomically negative/FISH+ case, we are performing ALK IHC to assess ALK protein expression, as well as DNA sequencing to evaluate for potential mutations within the MS targeted peptides. Of the two cases positive for ROS1 by the MS assay, one is known to be FISH positive and the other is undergoing FISH verification. RET protein expression has not yet been assessed in any known RET translocation positive cases; however, the RET technical performance suggests this is a promising assay and we are continuing to screen for RET positive control samples. While additional studies are needed to validate the clinically utility of the ALK, ROS1, and RET assay; multiplexed proteomic screening of patient tissue could be performed at the time of initial biopsy, allowing for simultaneous assessment of multiple clinically actionable gene rearrangements and biomarker targets.

Citation Format: Wei-Li Liao, Sheeno Thyparambil, Eunkyung An, Christopher P. Hartley, patrick Ma, Jaime Rodriguez, Ignacio Wistuba, Jon Burrows, Todd Hembrough, Laura J. Tafe. Multiplexed mass spectrometry-based assay to quantify translocation markers from non-small cell lung cancer (NSCLC) FFPE tissue. [abstract]. In: Proceedings of the AACR-IASLC Joint Conference on Molecular Origins of Lung Cancer; 2014 Jan 6-9; San Diego, CA. Philadelphia (PA): AACR; Clin Cancer Res 2014;20(2Suppl):Abstract nr B09.

Identification of RBCK1 as a novel regulator of FKBPL: implications for tumor growth and response to tamoxifen

FKBPL has been implicated in processes associated with cancer, including regulation of tumor growth and angiogenesis with high levels of FKBPL prognosticating for improved patient survival. Understanding how FKBPL levels are controlled within the cell is therefore critical. We have identified a novel role for RBCK1 as an FKBPL-interacting protein, which regulates FKBPL stability at the post-translational level via ubiquitination. Both RBCK1 and FKBPL are upregulated by 17-β-estradiol and interact within heat shock protein 90 chaperone complexes, together with estrogen receptor-α (ERα). Furthermore, FKBPL and RBCK1 associate with ERα at the promoter of the estrogen responsive gene, pS2, and regulate pS2 levels. MCF-7 clones stably overexpressing RBCK1 were shown to have reduced proliferation and increased levels of FKBPL and p21. Furthermore, these clones were resistant to tamoxifen therapy, suggesting that RBCK1 could be a predictive marker of response to endocrine therapy. RBCK1 knockdown using targeted small interfering RNA resulted in increased proliferation and increased sensitivity to tamoxifen treatment. Moreover, in support of our in vitro data, analysis of mRNA microarray data sets demonstrated that high levels of FKBPL and RBCK1 correlated with increased patient survival, whereas high RBCK1 predicted for a poor response to tamoxifen. Our findings support a role for RBCK1 in the regulation of FKBPL with important implications for estrogen receptor signaling, cell proliferation and response to endocrine therapy.

Development and clinical validation of an adeno/squamous multiplexed diagnostic assay for NSCLC

e19057

Background: The diagnosis of adenocarcinoma (ADC) vs. squamous cell carcinoma (SCC) in NSCLC is critical since new therapies (e.g. pemetrexed) are restricted to non-squamous NSCLC. Most diagnoses are made based on histopathology, though IHC is often performed as well. Since IHC is not quantitative, interpretation of intensity is subjective, and reproducibility can be problematic. Using the Liquid Tissue-SRM mass spectrometry (MS) platform, we have developed a quantitative, multiplexed clinical diagnostic assay to measure the adeno/squamous markers TTF-1/CK7 (ADC) and K5 and p63/40 (SCC) in FFPE tissue. This proteomic assay is epitope independent, and highly reproducible. Methods: Recombinant K5, K7, TTF-1 and p63/p40, were subjected to trypsin digestion mapping to identify peptides for MS analysis. Heavy isotope labeled peptides were synthesized as positive control peptides for quantitation. The multiplexed assay was technically validated on cell lines, and human tumor tissues. Results: ADC/SCC proteomic analysis was performed on a training set of 39 NSCLC tissues from U. of Chicago (20 ADC and 19 SCC). Principal Component Analysis was used to define optimal quantitative cutoffs for each of the four markers for the two tumor subtypes. The ADC diagnosis was unequivocal for all 20 ADC samples, however within the 19 SCC’s, one sample appeared to be ADC and two samples had markers for both ADC and SCC. Proteomic analysis of a test set of 194 NSCLC tumors (98 ADC and 98 SCC based on pathology reports) from MD Anderson Cancer Center was consistent with the observations in the training set. 93/98 ADC cases were confirmed by proteomic analysis, four ADC cases showed mixed or SCC phenotypes. Proteomic analysis confirmed 58/98 SCC cases but identified 27 cases as mixed ADC SCC or ADC based on TTF1/K5 expression. Further studies are ongoing to determine the clinical utility of these findings. Conclusions: These data demonstrate that quantitative proteomic analysis can define cut offs for ADC and SCC Biomarkers profiles in NSCLC tumors. These profiles can determine ADC, SCC and mixed phenotypes and provide physicians with accurate information to help them stratify their patients to the right evidence based treatment therapy.

Application of selected reaction monitoring for multiplex quantification of clinically validated biomarkers in formalin-fixed, paraffin-embedded tumor tissue

One of the critical gaps in the clinical diagnostic space is the lack of quantitative proteomic methods for use on formalin-fixed, paraffin-embedded (FFPE) tissue. Herein, we describe the development of a quantitative, multiplexed, mass spectrometry-based selected reaction monitoring (SRM) assay for four therapeutically important targets: epidermal growth factor receptor, human EGF receptor (HER)-2, HER3, and insulin-like growth factor-1 receptor. These assays were developed using the Liquid Tissue-SRM technology platform, in which FFPE tumor tissues were microdissected, completely solubilized, and then subjected to multiplexed quantitation by SRM mass spectrometry. The assays were preclinically validated by comparing Liquid Tissue-SRM quantitation of FFPE cell lines with enzyme-linked immunosorbent assay/electrochemiluminescence quantitation of fresh cells (R(2) > 0.95). Clinical performance was assessed on two cohorts of breast cancer tissue: one cohort of 10 samples with a wide range of HER2 expression and a second cohort of 19 HER2 IHC 3+ tissues. These clinical data demonstrate the feasibility of quantitative, multiplexed clinical analysis of proteomic markers in FFPE tissue. Our findings represent a significant advancement in cancer tissue analysis because multiplexed, quantitative analysis of protein targets in FFPE tumor tissue can be tailored to specific oncological indications to provide the following: i) complementary support for anatomical pathological diagnoses, ii) patient stratification to optimize treatment outcomes and identify drug resistance, and iii) support for the clinical development of novel therapies.

Abstract 1207: Development of a quantitative gastroesophageal cancer selected reaction monitoring mass Spectrometric Multiplex Assay for use in FFPE tumor tissues

Aberrant over-expression of receptor tyrosine kinases, (e.g. MET, HER, FGFR, and IGFR) as well as other oncogenic mediators (e.g. KRAS, PI3 Kinase and SRC) are known drivers of gastroesophageal adenocarcinoma (GEC), subdividing the disease into distinct molecular subsets. Inter/intrapatient tumor heterogeneity suggests that an expedient, reliable, medium throughput oncogene protein expression profiling will provide vital information to better personalize cancer care. To date, clinical quantification of protein in formalin fixed paraffin embedded (FFPE) tissues is limited to immunohistochemistry (IHC), which is semi-quantitative at best. Moreover, IHC of multiple proteins of interest is laborious, time consuming, wasteful of scarce tissue, and costly. We present a quantitative mass spectrometric (MS) assay for FFPE GEC utilizing Liquid Tissue - Selected Reaction Monitoring (SRM), with subsequent multiplex quantification of relevant oncoproteins in a panel of gastroesophageal cancer (GEC) cell lines and tissues.

Using trypsin digestion mapping of recombinant oncoproteins, we identified unique peptide sequences, and built quantitative MS assays which could be multiplexed into a single SRM analysis of 1μg of tumor protein. Assays were preclinically validated on 10 different formalin fixed (FF) cell lines.

We then tested the GEC-plex assay on a panel of FFPE GEC cell lines characterized by immunoblot (IB), IHC, and gene copy number by FISH. In addition to RON, we multiplexed SRM quantification of Met, EGFR, HER2, HER3, IGF1R, FGFR2, KRAS and cSRC. We evaluated 17 GEC lines including AGS wild type, scrambled shRNA (AGS-SC) and RON shRNA knockdown (AGS-KD) to assess ‘post-treatment’ changes in oncogene expression. We then evaluated 100 GEC human cancer tissues with paired peritoneal metastases when available and select paraneoplastic normal tissues using laser microdissection of tumor tissue from a single unstained 10μm thick section.

Validation of the GEC-plex SRM assay on GEC cell lines revealed very high concordance when compared to IB and IHC measurement. The AGS-WT/SC cells showed comparable levels of RON (284/323 amol/μg cell protein), while RON was not detected in AGS-KD cells, as expected. Measurement of oncoproteins in GEC cell lines and tissues correlated well with IHC and FISH data. Multiplex oncogene quantification of all cell lines and tissues, along with expression profile changes in the AGS RON KD line compared to AGS-WT/SC will be presented.

Taken together, these data demonstrate a sensitive, accurate, and quantitative assay to measure relevant actionable oncoproteins in FF cells. The GEC-plex multiplexed oncogene expression of these tumors was feasible and expedient using limited tissue from clinical samples, and is a novel clinically applicable approach for tumor characterization for baseline and post-treatment assessment.

Citation Format: Daniel V. Catenacci, Peng Xu, Les Henderson, Wei-Li Liao, Sheeno Thyparambil, Jon Burrows, Todd Hembrough. Development of a quantitative gastroesophageal cancer selected reaction monitoring mass Spectrometric Multiplex Assay for use in FFPE tumor tissues. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 1207. doi:10.1158/1538-7445.AM2013-1207

Abstract 41: Development of a quantitative colorectal cancer SRM assay for use in FFPE tumor tissues

Introduction: Aberrant over-expression of receptor tyrosine kinases, including the MET, HER, FGFR, and IGFR families along with other critical downstream oncogenic mediators including KRAS, BRAF, PI3 Kinase and SRC are known drivers of colorectal cancer (CRC), subdividing the disease into distinct molecular subsets. Inter-patient tumor heterogeneity suggests that an expedient, reliable, medium throughput oncogene protein expression profiling will provide vital information to better personalize cancer care. Moreover, intra-patient tumor heterogeneity from primary tumor to metastatic disease is likely to influence biomarker prediction of response to specific targeted agents. To date, clinical quantification of protein in formalin fixed paraffin embedded (FFPE) tissues is limited to immunohistochemistry (IHC), which is semi-quantitative at best. Moreover, IHC of multiple proteins of interest is laborious, time consuming, wasteful of scarce tissue, and costly. Other protein quantification methods (ELISA, ECL) would require non-standard tissue processing for analysis. We present a quantitative mass spectrometric (MS) assay for CRC utilizing Liquid Tissue - Selected Reaction Monitoring (SRM), with subsequent multiplex quantification of relevant oncoproteins in a cohort of CRC paired primary and metastatic tumor tissues.

Methods: Using trypsin digestion mapping of recombinant oncoproteins, we identified unique peptide sequences, and built quantitative MS assays which could be multiplexed into a single SRM analysis of 1μg of tumor protein. Assays were preclinically validated on 10 different formalin fixed (FF) cell lines.

We then tested the ‘CRC-plex’ MS assay with multiplexed SRM quantification of Met, RON, EGFR, HER2, HER3, IGF1R, FGFR2, KRAS and cSRC on 42 primary human CRC cancer tissues, with paired metastases when available obtained from core biopsy or metastatectomy, using laser capture microdissection of the target material from a single unstained 10μm thick section per sample.

Results: Validation of the CRC-plex SRM assay on cell lines and FFPE tissues revealed very high concordance when compared to IB and IHC. Multiplex oncogene quantification of all tissues, to the attomole/microgram level, will be presented, highlighting inter-patient and intra-patient (from primary to metastasis) heterogeneity of samples.

Conclusions:

Taken together, these data demonstrate a sensitive, accurate, and quantitative assay to measure relevant actionable oncoproteins in FFPE clinical samples. The CRC-plex multiplexed oncogene expression of these tumors was feasible and expedient using limited tissue from clinical samples, and is a novel clinically applicable approach for tumor characterization for baseline and/or post-treatment assessment.

Citation Format: Todd Hembrough, Wei-Li Liao, Les Henderson, Peng Xu, Sheeno Thyparambil, Jon Burrows, Daniel V. Catenacci. Development of a quantitative colorectal cancer SRM assay for use in FFPE tumor tissues. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 41. doi:10.1158/1538-7445.AM2013-41

Abstract 4471: Combined blockade of PI3K/AKT and EGFR/HER3 enhances antitumor activity in triple negative breast cancer

Background: Up to 60% of triple negative breast cancers (TNBCs) express high levels of EGFR. Moreover, TNBCs are associated with increased frequency of phosphatase and tension homologue (PTEN) loss of function, leading to hyperactivation of the phosphoinositide 3-kinase (PI3K)/AKT pathway. This provides the rationale for using PI3K/AKT inhibitors in this subset of patients. However, compensatory expression of receptor tyrosine kinases (RTKs) such as HER3 may limit efficacy of PI3K/AKT inhibitors. Therefore, we hypothesize that combined targeting of both EGFR and HER3 and the PI3K/AKT pathway will result in superior antitumor activity compared to single agent in TNBC. Materials and Methods: Several TNBC cell lines were treated with MEHD7945A, a dual-action antibody that targets both EGFR and HER3, AKT inhibitor GDC-0068, and pan-PI3K inhibitor GDC-0941. Cell viability was measured by CellTiter-Glo and Crystal Violet. Both cell line- and patient-derived xenograft models of TNBC were treated with MEHD7945A, GDC-0068, GDC-0941, or the combination of MEHD7945A with either GDC-0068 or GDC-0941. Tumor size and histology were examined. Protein expression was measured by Western blot, Mass Spectometry, CEER and immunohistochemistry. Results: GDC-0068 and GDC-0941 treatment resulted in variable inhibition of cell viability, with IC50s ranging from 170 nM to &gt;1 μM across all TNBC cell lines. In cells stimulated with either EGF or Heregulin MEHD7945A prevented EGFR/HER3 receptors phosphorylation and improved the antiproliferative activity of the PI3K/AKT inhibitors. To test the activity of these compounds in vivo we used three different models of TNBC, two cell line (MDA-MB-468 and HCC70)-based and a patient-derived xenograft. MEHD7945, GDC-0941 and GDC-0068 showed variable delay in tumor growth whereas combination of MEHD7945A with either GDC-0068 or GDC-0941 was always superior to single agent treatment. Both combinations either prevented tumor growth or led to tumor shrinkage with complete responses achieved in 1/2 mice in each cohorts. Of note, all the treatments (up to 9 weeks of therapeutic exposure) were well tolerated. Analysis of treated tumors reveals potent inhibition of the PI3K/AKT pathway, with decreased levels phospho-PRAS40 and phospho-S6. Moreover, we confirmed that MEHD7945A effectively prevented EGFR and HER3 phosphorylation consequent to PI3K inhibition. Conclusions: Combined therapy with MEHD7945A and either GDC-0068 or GDC-0941 was superior to monotherapy in preclinical models of TNBC. We are currently exploring the levels of expression/activation of EGFR and HER3 following PI3K/Akt blockade in samples from patients treated with GDC-0068. These findings provide the rationale for combined targeting of PI3K/AKT and EGFR/HER3 in triple negative breast cancers.

Citation Format: Maurizio Scaltriti, Jessica Tao, Dejan Juric, Neil Auricchio, Pau Castel, Natasha Morse, Phillip Kim, Sharat Singh, Saswati Hazra, Todd Hembrough, Jon Burrows, Jose Baselga. Combined blockade of PI3K/AKT and EGFR/HER3 enhances antitumor activity in triple negative breast cancer. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 4471. doi:10.1158/1538-7445.AM2013-4471

Use of formalin-fixed, paraffin-embedded tissue for proteomic biomarker discovery

Application of mass spectrometry to proteomic analysis of tissue is a highly desirable approach to discovery of disease biomarkers due to a direct correlation of findings to tissue/disease histology and in many respects obviating the need for model systems of disease. Both frozen and formalin-fixed, paraffin-embedded (FFPE) tissue can be interrogated; however, worldwide access to vastly larger numbers of highly characterized FFPE tissue collections derived from both human and model organisms makes this form of tissue more advantageous. Here, an approach to large-scale, global proteomic analysis of FFPE tissue is described that can be employed to discover differentially expressed proteins between different histological tissue types and thus discover novel protein biomarkers of disease.

Abstract P1-07-19: Mass Spectrometry Based Quantitative Analysis of the HER Family receptors in FFPE Breast Cancer Tissue

The human EGF receptor family (HER's) consists of two clinically validated drug targets (EGFR and HER2), a third (HER3) currently under investigation for its possible role in the acquisition of multidrug resistance and a fourth (HER4), the role of which is still matter of debate. Drugs inhibiting EGFR or HER2 show significant antitumor activity in the clinic, however, acquisition of resistance is a hallmark of these and most targeted therapies. In the case of EGFR and HER2, one of the emerging resistance mechanisms is the co-expression of HER3. Indeed, recent reports show that inhibition of the PI3K pathway leads to upregulation of HER3, and subsequent resistance. Clinical analysis of protein levels in formalin fixed paraffin embedded (FFPE) tissues is limited to immunohistochemistry (IHC), which is semi-quantitative and requires significant amounts of tissue. Moreover, the vast majority of research groups consider specific HER3 staining by IHC particularly challenging. However, accurate measurement of these targets is critical both for properly defining treatment groups and predicting patterns of resistance.

In order to address these issues, we used trypsin digestion mapping and stable isotope labeled peptides to develop a panel of quantitative mass spectrometric (MS) assays to measure the levels of EGFR, HER2, HER3 and other clinically relevant targets in FFPE breast cancer tissue. These quantitative MS assays were then multiplexed to analyze 1μg of tumor protein.

In this study, we multiplexed HER family analysis on 31 HER2 positive breast cancers. Tumor tissue was microdissected from FFPE sections, and subjected to quantitative MS analysis of EGFR, HER2, HER3 as well as IGF1R and cMET. Quantitation of HER2 showed a broad range of HER2 expression in these tissues. The highest expresser measured 26 fmol/ug tumor tissue, representing amplification and massive protein over expression. In contrast, five tissues showed low levels of HER2 expression, below 1 fmol/ug, similar to HER2 non-amplified cell lines. This suggests that MS quantitation can identify patients with low expression of HER2 who are unlikely to respond to trastuzumab therapy. As a matter of fact, 3 of these 5 low expressing patients had outcome data and showed no response to trastuzumab treatment.

In 28 of 31 patient tissue samples, HER3 showed low levels of expression (100–300 amol/ug tumor tissue) similar to HER3 expression in cell lines, and comparable to low expressing EGFR and HER2 cell lines. The remaining 3 patients had no detectable HER3. This study demonstrates the feasibility of measuring HER3 in multiplex in FFPE breast cancer tissue. Based on the low but widespread expression of HER3 in this cohort, it may be most useful to assess HER3 expression after initial treatment as a marker of potential resistance to targeted therapies.

Taken together, these data demonstrate that a sensitive and quantitative assay to measure oncoproteins in FFPE clinical samples may help stratify patients with variable expression of these targets. Our quantitation of oncogene expression from clinical samples uses a small amount of tissue, is clinically applicable and alleviates the problem of scoring either positive or negative for the expression of a given protein.

Citation Information: Cancer Res 2012;72(24 Suppl):Abstract nr P1-07-19.

Multiplexed mass spectometic quantitation of HER1-3, cMET, and IGF1R in FFPE tumor samples: Implications for targeted therapy and resistance

e21068

Background: The human EGF receptor family (HER’s) consists of two clinically validated drug targets (EGFR and HER2), and two receptors (HER3 and HER4) which are the subject of intensive preclinical and early clinical investigation. Although drugs inhibiting both EGFR and HER2 show significant antitumor activity in the clinic, the acquisition of resistance is a hallmark of these and other targeted therapies. In the case of both targets, one of the emerging resistance mechanisms is the co-expression of other receptor tyrosine kinases, including members of the EGFR superfamily, cMet and IGF1R. As an example, it was recently shown that HER2 co-expression mediates resistance in cetuximab treated head and neck cancer. Similarly, much attention has been paid to HER3 both as a bona fide drug target and a resistance mechanism. Methods: Using trypsin digestion mapping of recombinant proteins, we identified unique peptide sequences from each of these receptors, and built quantitative mass spectrometric (MS) assays which could be multiplexed into a single MS analysis of 1ug of tumor protein. Assays were preclinically validated on 10 formalin fixed cell lines, and FFPE human NSCLC primary tumor xenografts. Results: The validated multiplex assay was used to measure expression levels of HER1-3, cMET and IGF1R in two cohorts of clinical tumor tissue which had been treated with HER family antagonists. One, a set of gefitinib treated NSCLC tumors (N=15) , and a second, a cohort of advanced breast cancer tissues which had adjuvant treatment with trastuzumab(N=18). Here we present expression patterns for each of the RTKs studied, with the intent to begin to define the relationship between RTK expression and response to either gefitinib or trastuzumab treatment. Conclusions: It is important to not only understand primary mechanisms of tumor growth, but also mechanisms of resistance in patients undergoing targeted therapies. Our Liquid Tissue-SRM promises to be a platform which can deliver extremely high sensitivity, absolute specificity as well as multiplexing capabilities to assess critical oncology targets.

Abstract A50: Development of a quantitative RON SRM Assay for use in formalin fixed tumor tissues

Introduction: RON and Met, members of the Met family of tyrosine kinases, are implicated as mediators of tumor progression and metastasis in cancer. Over-expression of each receptor is prognostic of poor survival in resected and metastatic cancers, and expression of RON/Met in preclinical models and early phase clinical trials predicts response to RON/Met specific inhibitors. RON is expressed as a number of alternate splice variants/transcripts, complicating the quantification of the receptor by standard clinical methods. Inter/intrapatient tumor heterogeneity suggests that an expedient, reliable, medium throughput oncogene protein expression profiling will provide vital information to better personalize cancer care, with emphasis on serial biopsies to assess acquired treatment resistance mechanisms. To date, clinical quantification of protein in formalin fixed paraffin embedded (FFPE) tissues is limited to immunohistochemistry (IHC), which is semi-quantitative at best. Moreover, IHC of multiple proteins of interest is laborious, time consuming, wasteful of scarce tissue, and costly. Other protein quantification methods (ELISA, ECL) would require non-standard tissue processing for analysis. We sought to develop a quantitative mass spectrometric (MS) assay for RON utilizing Liquid Tissue – Selected Reaction Monitoring (SRM), with subsequent multiplex quantification of RON, Met, and other previously validated proteins in a panel of gastroesophageal cancer (GEC) cell lines and tissues.

Methods: Using trypsin digestion mapping of recombinant RON, we identified unique peptide sequences, and built quantitative MS assays which could be multiplexed into a single SRM analysis of 1μg of tumor protein. Assays were preclinically validated on 10 different formalin fixed (FF) cell lines. The final assay was validated and the N-terminal RON SRM demonstrated an LOD/LOQ of 62/125. Alternate peptides were chosen to quantify differences in RON splice variants/transcripts.

We then tested the RON MS assay using a panel of FF GEC cell lines previously characterized by immunoblot (IB) and IHC FFPE pellet. In addition to RON, we multiplexed SRM quantification of Met, EGFR, HER2, HER3, IGF1R, and cSRC. We evaluated 15 GEC lines including three AGS lines: wild type (AGS-WT), scrambled shRNA (AGS-SC) and RON shRNA knockdown (AGS-KD) to assess ‘post-treatment’ changes in oncogene expression profiles. We then evaluated 20 GEC human cancer tissues and 5 paraneoplastic normal tissues using laser capture microdissection of the target material from a single unstained 10μm thick section per sample.

Results: In the initial analysis, 4/10 cell lines (HCC827, Colo205, HT29, A431) expressed N-terminal RON (∼250 amol/μg cell protein). Validation of the RON SRM assay on GEC cell lines revealed very high concordance when compared to IB and IHC measurement. The AGS-WT/SC cells showed comparable levels of N-terminal RON (284/323 amol/ug cell protein), while RON was not detected in AGS-KD cells, as expected. Correlation of IB with RON intracellular/extracellular MS assay data will be presented. Measurement of RON in the GEC tissues correlated well with IHC. RON expression was seen in 75% of GEC tissues, and was lower/undetectable in adjacent normal tissues. Multiplex oncogene quantification of all cell lines and tissues, along with expression profile changes in the AGS RON KD line compared to AGS-WT/SC will be presented.

Conclusions: Taken together, these data demonstrate a sensitive, accurate, and quantitative assay to measure RON and its variants in FF cells. Multiplexed oncogene expression of these tumors was feasible and expedient using limited tissue, and is a novel clinically applicable approach for tumor characterization for baseline and post-treatment assessment.

Selected Reaction Monitoring (SRM) Analysis of Epidermal Growth Factor Receptor (EGFR) in Formalin Fixed Tumor Tissue

BACKGROUND

Analysis of key therapeutic targets such as epidermal growth factor receptor (EGFR) in clinical tissue samples is typically done by immunohistochemistry (IHC) and is only subjectively quantitative through a narrow dynamic range. The development of a standardized, highly-sensitive, linear, and quantitative assay for EGFR for use in patient tumor tissue carries high potential for identifying those patients most likely to benefit from EGFR-targeted therapies.

METHODS

A mass spectrometry-based Selected Reaction Monitoring (SRM) assay for the EGFR protein (EGFR-SRM) was developed utilizing the Liquid Tissue®-SRM technology platform. Tissue culture cells (n = 4) were analyzed by enzyme-linked immunosorbent assay (ELISA) to establish quantitative EGFR levels. Matching formalin fixed cultures were analyzed by the EGFR-SRM assay and benchmarked against immunoassay of the non-fixed cultured cells. Xenograft human tumor tissue (n = 10) of non-small cell lung cancer (NSCLC) origin and NSCLC patient tumor tissue samples (n = 23) were microdissected and the EGFR-SRM assay performed on Liquid Tissue lysates prepared from microdissected tissue. Quantitative curves and linear regression curves for correlation between immunoassay and SRM methodology were developed in Excel.

RESULTS

The assay was developed for quantitation of a single EGFR tryptic peptide for use in FFPE patient tissue with absolute specificity to uniquely distinguish EGFR from all other proteins including the receptor tyrosine kinases, IGF-1R, cMet, Her2, Her3, and Her4. The assay was analytically validated against a collection of tissue culture cell lines where SRM analysis of the formalin fixed cells accurately reflects EGFR protein levels in matching non-formalin fixed cultures as established by ELISA sandwich immunoassay (R2 = 0.9991). The SRM assay was applied to a collection of FFPE NSCLC xenograft tumors where SRM data range from 305amol/μg to 12,860amol/μg and are consistent with EGFR protein levels in these tumors as previously-reported by western blot and SRM analysis of the matched frozen tissue. In addition, the SRM assay was applied to a collection of histologically-characterized FFPE NSCLC patient tumor tissue where EGFR levels were quantitated from not detected (ND) to 670amol/μg.

CONCLUSIONS

This report describes and evaluates the performance of a robust and reproducible SRM assay designed for measuring EGFR directly in FFPE patient tumor tissue with accuracy at extremely low (attomolar) levels. This assay can be used as part of a complementary or companion diagnostic strategy to support novel therapies currently under development and demonstrates the potential to identify candidates for EGFR-inhibitor therapy, predict treatment outcome, and reveal mechanisms of therapeutic resistance.