e17551 Background: Tumor-marker gangliosides (TMGs) have enormous potential for early-stage cancer detection as diagnostic biomarkers despite being relatively understudied in this context. AOA Dx is focused on the analytical development of three separate platforms for the quantitation of TMGs in human serum. The development of these platforms for TMG quantitation may allow for the identification of diagnostic signatures for early-stage cancer detection. Methods: First, we are developing a pipeline of antibody-based assays to target TMGs. To aid in development of multiple immunoassays, we collected specificity and affinity data on commercial and proprietary antibodies targeting TMGs using glycoarrays. We are also currently using two immune-based platforms to target TMGs. We have developed an enzyme-linked immunosorbent assay (ELISA) and we have implemented high-performance thin-layer chromatography (HPTLC) to detect individual and total gangliosides. Additionally, we are applying both targeted and untargeted mass spectrometry to human serum from confirmed cancer diagnoses. Results: The specificity and affinity data from the glycoarrays confirm that our TMG antibodies have negligible cross-reactivity and are suitable for diagnostic platform development. Additionally, our developed ELISA allows for the quantification of TMGs in diverse and complex matrices including human serum and plasma, cell lines, and exosomes. HPTLC also detects individual and total gangliosides in each of these matrices, which allows for high-throughput analysis for TMG quantitation. Finally, the application of both targeted and untargeted mass spectrometry has identified multiple TMGs characterized by unique lipid tails. Notably, MS analysis shows that the serum of melanoma and ovarian cancer patients exhibited significantly increased levels of several ganglioside species compared to age-matched healthy serum, further highlighting the potential of TMGs as a promising avenue for cancer diagnosis. Further experiments will focus on refining all platforms. We will also expand the demographic representation of our human serum sample cohort to confirm the initial findings from our mass spectrometry experiments and continue to use this platform to identify additional TMGs of interest. Conclusions: AOA Dx is advancing the development of a multi-platform approach for the detection of TMGs. Our objective is the identification of a diagnostic disease signature for early-stage cancer detection. The validation of this type of diagnostic panel would allow for expedited diagnosis and treatment of cancers currently diagnosed at late stages, ultimately reducing healthcare costs and increasing survival rates. Future research will aim to validate these biomarkers in independent prospective studies.

Abstract Tumor-marker gangliosides (TMGs) have enormous potential for early-stage cancer detection as diagnostic biomarkers despite being relatively understudied in this context. AOA Dx is focused on the development of a mass spectrometry platform for the quantitation of TMGs in human serum, particularly disialogangliosides GD2 and GD3. The development of a mass spectrometry platform for TMG quantitation may allow for the identification of diagnostic signatures for early-stage cancer detection. Briefly, we monitored fragment moieties characteristic of gangliosides in an untargeted fashion by mass spectrometry. We then identified those differentially altered in cancerous groups compared to normal, and subsequently performed targeted MRM analysis. Through these investigations, we have identified multiple TMGs, specifically multiple types of GD2 and GD3 species characterized by unique lipid tails across different cancer types in human serum from confirmed cancer diagnoses. Other ganglioside classes including GMs and relatively understudied GTs were also identified in this study. Notably, the serum of melanoma and ovarian cancer patients exhibited significantly increased levels of several ganglioside species compared to age-matched healthy serum, highlighting the potential of TMGs as a promising avenue for cancer diagnosis. Further experiments will focus on refining this mass spectrometry method and expand demographic representation to confirm our initial findings and identify additional TMGs of interest. In addition, we intend to apply immune-based platforms such as thin-layer chromatography and ELISA, which have already shown promising results in the detection and quantitation of these compounds. Taken together, AOA Dx is advancing the development of a high-throughput mass spectrometry platform designed for the detection of TMGs, with a primary focus on GD2 and GD3. Our objective is the identification of a diagnostic disease signature for early-stage cancer detection. The validation of this type of diagnostic panel would allow for expedited diagnosis and treatment of cancers currently diagnosed at late stages, ultimately reducing healthcare costs and increasing survival rates. Future research will aim to validate these biomarkers in independent prospective studies. Citation Format: Rachel Culp-Hill, Collin Hill, Adele Blackler, William Ricketts. Identification of tumor marker gangliosides for early cancer detection: A mass spectrometry approach [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 2447.

Human protein biomarker discovery relies heavily on pre-clinical models, in particular established cell lines and patient-derived xenografts, but confirmation studies in primary tissue are essential to demonstrate clinical relevance. We describe in this study the process that was followed to clinically translate a 5-protein response signature predictive for the activity of an anti-HER3 monoclonal antibody (lumretuzumab) originally measured in fresh frozen xenograft tissue. We detail the development, qualification, and validation of the multiplexed targeted mass spectrometry assay used to assess the signature performance in formalin-fixed, paraffin-embedded human clinical samples collected in a phase Ib trial designed to evaluate lumretuzumab in patients with metastatic breast cancer. We believe that the strategy delineated here provides a path forward to avoid the time- and cost-consuming step of having to develop immunological reagents against unproven targets. We expect that mass spectrometry-based platforms may become part of a rational process to rapidly test and qualify large number of candidate biomarkers to identify the few that stand a chance for further development and validation.

Mass spectrometry (MS) is a powerful platform for the discovery and routine determination of biochemical entities that mark the presence, type, and progression of disease. More so than most other analytical strategies, MS is particularly versatile and can be applied to the characterization and precise quantification of components in biological matrices including cell lines, formalin-fixed tissue, frozen tissue, blood, urine, and cerebral spinal fluid. Over the last few decades, there has been intensive research aimed at the discovery and development of new MS-based biochemical tests. In this chapter, we outline some of these efforts and discuss the challenges in the application of MS to the development of companion and complementary diagnostics.

Background The VeriStrat test provides accurate predictions of outcomes in all lines of therapy for patients with non-small cell lung cancer (NSCLC). We investigated the predictive and prognostic role of VeriStrat in patients enrolled on the MARQUEE phase III trial of tivantinib plus erlotinib (T+E) versus placebo plus erlotinib (P+E) in previously treated patients with advanced NSCLC. Methods Pretreatment plasma samples were available for 996 patients and were analyzed by matrix-assisted laser desorption/ionization-time of flight mass spectrometry to generate VeriStrat labels (good, VS-G, or poor, VS-P). Results Overall, no significant benefit in overall survival (OS) and progression-free survival (PFS) were observed for the addition of tivantinib to erlotinib. Regardless of treatment arm, patients who were classified as VS-G had significantly longer PFS (3.8 mo for T+E arm, 2.0 mo for P+E arm) and OS (11.6 mo for T+E, 10.2 mo for P+E arm) than patients classified as VS-P (PFS: 1.9 mo for both arms, hazard ratio [HR], 0.584; 95% confidence interval [CI], 0.468-0.733; p < .0001 for T+E, HR, 0.686; 95% CI, 0.546-0.870; p = .0015 for P+E; OS: 4.0 mo for both arms, HR, 0.333; 95% CI, 0.264-0.422; p < .0001 for T+E; HR, 0.449; 95% CI, 0.353-0.576; p < .0001 for P+E). The VS-G population had higher OS than the VS-P population within Eastern Cooperative Oncology Group (ECOG) performance score (PS) categories. VS-G patients on the T+E arm had longer PFS, but not OS, than VS-G patients on the P+E arm (p = .0108). Among EGFR mutation-positive patients, those with VS-G status had a median OS more than twice that of any other group (OS: 31.6 mo for T+E and 22.8 mo for P+E), whereas VS-P patients had similar survival rates as VS-G, EGFR-wild type patients (OS: 13.7 mo for T+E and 6.5 mo for P+E). Conclusion In these analyses, VeriStrat showed a prognostic role within EGOC PS categories and regardless of treatment arm and EGFR status, suggesting that VeriStrat could be used to identify EGFR mutation-positive patients who will have a poor response to EGFR tyrosine kinase inhibitors. Implications for Practice This study suggests that VeriStrat testing could enhance the prognostic role of performance status and smoking status and replicates findings from other trials that showed that the VeriStrat test identifies EGFR mutation-positive patients likely to have a poor response to EGFR tyrosine kinase inhibitors (TKIs). Although these findings should be confirmed in other populations, VeriStrat use could be considered in EGFR mutation-positive patients as an additional prognostic tool, and these results suggest that EGFR mutation-positive patients with VeriStrat "poor" classification could benefit from other therapeutic agents given in conjunction with TKI monotherapy.

Abstract Hepatocellular carcinoma (HCC) is the most common type of primary liver cancer. Well differentiated HCC can sometimes be extremely difficult to be distinguished from other hepatocellular mass lesions such as hepatocellular adenoma and dysplastic liver nodule due to considerable morphologic overlaps. Immunohistochemical markers may have a limited utility, especially on core biopsy. Choice of treatment depends on the extent and location of the cancer, and the overall health of the patient. For patients who are healthy enough to undergo surgery and who have early-stage cancer confined to the liver, treatment may involve hepatic resection; however many patients develop a cancer recurrence, which is the main cause of death in long-term evaluations. Recurrence rates after treatment with resection are high, highlighting the importance of finding effective adjuvant treatments and markers that aid in determining differences between hepatocellular lesions. To explore differences between hepatocellular lesions that could be indicators of tumor behavior, we used targeted proteomic analysis to assess different protein biomarkers in formalin-fixed paraffin-embedded (FFPE) HCC tumor tissue Twenty-two FFPE HCC tissue blocks were obtained and a pathologist marked a minimum 8mm2 of tumor area. Following laser microdissection, proteins were extracted using the Liquid-Tissue® process and subjected to selected reaction monitoring mass spectrometry to quantify the amounts of 30 different targeted proteins. As anticipated, well differentiated HCC, hepatocellular adenoma and dysplastic nodule expressed high rates of P-glycoprotein and the majority expressed multi-drug resistance gene protein (MDR1). Such markers may account in part for the chemotherapy refractory nature of HCC. All 22 patients expressed high levels of hENT1 and lacked expression of RRM1, indicating that gemcitabine-based therapy would be an appropriate choice. All 22 patients lacked expression of marker of sensitivity to anthracycline (TOPO2A) and the majority of patients did not express a marker of resistance to platinum therapy (ERCC1). Of the 22 patients whose tumors expressed EGFR, 5 had expression above the 75%ile and would thus be eligible for EGFR small molecule inhibitor therapy. Dysplastic liver nodule patients did not expressed significant level of EGFR. Further, multiplex-targeted proteomics discovered patients expressing cMET and IDO1, which indicate eligibility for clinical trials of targeted therapies or immunotherapies. 60% of dysplastic liver nodule patients did not expressed cMET at any level This study retrospectively evaluates HCC patients in an attempt to identify predictors of tumor behavior. Proteomic and genomic screening should be performed to identify differences between various hepatocellular lesions. Prospective evaluation of molecular and genetic profile is warranted in HCC patients to be distinguished from other hepatocellular mass lesions. Citation Format: Fabiola Cecchi, Nam Ku, Hanlin Wang, Adele Blackler, Todd Hembrough, Shahrooz Rabizadeh, Patrick Soon-Shiong, Jiaoti Huang. Targeted proteomic analysis of hepatocellular carcinoma and its histologic mimickers. [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 4935.

Background Combined targeted strategy with letrozole (Le) and lapatinib (La) improves progression-free survival (PFS) in patients with metastatic breast cancer (MBC) co-expressing hormone receptor-positive (HR+) and HER2+ but not in HR+/HER2-negative (HER-) disease (Johnston J Clin Oncol 2009). However, among HER2+ tumors, quantitative levels of HER2 are heterogeneous with a broad dynamic range corresponding to approximately 163.7 to 17446.7 amol/µg as previously reported (Nuciforo SABCS 2014). In addition, within HER2- tumors, quantitative measurement of HER family proteins may identify those patients most likely to benefit from the addition of La to Le. In this retrospective study, we tested the prognostic and predictive ability of HER proteins quantification in clinically HER2+ tumor samples from the EGF30008 study. Methods Formalin-fixed paraffin-embedded primary tumor tissues sections from HER2+ MBC population were used. After laser microdissection, tissue lysates were prepared for selected reaction monitoring mass spectrometry (SRM-MS) analysis. Absolute quantitation was accomplished through simultaneous detection of endogenous target and synthetic labeled heavy peptide identical to analytical targets (EGFR, HER2, HER3). HER2 protein levels were correlated with PAM50 molecular subtypes, ERBB2 and ESR1 genes by nCounter. PFS and overall survival (OS) were analyzed by Kaplan–Meier and log-rank test. To determine whether HER2 protein levels were predictive of La benefit, we tested the interaction term of HER2 protein as a continuous variable by treatment arm in a Cox model. Results Within the HER2+ study cohort (n=219), 107 had an available tumor block; 84 cases had sufficient material for HER expression measurement by SRM-MS. Average HER2 levels were 2321.1 amol/ug (median, 817.6). HER2 levels were lower in Le+La (n=43; mean, 1761 amol/ug) compared to Le (n=41; mean, 2908 amol/ug) arms, although the difference was non-significant (p=0.108). No expression of EGFR and HER3 was observed. HER2 protein levels were significantly different among PAM50 subtypes with HER2-enriched (HER2E) tumors showing the highest expression followed by Basal-like, Luminal A, Luminal B, and Normal-like (p Conclusions Levels of HER2 protein in HER2+ MBC are extremely heterogeneous. An association between HER2 protein and gene expression by nCounter was observed. HER2E tumors by PAM50 showed the highest levels of HER2 protein. Within the group of HER2+ MBC by standard IHC/FISH, tumors with high HER2 protein had a statistically non-significant worse outcome and do not seem to benefit from La. Further validation of these findings is warranted. Citation Format: Nuciforo P, Thyparambil S, Galvan P, Vilaro M, Jimenez J, Liao W-L, Cecchi F, Blackler A, Press MF, Gagnon R, Ellis C, Hembrough T, Johnston S, Prat A. Quantitative HER family proteins assessment as prognostic and predictive biomarkers in the EGF30008 clinical trial. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P3-07-08.

Lung cancer remains the leading cause of cancer mortality in United States and globally. Pemetrexed combined with platinum chemotherapy is specifically indicated for treatment of non-squamous non-small cell lung cancer (non-sq NSCLC). Pemetrexed is a folate-analog metabolic inhibitor that disrupts folate-dependent processes essential for cell replication. Pemetrexed inhibits thymidylate synthase (TS), dihydrofolate reductase (DHFR), and glycinamide ribonucleotide formyltransferase (GARFT), which are folate-dependent enzymes involved in the de novo biosynthesis of thymidine and purine nucleotides. Folate receptor alpha (FRalpha) is a folate/antifolate transporter protein that is overexpressed by a number of epithelial tumors. The purpose of this study is to identify proteomic biomarkers predictive of response to pemetrexed-based chemotherapy in non-sq NSCLC. Patients with advanced non-sq NSCLC who received pemetrexed-based chemotherapy at West Virginia University from 2009 to 2014 were retrospectively identified. Formalin-fixed, paraffin-embedded tumor biopsies were laser microdissected, solubilized, enzymatically digested and subjected to quantitative proteomic analysis. A multiplexed, selected reaction monitoring (SRM) mass spectrometry (MS) assay was used to determine the absolute levels of 46 different candidate proteomic markers, including those in the folate receptor pathway. TS analysis was also performed by IHC. The Kaplan-Meier method and log-rank test were used in statistical analysis of overall survival (OS) and progression-free survival (PFS). The 74 patients included in the study had a median follow-up of 26 months, a median OS of 16.6 months (95%CI: 11.6 - 43.4), and a median PFS of 9.61 months (95%CI: 8.43, 12.98). There were 65 patients who received pemetrexed-based regimen as a first line therapy and 9 patients as subsequent salvage treatment. In a comparison between patients who survived >24 months and < 8 months, there were no significant differences between the two groups in terms of sex, age, ECOG performance status, TNM stage at diagnosis, and smoking history. Among the 37 patients with sufficient tumor specimens available for multiplexed proteomic analysis, 30 biomarkers were detected with varying levels of expression. Sixteen additional biomarkers were undetectable. TS protein expression was detected in by SRM in 2 patients and by IHC in 32 patients (tumor staining>1); however, TS IHC was not predictive of outcome (PFS-HR ratio = 1.06). Patients whose tumors expressed low levels of GARFT protein (≤900 amol/μg; n=7) had statistically significantly longer median PFS than those whose tumors expressed high levels of GARFT (>900 amol/μg; n=30) (40.6 vs. 11.4 months; p = 0.014). Patients with high FRalpha protein expression (>1510 amol/μg, n=9) had significantly longer median PFS than those with low FRalpha expression (≤1510 amol/μg; n=28) (>50 vs. 11.4 months; p= 0.021). Moreover, the 23 patients with both high GARFT expression (>900 amol/μg) and low FRalpha expression (≤1510 amol/μg) faired considerably worse than the remainder of patients (median PFS 10.1 vs. 40.6 months; p=0.0003). Multiplexed mass spectrometry-based proteomics offers a feasible and promising approach for tumor biomarker profiling and quantification to predict therapeutic response. Of note, our results show that FRalpha and GARFT protein expression may be predictive of response to pemetrexed-based treatment in patients with non-sq NSCLC. Further investigation is needed to validate the utility of these biomarkers for guiding personalized treatment decisions in clinical practice.

Protein-targeted therapies are expected to selectively kill tumor cells that express the targeted protein biomarker. Although a tumor mass may initially respond to targeted therapies based on expression of the targeted protein, all cells within a tumor may not express the targeted protein above a critical threshold level; therefore, those cells that do not express, or that downregulate expression of, the targeted protein may not be responsive to therapy. The ability to monitor the dynamic expression of these protein biomarkers throughout the course of therapy may allow for treatment to be personalized in real-time in response to the evolving nature of the tumor. This report demonstrates, by monitoring a single patient through multiple therapies, how targeted mass spectrometry is an effective, quantitative method that provides real-time analysis of multiple therapeutically associated targeted proteins that can be used to personalize a patient's treatment strategy throughout the course of care.

Abstract Background: Standard treatment for muscle-invasive bladder cancer (MIBC) includes chemotherapy with either gemcitabine-cisplatin (GC) or methotrexate, vinblastine, adriamycin and cisplatin (MVAC). These regimens have similar clinical complete response rates of approximately 30%. While no targeted treatment has been approved for bladder cancer, clinical trials have identified biochemical markers that predict the chemoresponsiveness of MIBC tumors to specific chemotherapeutic agents. For example, patients with high hENT1 and low RRM1 expression responded better to GC-based chemotherapy than their counterparts, and HER2 overexpression predicted resistance to cisplatin-based therapy. To quantify targets that are known indicators of tumor behavior, we used targeted proteomic analysis to assess 30 different protein biomarkers in formalin-fixed paraffin-embedded (FFPE) MIBC tumor tissue. Methods: Twelve FFPE MIBC tissue blocks were obtained and a pathologist marked a minimum 8mm2 of tumor area from 1 or 2 slides. Following laser microdissection of the marked areas, proteins were extracted using the Liquid-Tissue® process and subjected to selected reaction monitoring mass spectrometry to quantify the amounts of 30 different targeted proteins in each patient sample. Results: Of the 12 patient samples, 7 (58%) expressed high levels of hENT1 and 11 (92%) expressed low levels of RRM1, indicating that gemcitabine-based therapy would be an appropriate choice. A single patient expressed high levels of RRM1, an indication for non-gemcitabine based therapy. All 12 patients expressed TUBB3, a marker of resistance to taxane (vinblastine) and 10 patients (83%) lacked expression of FR-alpha, a marker of sensitivity to methotrexate. The majority of patients expressed a marker of sensitivity to anthracycline (TOPO2A) and did not express a resistance biomarker for platinum therapy (ERCC1). Of 3 patients whose tumors expressed HER2, 2 had overexpression (>750 amol/ug) and would thus be eligible for HER2 basket trials. Further, multiplex-targeted proteomics discovered patients expressing FGFR1 (17%), cMET (33%), Axl (17%) and IDO1 (25%), which would make them eligible for clinical trials of targeted or immunotherapies. Conclusion: MIBC is heterogeneous and expresses a wide range of proteins. Yet, it continues to be treated with only 2 chemotherapeutic regimens. Multiplexed proteomics is currently being used in clinical practice to inform personalized patient care decisions with identification and the relative quantities of actionable proteins known to predict tumor behavior. Citation Format: Fabiola Cecchi, Sheeno Thyparambil, Adele Blackler, Todd Hembrough, Shahrooz Rabizadeh, Patrick Soon-Shiong, Henry Frierson, Daniel Theodorescu. Targeted proteomic analysis for personalized treatment of muscle invasive bladder cancer. [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 449.

Abstract Background Combined targeted strategy with letrozole (Le) and lapatinib (La) improves progression-free survival (PFS) in patients with metastatic breast cancer (MBC) co-expressing hormone receptor-positive (HR+) and HER2+ but not in HR+/HER2-negative (HER-) disease (Johnston J Clin Oncol 2009). However, among HER2+ tumors, quantitative levels of HER2 are heterogeneous with a broad dynamic range corresponding to approximately 163.7 to 17446.7 amol/µg as previously reported (Nuciforo SABCS 2014). In addition, within HER2- tumors, quantitative measurement of HER family proteins may identify those patients most likely to benefit from the addition of La to Le. In this retrospective study, we tested the prognostic and predictive ability of HER proteins quantification in clinically HER2+ tumor samples from the EGF30008 study. Methods Formalin-fixed paraffin-embedded primary tumor tissues sections from HER2+ MBC population were used. After laser microdissection, tissue lysates were prepared for selected reaction monitoring mass spectrometry (SRM-MS) analysis. Absolute quantitation was accomplished through simultaneous detection of endogenous target and synthetic labeled heavy peptide identical to analytical targets (EGFR, HER2, HER3). HER2 protein levels were correlated with PAM50 molecular subtypes, ERBB2 and ESR1 genes by nCounter. PFS and overall survival (OS) were analyzed by Kaplan–Meier and log-rank test. To determine whether HER2 protein levels were predictive of La benefit, we tested the interaction term of HER2 protein as a continuous variable by treatment arm in a Cox model. Results Within the HER2+ study cohort (n=219), 107 had an available tumor block; 84 cases had sufficient material for HER expression measurement by SRM-MS. Average HER2 levels were 2321.1 amol/ug (median, 817.6). HER2 levels were lower in Le+La (n=43; mean, 1761 amol/ug) compared to Le (n=41; mean, 2908 amol/ug) arms, although the difference was non-significant (p=0.108). No expression of EGFR and HER3 was observed. HER2 protein levels were significantly different among PAM50 subtypes with HER2-enriched (HER2E) tumors showing the highest expression followed by Basal-like, Luminal A, Luminal B, and Normal-like (p<0.001). A correlation between HER2 protein, ERBB2 (r=0.5, p<0.001) and ESR1 (r=-0.5, p=0.001) gene expression was found. In patients with disease that expresses HER2 protein levels above the median a trend towards worse PFS (2.9 vs 7.7 months, p=0.092) and OS (21 vs 39 months, p=0.071) were observed. A statistically significant interaction was observed between HER2 protein levels and La treatment for both PFS (p=0.049) and OS (p<0.001). HER2+ tumors with lower expression of HER2 benefited more from La than those with higher expression. Conclusions Levels of HER2 protein in HER2+ MBC are extremely heterogeneous. An association between HER2 protein and gene expression by nCounter was observed. HER2E tumors by PAM50 showed the highest levels of HER2 protein. Within the group of HER2+ MBC by standard IHC/FISH, tumors with high HER2 protein had a statistically non-significant worse outcome and do not seem to benefit from La. Further validation of these findings is warranted. Citation Format: Nuciforo P, Thyparambil S, Galván P, Vilaro M, Jimenez J, Liao W-L, Cecchi F, Blackler A, Press MF, Gagnon R, Ellis C, Hembrough T, Johnston S, Prat A. Quantitative HER family proteins assessment as prognostic and predictive biomarkers in the EGF30008 clinical trial. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P3-07-08.

74 Background: KRAS mutation is rare ( < 5%) in gastroesophageal cancer (GEC). However, the incidence of KRAS gene amplification (amp+), consequent protein levels, and prognostic and/or therapeutic implications are unknown. Methods: 410 GEC samples and 30 cell lines were assessed for KRAS gene copy number (GCN) by fluorescence in situ hybridization (FISH) (n = 90), Kras expression by selected reaction monitoring mass spectrometry (Kras-SRM-MS) (n = 393), and Kras-SRM level evaluated for correlation with KRAS amp+ status (n = 73). Survival analysis was performed comparing KRAS amp+ versus non-amp+ patients. When possible, concurrent 315 gene next-generation sequencing was also performed. Four KRAS-amplified xenograft lines (CAT-2,12,14,15) were established from malignant effusions. Tumorigenic activity of KRAS amp+ lines (CAT lines, MKN-1) were assessed using MTT and soft agar assays in vitro and subcutaneous xenograft models, compared to non-amp+ lines. Inhibitory assays were performed using KRAS siRNA and CRIPSR, and commercial inhibitors targeting downstream effectors MEK and/or PIK3CA. Results: KRAS FISH revealed clustered gene amp+ in 28.9% (26/90); these patients had worse prognosis than non-amp+ patients. GCN significantly correlated with Kras expression. All KRAS amp+ cell lines significantly overexpressed Kras protein and were tumorigenic in xenograft subcutaneous models. KRAS siRNA and KRAS CRISPR of KRAS amp+ cell lines demonstrated inhibition in MTT viability and soft agar assays, compared to appropriate controls, and demonstrated significant and durable xenograft growth reduction. Conversely, inhibition using MEK and/or PI3K inhibitors demonstrated only transient growth reduction in vivo. Conclusions: KRAS gene amp+ was observed in a large subset (26%) of GEC patients, which correlated with extreme expression by mass spectrometry. Established xenograft lines serve as models to investigate therapeutic strategies for KRAS amp+ patients. Inhibition using MEK/PIK3CA inhibitors provided transient benefit for KRAS amp+ tumors while durable inhibition was observed with Kras protein knockdown, suggesting potential benefit from novel siRNA therapeutics currently in development.

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.

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/mg 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, trastuzumabtreated 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.

e18242 Background: Tumor molecular profiling is increasingly being used to develop personalized treatment strategies for cancer patients (pts). The OncoPlex Dx (OPDx) test (NantOmics) uses a quantitative, multiplexed, mass spectrometry assay to measure protein expression in tumors. Here we provide a model to evaluate the cost implications and clinical outcomes of including the OPDx Test to guide treatment strategies for metastatic breast cancer (mBC) pts from a US payer (CMS) perspective.Methods: A decision analysis model was developed in Excel 2010; time frame, 1 treatment course. The budget impact of using the OPDx Test was determined from diagnostic, therapeutic, and hospitalization costs and was compared to standard testing/care (empiric care). Pts with mBC planning 1st- or 2nd-line therapy enter the model and receive the OPDx Test (27-protein panel) or standard test (HER2, ER, PR). The model assumes 2 scenarios: 1) 100% of oncologists adopt the test results; 2) 25% of oncologists adopt the test results, 75% use empiric care. Published data informed PFS, serious adverse events, and clinical pathways. Sensitivity analyses assessed the impact of parameter uncertainty on model results. Results: 1st-line pts: PFS (OPDx Test vs empiric care) was 18.7 vs 17.1 months (mo) (scenario 1) and 17.3 vs 17.1 mo (scenario 2) resulting in an incremental cost of $93 and $157 per mo of PFS; for scenario 1 and 2, respectively, inclusion of the OPDx Test increased overall treatment costs by $8,599 and $1,477 per pt or $0.03 and $0.02 per member per month (PMPM). 2nd-line pts: PFS (OPDx Test vs empiric care) was 7.1 vs 6.6 mo (scenario 1) and 6.6 vs 6.6 mo (scenario 2) resulting in an incremental cost of $478 and $828 per mo of PFS; for scenario 1 and 2, respectively, inclusion of the OPDx Test increased overall treatment costs by $8,599 and $1,378 per pt or $0.08 and $0.07 PMPM. Sensitivity analysis yielded an average cost of (1st-line/2nd-line) $4,409/$3,193 per pt and a mean improvement in PFS of 0.75/0.16 mo.Conclusions: Integration of the OPDx Test to personalize treatment strategies based on pt tumor biology has the potential to improve outcomes while incurring minimal extra cost.

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.

4050 Background: Trastuzumab-based chemotherapy is standard treatment for HER2-positive advanced gastric cancer (AGC). Although increased HER2 gene amplification by fluorescent in situ hybridization (FISH) has been correlated with sensitivity to trastuzumab, the predictive value of HER2 protein expression levels for trastuzumab sensitivity has not been reported. In this work, we quantitate levels of HER2 using a mass spectrometry-based assay and identify a cutoff for HER2 protein levels that is predictive of enhanced response to trastuzumab. Methods: A multiplexed, selected reaction monitoring (SRM) mass spectrometry assay was used to determine the absolute level of the HER2 protein in patient tumors. HER2 immunohistochemistry (IHC) status, HER2/CEP17 ratio, HER2 gene copy number, and HER2 protein levels were compared in 249 AGC tumors, 95 of which were treated with trastuzumab. Overall survival (OS) in the trastuzumab cohort was correlated with HER2 protein levels and a predictive cutoff was determined by the lowest p value of log rank test. Results: While HER2 protein quantitation by mass spectrometry positively correlated with both FISH and IHC, a wide range of HER2 protein levels was observed in tumors classified as HER2-positive by conventional methods. Ninety five trastuzumab treated patients were stratified into two groups based on HER2 protein level: HER2 high expressers and HER2 moderate expressers. Patients classified as HER2 high expressers (n = 48), with HER2 levels above 2383 amol/ug, had twice the overall survival (OS) of patients (n = 47) classified as moderate expressers (OS: 35.0 vs. 17.5 months, HR 0.5, p= 0.007). Conclusions: We used a non-antibody based assay to quantify absolute levels of HER2 protein in samples from AGC patients. We found high variability in HER2 expression within a patient population that had been classified as 3+ by IHC. High levels of HER2 correlated with increased overall survival following trastuzumab. This study demonstrates the HER2 measurement by SRM could guide physicians in their patient's selection for trastuzumab-based chemotherapy.