Abstract 4787: Novel upfront sample enrichment nanotechnology identifies prostate, breast, colon, ovarian, lung, pancreatic, and melanoma cancer specific biomarker candidates

BACKGROUND: Routine laboratory blood tests for biomarkers could dramatically simplify and improve cancer diagnosis, prognosis and tailored therapy. The tumor and its microenvironment, produce cascades of information that enrich the blood proteome with potential cancer biomarkers that could be highly informative about the establishment, progression and metastatic dissemination of cancer. Nevertheless, the identification of low abundance and labile cancer specific biomarkers in blood remains extremely challenging. Low abundance markers are masked by high abundance proteins such as albumin, and by non-specific markers whose changes accompany many diseases. In this study, we analyzed a large cohort of human serum samples from a wide-range of cancer conditions and benign states, and utilized a rapid and powerful nanoparticle-based biomarker capture technology. METHODS- We utilized isopropylacrylamide (NIPAm) core shell hydrogel particles, functionalized with two chemical baits, Cibacron blue F3GA and vinylsulfonic acid, for biomarker capture from 450 serum/plasma samples. Twenty age and stage-matched cancer and 20 to 40 benign/inflammatory controls were processed for each of the 7 cancer types, and proteins eluted from the particles were analyzed by high resolution LC-MS/MS analysis using an LTQ-Orbitrap (Thermo Fisher). All specimens were analyzed in a randomized, batch fashion, followed by an accurate comparison of the results in order to 1) identify a panel of biomarkers for each cancer type and distinguish protein which are involved in commons cancer mechanism and proteins which could uniquely indicate a particular cancer type and 2) avoid the technological bias that could be associated with the comparison of separated studies. RESULTS: For each cancer type we obtained a panel of hundreds of candidates biomarkers, a large number of them not previous identified by MS and/or never measured in plasma. Within the proteins identified are kinases, cytokines, growth factors, structural and nuclear proteins. Each panel of candidate biomarkers includes a) proteins unique for a cancer type, such as the tyrosine kinase Tec, specific for prostate cancer; b) proteins common to many cancer types such as, PRKAG2, CD9, Lipocalin 2, Annexin I, and SDFR-1 and c) numerous proteins whose role in cancer is novel or not well-described. CONCLUSIONS: Cancer-specific low abundance marker candidates have been identified using NanoTrap ™ nanoparticles, a novel rapid upfront sample processing biomarker capture technique. We are developing a protocol for the validation of the biomarkers based on MRM-MS. Further investigation will be required to understand the biological meaning and clinical value of the proteins identified.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 4787. doi:1538-7445.AM2012-4787

Functional protein pathway activation mapping of the progression of normal skin to squamous cell carcinoma

Reverse phase protein microarray analysis was used to identify cell signaling derangements in squamous cell carcinoma (SCC) compared with actinic keratosis (AK) and upper inner arm (UIA). We analyzed two independent tissue sets with isolation and enrichment of epithelial cells by laser capture microdissection. Set 1 served as a pilot and a means to identify protein pathway activation alterations that could be further validated in a second independent set. Set 1 was comprised of 4 AK, 13 SCC, and 20 UIA. Set 2 included 15 AK, 9 SCCs, and 20 UIAs. Activation of 51 signaling proteins, known to be involved in tumorigenesis, were assessed for set 1 and showed that the MEK-ERK [mitogen-activated protein (MAP)/extracellular signal-regulated (ERK; MEK)] pathway was activated in SCC compared with AK and UIA, and that epidermal growth factor receptor (EGFR) and mTOR pathways were aberrantly activated in SCC. Unsupervised two-way hierarchical clustering revealed that AK and UIA shared a common signaling network activation architecture while SCC was dramatically different. Statistical analysis found that prosurvival signaling through phosphorylation of ASK and 4EBP1 as well as increased Bax and Bak expression was higher in AK compared with UIA. We expanded pathway network activation mapping in set 2 to 101 key signaling proteins, which corroborated activation of MEK-ERK, EGFR, and mTOR pathways through discovery of a number of upstream and downstream signaling molecules within these pathways to conclude that SCC is indeed a pathway activation-driven disease. Pathway activation mapping of SCC compared with AK revealed several interconnected networks that could be targeted with drug therapy for potential chemoprevention and therapeutic applications.

Ductal carcinoma in situ: challenges, opportunities, and uncharted waters

Ductal carcinoma in situ (DCIS) is a heterogeneous group of diseases that differ in biology and clinical behavior. Until 1980, DCIS represented less than 1% of all breast cancer cases. With the increased utilization of mammography, DCIS now accounts for 15% to 25% of newly diagnosed breast cancer cases in the United States. Although our ability to detect DCIS has radically improved, our understanding of the pathophysiology and factors involved in its progression to invasive carcinoma is still poorly defined. In many patients, DCIS will never progress to invasive breast cancer and these women are overtreated. In contrast, some DCIS cases are clinically aggressive and the women may be undertreated. We are able to define some of the predictors of aggressive DCIS compared with DCIS of low malignant potential. However, our ability to risk-stratify DCIS is still in its infancy. Clinical risk factors that predict aggressive disease and increased risk of local recurrence include young age at diagnosis, large lesion size, high nuclear grade, comedo necrosis, and involved margins. Treatment factors such as wider surgical margins and radiation therapy reduce the risk of local recurrence. DCIS represents a key intermediate in the stepwise progression to malignancy, but not all aggressive breast cancers appear to have a DCIS intermediate, notably within triple-negative breast cancer. Ongoing studies of the genetic and epigenetic alterations in precancerous breast lesions (atypia and DCIS) as well as the breast microenvironment are important for developing effective early detection and individualized targeted prevention.

Mechanism of cell adaptation: when and how do cancer cells develop chemoresistance?

Chemotherapy treatments are considered essential tools to defeat cancer progression and dissemination to improve patients' quality of life and survival. Although most malignancies initially respond to chemotherapeutic treatments, after an unpredictable period, tumor cells develop mechanisms of resistance to the treatment. Different cell compartments are involved in the mechanism of chemoresistance, and multiple mechanisms can be activated by single cells at different times of the cancer progression. Alteration of drug metabolism, derangement of intracellular pathways' signaling, cross-talk between different membrane receptors, and modification of apoptotic signaling and interference with cell replication are all mechanisms that the cell uses to overcome the effect of pharmacological compounds.In this review, we describe different adaptation, mostly at the level of the proteome, which cancer cells use to develop resistance to cancer treatment.

Development of a novel proteomic approach for mitochondrial proteomics from cardiac tissue from patients with atrial fibrillation

Atrial fibrillation (AF) is the most common cardiac arrhythmia affecting approximately 2.2 million Americans. Because several studies have suggested that changes in mitochondrial function and morphology may contribute to AF, we developed a novel proteomic workflow focused on the identification of differentially expressed mitochondrial proteins in AF patients. Right human atrial tissue was collected from 20 patients, 10 with and 10 without AF, and the tissue was subjected to hydrostatic pressure cycling-based lysis followed by label-free mass spectrometric (MS) analysis of mitochondrial enriched isolates. Approximately 5% of the 700 proteins identified by MS analysis were differentially expressed between the AF and non-AF samples. We chose four differentially abundant proteins for further verification using reverse phase protein microarray analysis based on their known importance in energy production and regulatory association with atrial ion channels: four and a half LIM, destrin, heat shock protein 2, and chaperonin-containing TCP1. These initial study results provide evidence that a workflow to identify AF-related proteins that combines a powerful upfront tissue cell lysis with high resolution MS for discovery and protein array technology for verification may be an effective strategy for discovering candidate markers in highly fibrous tissue samples.

Abstract 2917: Functional protein pathway activation mapping of the progression of normal skin to squamous cell carcinoma

In order to identify important cell signaling derangements in squamous cell carcinoma (SCC) and its precursor actinic keratosis (AK) as a means to uncover important molecular targets and further characterize this disease, we analyzed two independent tissue study sets using Reverse Phase Protein Microarrays (RPMA). Set 1 served as a pilot as well as a means to generate candidate pathway alterations that could be further validated in a second independent sample set. Study Set 1 was comprised of 4 AK, 6 advanced SCC (≥ 2 cm), 7 non-advanced SCC, and 20 normal appearing skin samples [upper-inner arm, (UIA)]. Set 2 included15 AK, 5 advanced SCC, 4 non-advanced SCC and 20 UIA. LCM was used to isolate pure populations of epithelial cells. Fifty-one key signaling proteins and phosphorylated proteins were assessed for set 1 showing that the MEK-ERK pathway was activated in SCC compared to AK and normal skin, that EGFR was aberrantly activated in SCC, and that the mTOR pathway was highly activated in SCC. Unsupervised clustering revealed dramatic differences in SCC signaling architecture. Statistical analysis (p<0.01) found that pro-survival signaling through phosphorylation of ASK, and 4EBP1 as well as increased Bax and Bak expression were higher in AK vs UIA. We then expanded our pathway network activation mapping in set 2 to 108 key signaling proteins. We corroborated the MEK-ERK, EGFR and mTOR pathway activation and identified an expanded number of upstream and downstream signaling molecules within these pathways, and that SCC is indeed a pathway activation-driven disease.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 2917. doi:10.1158/1538-7445.AM2011-2917

Breast cancer stem cells: a new target for therapy

Normal adult tissue stem cells awake from a dormant state to grow, differentiate, and regenerate damaged tissue. They also travel in the circulation and colonize distant organs at sites undergoing tissue repair. These same traits are utilized or co-opted by metastatic cancer cells. The cancer stem cell theory proposes that tumors emerge from a subpopulation of cancer cells that possess stem cell properties. This theory has profound implications for therapy. A small number of cancer stem cells may lie dormant following conventional therapy and tumor remission, only to re-emerge and regenerate the entire recurrent cancer. Consequently, it has been proposed that targeting cancer stem cells is the only way to obtain durable cancer treatment responses. Several strategies for targeting cancer stem cells have been proposed. Nevertheless, a number of issues must be investigated and resolved before effective treatments targeting cancer stem cells can enter clinical testing.

Phosphoproteomic biomarkers predicting histologic nonalcoholic steatohepatitis and fibrosis

The progression of nonalcoholic fatty liver disease (NAFLD) has been linked to deregulated exchange of the endocrine signaling between adipose and liver tissue. Proteomic assays for the phosphorylation events that characterize the activated or deactivated state of the kinase-driven signaling cascades in visceral adipose tissue (VAT) could shed light on the pathogenesis of nonalcoholic steatohepatitis (NASH) and related fibrosis. Reverse-phase protein microarrays (RPMA) were used to develop biomarkers for NASH and fibrosis using VAT collected from 167 NAFLD patients (training cohort, N = 117; testing cohort, N = 50). Three types of models were developed for NASH and advanced fibrosis: clinical models, proteomics models, and combination models. NASH was predicted by a model that included measurements of two components of the insulin signaling pathway: AKT kinase and insulin receptor substrate 1 (IRS1). The models for fibrosis were less reliable when predictions were based on phosphoproteomic, clinical, or the combination data. The best performing model relied on levels of the phosphorylation of GSK3 as well as on two subunits of cyclic AMP regulated protein kinase A (PKA). Phosphoproteomics technology could potentially be used to provide pathogenic information about NASH and NASH-related fibrosis. This information can lead to a clinically relevant diagnostic/prognostic biomarker for NASH.

Reverse-phase phosphoproteome analysis of signaling pathways induced by Rift valley fever virus in human small airway epithelial cells

Rift valley fever virus (RVFV) infection is an emerging zoonotic disease endemic in many countries of sub-Saharan Africa and in Egypt. In this study we show that human small airway epithelial cells are highly susceptible to RVFV virulent strain ZH-501 and the attenuated strain MP-12. We used the reverse-phase protein arrays technology to identify phosphoprotein signaling pathways modulated during infection of cultured airway epithelium. ZH-501 infection induced activation of MAP kinases (p38, JNK and ERK) and downstream transcriptional factors [STAT1 (Y701), ATF2 (T69/71), MSK1 (S360) and CREB (S133)]. NF-κB phosphorylation was also increased. Activation of p53 (S15, S46) correlated with the increased levels of cleaved effector caspase-3, -6 and -7, indicating activation of the extrinsic apoptotic pathway. RVFV infection downregulated phosphorylation of a major anti-apoptotic regulator of survival pathways, AKT (S473), along with phosphorylation of FOX 01/03 (T24/31) which controls cell cycle arrest downstream from AKT. Consistent with this, the level of apoptosis inhibitor XIAP was decreased. However, the intrinsic apoptotic pathway marker, caspase-9, demonstrated only a marginal activation accompanied by an increased level of the inhibitor of apoptosome formation, HSP27. Concentration of the autophagy marker, LC3B, which often accompanies the pro-survival signaling, was decreased. Cumulatively, our analysis of RVFV infection in lung epithelium indicated a viral strategy directed toward the control of cell apoptosis through a number of transcriptional factors. Analyses of MP-12 titers in challenged cells in the presence of MAPK inhibitors indicated that activation of p38 represents a protective cell response while ERK activation controls viral replication.

Platform for establishing interlaboratory reproducibility of selected reaction monitoring-based mass spectrometry peptide assays

Mass spectrometry (MS) is an attractive alternative to quantification of proteins by immunoassays, particularly for protein biomarkers of clinical relevance. Reliable quantification requires that the MS-based assays are robust, selective, and reproducible. Thus, the development of standardized protocols is essential to introduce MS into clinical research laboratories. The aim of this study was to establish a complete workflow for assessing the transferability and reproducibility of selected reaction monitoring (SRM) assays between clinical research laboratories. Four independent laboratories in North America, using identical triple-quadrupole mass spectrometers (Quantum Ultra, Thermo), were provided with standard protocols and instrumentation settings to analyze unknown samples and internal standards in a digested plasma matrix to quantify 51 peptides from 39 human proteins using a multiplexed SRM assay. The interlaboratory coefficient of variation (CV) was less than 10% for 25 of 39 peptides quantified (12 peptides were not quantified based upon hydrophobicity) and exhibited CVs less than 20% for the remaining peptides. In this report, we demonstrate that previously developed research platforms for SRM assays can be improved and optimized for deployment in clinical research environments.

Functional protein network activation mapping reveals new potential molecular drug targets for poor prognosis pediatric BCP-ALL

BACKGROUND

In spite of leukemia therapy improvements obtained over the last decades, therapy is not yet effective in all cases. Current approaches in Acute Lymphoblastic Leukemia (ALL) research focus on identifying new molecular targets to improve outcome for patients with a dismal prognosis. In this light phosphoproteomics seems to hold great promise for the identification of proteins suitable for targeted therapy.

METHODOLOGY/PRINCIPAL FINDINGS

We employed Reverse Phase Protein Microarrays to identify aberrantly activated proteins in 118 pediatric B-cell precursor (BCP)-ALL patients. Signal transduction pathways were assayed for activation/expression status of 92 key signalling proteins. We observed an increased activation/expression of several pathways involved in cell proliferation in poor clinical prognosis patients. MLL-rearranged tumours revealed BCL-2 hyperphosphorylation through AMPK activation, which indicates that AMPK could provide a functional role in inhibiting apoptosis in MLL-rearranged patients, and could be considered as a new potential therapeutic target. Second, in patients with poor clinical response to prednisone we observed the up-modulation of LCK activity with respect to patients with good response. This tyrosine-kinase can be down-modulated with clinically used inhibitors, thus modulating LCK activity could be considered for further studies as a new additional therapy for prednisone-resistant patients. Further we also found an association between high levels of CYCLIN E and relapse incidence. Moreover, CYCLIN E is more expressed in early relapsed patients, who usually show an unfavourable prognosis.

CONCLUSIONS/SIGNIFICANCE

We conclude that functional protein pathway activation mapping revealed specific deranged signalling networks in BCP-ALL that could be potentially modulated to produce a better clinical outcome for patients resistant to standard-of-care therapies.

Investigation of the ovarian and prostate cancer peptidome for candidate early detection markers using a novel nanoparticle biomarker capture technology

Current efforts to identify protein biomarkers of disease use mainly mass spectrometry (MS) to analyze tissue and blood specimens. The low-molecular-weight "peptidome" is an attractive information archive because of the facile nature by which the low-molecular-weight information freely crosses the endothelial cell barrier of the vasculature, which provides opportunity to measure disease microenvironment-associated protein analytes secreted or shed into the extracellular interstitium and from there into the circulation. However, identifying useful protein biomarkers (peptidomic or not) which could be useful to detect early detection/monitoring of disease, toxicity, doping, or drug abuse has been severely hampered because even the most sophisticated, high-resolution MS technologies have lower sensitivities than those of the immunoassays technologies now routinely used in clinical practice. Identification of novel low abundance biomarkers that are indicative of early-stage events that likely exist in the sub-nanogram per milliliter concentration range of known markers, such as prostate-specific antigen, cannot be readily detected by current MS technologies. We have developed a new nanoparticle technology that can, in one step, capture, concentrate, and separate the peptidome from high-abundance blood proteins. Herein, we describe an initial pilot study whereby the peptidome content of ovarian and prostate cancer patients is investigated with this method. Differentially abundant candidate peptidome biomarkers that appear to be specific for early-stage ovarian and prostate cancer have been identified and reveal the potential utility for this new methodology.

Abstract 4584: Verification of ovarian cancer biomarker candidates by nanoparticle-capture MRM

Background: Detection of early stage ovarian cancer offers the best opportunity to reduce mortality. In the attempt to improve Ovarian Cancer prognosis there is a sheer need for new sensitive and specific early detection biomarkers.

We have recently proposed a new workflow to overcome the limitations that characterize serum protein biomarker discovery. A new class of hydrogel (NIPAm) nanoparticle, with the incorporation of an affinity bait (AAC), had been developed and tested, showing to successfully separate from albumin, harvest, concentrate, and protect from degradation low abundance and LMW potential protein biomarkers, amenable for downstream mass spectrometry (LTQ-Orbitrap) analysis. Applying such workflow to a set of 40 serum samples from ovarian cancer patients and benign controls a list of 163 differentially expressed peptides was generated.

Our novel nanoparticle technology provides a rapid and near 100% efficient means to capture and greatly amplfy the resting concentration of LMW protein analytes. Since most of these markers do not have well performing specific antibodies commercially available, in this work we utilized MRM to verify, in an independent study set of 20 cancer samples and 24 benign controls, their differential expression as first identified by Orbitrap-MS/MS.

Method: NIPAm/AAC type of core-shell hydrogel nanoparticle was used for both orbitrap-LTQ based discovery and MRM verification such that the same analyte fractionation workflow was used but different downstream mass spectrometry. MRM was performed on a Thermo Quantum triple quadropole-MS using the nanoparticle trapped analyte archive as the input for analysis. On the basis of their biological significance and following manual verification of the raw LTQ-Orbitrap analysis data, a list of 35 biomarker candidates was selected for MRM verification. Among which i.e.: gelsolin isoform b, integrin α 2b preproprotein, apolipoprotein B precursor, fibronectin 1 isoform 2 preproprotein, LPS-binding protein precursor, ceruloplasmin, α-1apolipoprotein L1 isoform a precursor, leucine-rich α-2-glycoprotein 1, apolipoprotein C-IV, thrombospondin 1 precursor, pro-platelet basic protein precursor, serum amyloid A4, apolipoprotein H precursor, gelsolin isoform b, UNC-112 related protein 2 long form, H4 histone familymember J, cadherin 1, apolipoprotein AV, H2A histone family, member D, apolipoprotein C-III precursor, heterogeneous nuclear ribonucleoprotein AB isoform a, ras suppressor protein 1 isoform 2, cofilin 1 (non-muscle), a disintegrin & metalloproteinase domain 7, transgelin 2, S100-A7, mucin 16.

Conclusions: Several ovary candidate biomarkers were verified by Nanoparticle capture-MRM, thus providing data supporting the use and continued improvement of this novel biomarker discovery system for the identification of protein biomarker panels for early disease detection and therapeutic monitoring.

Note: This abstract was not presented at the AACR 101st Annual Meeting 2010 because the presenter was unable to attend.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 4584.

Improved reproducibility of reverse-phase protein microarrays using array microenvironment normalization

We introduce a novel experimental methodology for the reverse-phase protein microarray platform which reduces the typical measurement CV as much as 70%. The methodology, referred to as array microenvironment normalization, increases the statistical power of the platform. In the experiment, it enabled the detection of a 1.1-fold shift in prostate specific antigen concentration using approximately six technical replicates rather than the 37 replicates previously required. The improved reproducibility and statistical power should facilitate clinical implementation of the platform.

Multiplexed cell signaling analysis of metastatic and nonmetastatic colorectal cancer reveals COX2-EGFR signaling activation as a potential prognostic pathway biomarker

The identification of prognostic determinants of colorectal cancer (CRC), including prediction of occult metastasis, is of urgent consideration, based on the tremendous differences in outcome and survival between patients who present with metastasis or develop metastasis versus those patients with organ-confined or nonrecurrent disease. Currently, a great deal of attention has been focused on using gene expression profiles of tumor specimens as a launch point for prognostic biomarker discovery. In our study, we chose to focus on functional protein-based pathway biomarkers as a new information archive because it is these proteins that form the functional signaling networks that control cell growth, motility, apoptosis, survival, and differentiation. We used reverse-phase protein microarray analysis of laser capture microdissected CRC tumor specimens to profile broad cell signaling pathways from patients who presented with liver metastasis versus patients who remained recurrence free after follow-up. Our results indicate that members of the EGFR and COX2 signaling pathways appear differentially activated in the primary tumors of patients with synchronous metastatic disease. If validated in larger study sets, this pathway defect might be useful as a prognostic clinical tool as well as a guide to potential therapeutic intervention strategies that target occult disease and/or preventative measure.

Emerging concepts in biomarker discovery; the US-Japan Workshop on Immunological Molecular Markers in Oncology

Supported by the Office of International Affairs, National Cancer Institute (NCI), the "US-Japan Workshop on Immunological Biomarkers in Oncology" was held in March 2009. The workshop was related to a task force launched by the International Society for the Biological Therapy of Cancer (iSBTc) and the United States Food and Drug Administration (FDA) to identify strategies for biomarker discovery and validation in the field of biotherapy. The effort will culminate on October 28th 2009 in the "iSBTc-FDA-NCI Workshop on Prognostic and Predictive Immunologic Biomarkers in Cancer", which will be held in Washington DC in association with the Annual Meeting. The purposes of the US-Japan workshop were a) to discuss novel approaches to enhance the discovery of predictive and/or prognostic markers in cancer immunotherapy; b) to define the state of the science in biomarker discovery and validation. The participation of Japanese and US scientists provided the opportunity to identify shared or discordant themes across the distinct immune genetic background and the diverse prevalence of disease between the two Nations. Converging concepts were identified: enhanced knowledge of interferon-related pathways was found to be central to the understanding of immune-mediated tissue-specific destruction (TSD) of which tumor rejection is a representative facet. Although the expression of interferon-stimulated genes (ISGs) likely mediates the inflammatory process leading to tumor rejection, it is insufficient by itself and the associated mechanisms need to be identified. It is likely that adaptive immune responses play a broader role in tumor rejection than those strictly related to their antigen-specificity; likely, their primary role is to trigger an acute and tissue-specific inflammatory response at the tumor site that leads to rejection upon recruitment of additional innate and adaptive immune mechanisms. Other candidate systemic and/or tissue-specific biomarkers were recognized that might be added to the list of known entities applicable in immunotherapy trials. The need for a systematic approach to biomarker discovery that takes advantage of powerful high-throughput technologies was recognized; it was clear from the current state of the science that immunotherapy is still in a discovery phase and only a few of the current biomarkers warrant extensive validation. It was, finally, clear that, while current technologies have almost limitless potential, inadequate study design, limited standardization and cross-validation among laboratories and suboptimal comparability of data remain major road blocks. The institution of an interactive consortium for high throughput molecular monitoring of clinical trials with voluntary participation might provide cost-effective solutions.

Semi-quantitative protein analysis of HER2 and ER levels in human breast cancer reveals broad expression ranges within HER2+ and ER+ phenotypes

11014

Background: ER and HER2 measurements underpin a majority of breast cancer clinical testing, yet determination of ER and HER2 protein levels are routinely performed using subjective approaches. We have developed a semi-quantitative calibrated protein microarray, the Reverse Phase Protein Microarray (RPMA), to more adequately determine accurate and precise protein expression levels in clinical tissue specimens. We utilized this method to determine HER2 and ER expression levels and compared the results to those values reported from the clinical laboratory. Methods: Pure tumor epithelium from 149 frozen pre-treatment human breast cancer tissue specimens (from the I-SPY TRIAL: CALGB 150007/150012, ACRIN 6657) were procured via Laser Capture Microdissection and protein pathway mapping was performed whereby the ER (N=112) and HER2 (N= 118) levels were directly measured and compared with reported IHC values. Results: Overall, RPMA measurements of HER2 had excellent correlation with IHC and FISH HER2 determination with no IHC or FISH false positives (88/88). 7 out of 30 of the FISH/IHC+ cases were found by RPMA to have HER2 values as low or lower than the FISH/IHC- cases with the HER2+ population having RPMA expression levels that varied by as much as 10-fold. There was less concordance between RPMA ER values and IHC ER values. Detailed analysis of a more homogeneous ER+ population (Allred =8) revealed a large dynamic range of expression of ER (10–20 fold) by RPMA. The HER2 and ER RPMA results were independently validated by Western Blot using a separate biopsy. Conclusions: Discreet protein expression values obtained by RPMA for ER and HER2 reveal distinctly broad expression values, with as much as 10–20 fold dynamic range in expression, even in a homogeneous (e.g. Allred score of 8) population. Such dynamic differences in protein expression may produce dramatic effects in therapeutic response rate. These findings, if found to be clinically useful, point to a potential need for more fine-tuned protein expression determination by quantitative high-throughput technologies for patient stratification even for standard-of-care FDA approved therapies.

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