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To address the clinical relevance of molecular detection of occult breast cancer in sentinel lymph nodes and nonsentinel axillary lymph nodes (ALN), we initiated the Minimally Invasive Molecular Staging of Breast Cancer (MIMS) trial, a multi-institutional prospective cohort study. This trial represents the first prospective cohort study in which a multimarker, real-time reverse transcription polymerase chain reaction (RT-PCR) analysis was applied to the detection of breast cancer micrometastases in ALN. Sentinel and/or nonsentinel ALN from 501 breast cancer subjects with T1–T3 primary tumors were analyzed by standard histopathology and multimarker, real-time RT-PCR analysis. Seven breast cancer-associated genes (mam, mamB, PIP, CK19, muc1, PSE, and CEA) known to be overexpressed in metastatic breast cancer compared with control lymph nodes were used. Follow-up data were collected for 5 years. Of the 501 breast cancer subjects enrolled, 348 were node negative and completed the 5-year follow-up. Of these patients (n = 94), 27% demonstrated evidence of molecular overexpression. The 5-year relapse-free survival rate was 95.4% (95% confidence interval [95% CI], 92.4–97.2%). No single gene or combination of study genes was predictive of recurrence. The genes in this study panel failed to be predictive of clinical relapse. This may be a function of several factors: the low event rate at 5 years, the particular gene set, the methodology used for detection/analysis or that our original hypothesis was wrong and that the presence of positive marker signal by real-time RT-PCR is not associated with a worsened clinical outcome.

Background Pathologic evaluation may lack the sensitivity required for accurate staging of the axilla in breast cancer patients. We have completed enrollment of a multi-institutional prospective cohort study designed to determine if molecular analyses can improve axillary staging. In subset analyses, we have attempted to address the following questions: (1) Does molecular analysis improve the sensitivity of sentinel lymph node biopsy (SLNB) and (2) is the sentinel lymph node (SLN) hypothesis valid at the molecular level? Methods Four hundred eighty-nine subjects with T1, T2, or T3 breast cancer and no evidence of axillary lymph node (ALN) involvement were enrolled. ALNs were analyzed by routine pathology (hematoxylin-eosin staining), and by multimarker real-time reverse transcriptase-polymerase chain reaction analysis CRT-PCR to detect breast cancer metastases. Pathology and molecular data for both SLNs and nonsentinel ALNs were available for a subset of 207 subjects. Results The sensitivity of pathologic analysis of the SLN to predict the pathologic status of ALNs was 84.1%. The sensitivity of combining pathologic with molecular analysis of the SLN to predict the pathologic status of ALNs was 92.8%, a statistically significant increase in sensitivity (P = .031 by the McNemar test for correlated proportions). Finally, the sensitivity of combining pathologic with molecular analysis of the SLN to predict the pathologic or molecular status of ALNs was 85.4%. Conclusions The combination of pathologic and molecular analysis of SLNs resulted in the highest sensitivity for prediction of the pathologic status of ALNs. The data also provide evidence that the SLN hypothesis remains valid at the molecular level.

Esophageal adenocarcinoma (EA) is increasing faster than any other cancer in the U.S. In this report, we first show that EA can be distinguished from normal esophagus (NE) and esophageal squamous cell carcinoma by plotting expression values for EpCam, TFF1, and SBEM in three-dimensional Euclidean space. For monitoring progression of Barrett's esophagus (BE) to EA, we developed a highly sensitive assay for limited quantities of tissue whereby 50 ng of RNA are first converted to cDNA using 16 gene-specific primers. Using a set of training tissues, we developed a novel quantitative three-tiered algorithm that allows for accurate (overall accuracy = 61/63, 97%) discrimination of BE versus EA tissues using only three genes. The gene used in the first tier of the algorithm is TSPAN: samples not diagnosed as BE or EA by TSPAN in the first tier are then subjected to a second-tier analysis using ECGF1, followed by a third-tier analysis using SPARC. Addition of TFF1 and SBEM to the first tier (i.e., a five-gene marker panel) increases the overall accuracy of the assay to 98% (62/63) and results in mean molecular diagnostic scores (± SD) that are significantly different between EA and BE samples (3.19 ± 1.07 versus −2.74 ± 1.73, respectively). Our results suggest that relatively few genes can be used to monitor progression of BE to EA.

The clinical management of non-small cell lung cancer (NSCLC) would benefit greatly by a test that was able to detect small amounts of NSCLC in the peripheral blood. In this report, we used a novel strategy to enrich tumor cells from the peripheral blood of 24 stage I to IV NSCLC patients and determined expression levels for six cancer-associated genes (lunx, muc1, KS1/4, CEA, CK19, and PSE). Using thresholds established at three standard deviations above the mean observed in 15 normal controls, we observed that lunx (10 of 24, 42%), muc1 (5 of 24, 21%), and CK19 (5 of 24, 21%) were overexpressed in 14 of 24 (58%) peripheral blood samples obtained from NSCLC patients. Patients who overexpressed either KS1/4 (n = 2) or PSE (n = 1) also overexpressed either lunx or muc1. Of patients with presumed curable and resectable stage I to II disease (n = 7), at least one marker was overexpressed in three (43%) patients. In advanced stage III to IV patients (n = 17), at least one marker was overexpressed in 11 patients (65%). These results provide evidence that circulating tumor cells can be detected in NSCLC patients by a high throughput molecular technique. Further studies are needed to determine the clinical relevance of gene overexpression.

Non-small cell lung cancer (NSCLC) is the most common cancer-related cause of death for both men and women in the US. Standard therapies for patients with NSCLC include surgery, chemotherapy, and radiation therapy, and the stage of disease dictates choice of therapy. The current staging system for lung cancer uses the American Joint Committee on Cancer TNM system, and its goal is to classify patients into groups based on the extent of disease. This system relies heavily on the pathologic evaluation of the primary tumor (T), regional nodes (N), and distant metastases (M). Patients in whom mediastinal lymph nodes (MLNs) are involved (N2 or N3) are classified with stage III disease (1) and are generally considered inoperable. The recent identification of genes overexpressed in lung cancer (2)(3)(4) combined with advances in real-time reverse transcription-PCR (RT-PCR) provide the opportunity to establish sensitive and specific ways to analyze MLNs. In addition, molecular biology approaches using real-time RT-PCR are well suited to the analysis of lymph node tissue procured through minimally invasive procedures such as endoscopic ultrasound-guided fine-needle aspiration (EUS-FNA). This technique enables reliable biopsy of MLNs without the need for general anesthesia or surgery (5). Given the advantages of EUS-FNA, we investigated the possibility that metastatic disease could be reliably detected in MLNs of NSCLC patients by real-time RT-PCR. To define the ability of real-time RT-PCR to detect metastatic NSCLC in MLNs, we procured by EUS-FNA nine MLNs containing metastatic NSCLC (five adenocarcinomas, one large cell carcinoma, one squamous cell carcinoma, and two uncharacterized carcinomas). For negative controls, we collected 30 cervical lymph nodes obtained by surgical resection. Protocols for tissue procurement and patient consent governing all aspects of this study were reviewed and approved by the Medical University of South Carolina Institutional Review Board. For EUS-FNA, a …

Prostate Specific Ets factor is a recently identified transcriptional activator that is overexpressed in prostate cancer. To determine whether this gene is overexpressed in breast cancer, we performed a virtual Northern blot using data available online at the Cancer Genome Anatomy Project website. Ninety-five SAGE libraries were probed with a unique sequence tag to the Prostate Specific Ets gene. The results indicate that Prostate Specific Ets is expressed in 14 out of 15 breast cancer libraries (93%), nine out of 10 prostate cancer libraries (90%), three out of 40 libraries from other cancers (7.5%), and four out of 30 normal tissue libraries (13%). To determine the possibility that the Prostate Specific Ets gene is a novel marker for detection of metastatic breast cancer in axillary lymph nodes, quantitative real-time RT–PCR analyses were performed. The mean level of Prostate Specific Ets expression in lymph nodes containing metastatic breast cancer (n=22) was 410-fold higher than in normal lymph node (n=51). A receiver operator characteristic curve analysis indicated that Prostate Specific Ets was overexpressed in 18 out of 22 lymph nodes containing metastatic breast cancer (82%). The receiver operator characteristic curve analysis also indicated that the diagnostic accuracy of the Prostate Specific Ets gene for detection of metastatic breast cancer in axillary lymph nodes was 0.949. These results provide evidence that Prostate Specific Ets is a potentially informative novel marker for detection of metastatic breast cancer in axillary lymph nodes, and should be included in any study that involves molecular profiling of breast cancer. British Journal of Cancer (2002) 86, 899–904. DOI: 10.1038/sj/bjc/6600190 www.bjcancer.com © 2002 Cancer Research UK

To augment cytological diagnosis of pancreatic ductal adenocarcinoma (PDAC) in tissue samples obtained by minimally invasive endoscopic ultrasound-guided fine needle aspiration, we investigated whether a small set of molecular markers could accurately distinguish PDAC from chronic pancreatitis (CP). Expression levels of 29 genes were first determined by quantitative real-time RT-PCR in a training set of tissues in which the final diagnosis was PDAC (n=20) or CP (n=10). Using receiver operator characteristic curve analysis, we determined that the single gene with the highest diagnostic accuracy for discrimination of CP vs. PDAC in the training study was urokinase plasminogen activator receptor (UPAR; AUC value = 0.895, 95% CI=0.728-0.976). In the set of test tissues (n=14), the accuracy of UPAR decreased to 79%. However, we observed that the addition of 6 genes (EPCAM2, MAL2, CEA5, CEA6, MSLN and TRIM29; referred to as the 6-gene classifier) to UPAR resulted in high accuracy in both training and testing sets. Excluding 3 samples (out of 44; 7%) for which results of the UPAR/6-gene classifier were "undefined," the accuracy of the UPAR/6-gene classifier was 100% in training samples (n=29), 92% in 12 test samples (p=0.004 that results were randomly generated; p=0.046 that the UPAR/6-gene classifier was comparable to UPAR alone; chi2 test), 100% in 3 samples for which the initial cytological diagnosis was "suspicious" and 98% (40/41) overall. Our results provide evidence that molecular marker expression data can be used to augment cytological analysis.

The primary objective of cancer staging is to be able to classify patients by the extent of disease into groups with similar clinical outcomes and so facilitate patient management. In the setting of breast cancer, one of the most important prognostic indicators is the presence of axillary lymph node (ALN) metastases. Frequently, ALN disease status is the critical parameter for determining whether adjuvant systemic chemo or hormonal therapy is recommended.1–3 As a result, staging for newly diagnosed clinical stage I and II breast cancer patients has traditionally included an ipsilateral ALN dissection (ALND). Unfortunately, standard H&E histopathologic analysis of ALN has limitations. A number of studies have shown that performing additional tissue sections and/or immunohistochemical staining (IHC) of ALN increases metastases detection by up to 25%.4–6 Furthermore, these retrospective studies suggest that the prognosis for patients with occult disease is similar to patients with pathology-positive ALN.4,5,7 These findings imply that the development of more sensitive methods to detect micrometastatic disease in ALN could significantly improve breast cancer staging. The recent identification of genes overexpressed in breast cancer combined with advances in molecular biology provide such an opportunity for improving breast cancer staging.8–16 We and others have shown that the reverse transcription polymerase chain reaction (RT-PCR) is capable of detecting metastatic disease in ALN of breast cancer patients,15,17 with a sensitivity of up to one cancer cell per 107 normal cells.18–20 Ironically, the exquisite sensitivity of RT-PCR has hindered its clinical application because the majority of potential markers have some baseline expression in normal tissues.21,22 Due to the fact that conventional RT-PCR techniques are at best semiquantitative, it has been difficult to differentiate between baseline gene expression in normal tissues and increased gene expression associated with breast cancer.8,21,23–29 As a result, some investigators consider PCR technology to be problematic for clinical application with false positive and/or clinically irrelevant results a concern.8,21,23,25–27,29–31 Real-time RT-PCR solves these limitations through the use of an online fluorescence detection system that precisely quantifies the amount of PCR product. We have previously shown that real-time RT-PCR can differentiate between baseline gene expression in normal tissues and cancer-associated gene overexpression.32,33 For example, CEA, CK19, and muc1 have detectable baseline expression in normal lymph nodes, but expression levels in ALN with metastatic breast cancer is 5-fold to 3500-fold higher.32 Our data indicate that a combination of multimarker analysis and quantitative real-time RT-PCR can be a precise and powerful tool for the detection of breast cancer ALN metastases. Furthermore, the genes mam, PIP, PDEF, CK19, CEA, muc1, and mamB have particular promise for breast cancer detection.15,32,33 Although these results suggest that molecular markers could serve as valid surrogates for metastatic and micrometastatic breast cancer, their clinical relevance is unproven. To address this, the Minimally Invasive Molecular Staging of Breast Cancer (MIMS) trial was initiated. This trial represents the first prospective cohort study in which a multimarker, real-time RT-PCR analysis was applied to the detection of breast cancer micrometastases in ALN. Sentinel and/or nonsentinel ALN from 489 breast cancer subjects with T1–T3 primary tumors were analyzed by standard histopathology and multimarker, real-time RT-PCR analysis. The study was designed with sufficient statistical power to correlate molecular analyses with clinical outcome at 5 years. Although the clinical outcome data are not yet available, we show in this interim report that real-time RT-PCR is able to sensitively detect metastatic breast cancer in ALN and that overexpression of breast cancer–associated genes in subjects with pathology-negative ALN is correlated with traditional indicators of poor prognosis.

Background The rapid evolution of molecular technology and novel markers provides the opportunity to establish a more effective means to detect micrometastatic breast cancer. Given the controversies concerning application and clinical relevance, this review critically evaluates the current status of these molecular staging technologies. Data sources Breast cancer literature addressing (1) molecular detection methodologies (immunohistochemistry, reverse transcriptase polymerase chain reaction, and microarray analysis); (2) specific tissue applications such as lymph nodes, bone marrow aspirate, and peripheral blood; (3) expert commentary concerning the clinical applications and pitfalls of these technologies; and (4) recent data from our molecular diagnostics laboratory. Conclusions Molecular detection technologies such as reverse transcriptase polymerase chain reaction and microarray analyses are being developed that will likely have future application as cancer diagnostics. Further work is needed to establish assays that are validated by prospective clinical studies. Early identification of clinically relevant disease could lead to new treatment or staging approaches for breast cancer.

Identification of Molecular Markers That Discriminate Between Pancreatic Ductal Adenocarcinoma and Chronic Focal Pancreatitis Using Endoscopic Ultrasound Fine Needle Aspiration and Real-Time RT-PCR David H. Robbins, Yian Chen, Kaidi Mikhitarian, Carlton Barnett, David Cole, William Gillanders, Mike Mitas, Brenda Hoffman Chronic pancreatitis (CP) is an incapacitating disease marked by progressive destruction and replacement of the pancreatic parenchyma with fibrous tissue. At some point in the progression of this disease, chronic pancreatitis may present as a discrete mass, typically of the pancreatic head, and this clinical entity, chronic focal pancreatitis (CFP), is often indistinguishable from malignant disease. Since the clinical, radiographic, endosonographic, gross, and histopathologic features of CFP and pancreatic ductal adenocarcinoma cancer (PDAC) are very similar, reliably distinguishing between them without surgical exploration is a challenging diagnostic dilemma. The recent identification of genes overexpressed in PDAC and chronic pancreatitis by gene profiling provides the opportunity to more precisely characterize suspicious lesions using molecular markers. To determine whether a panel of molecular markers could accurately discriminate PDAC from CFP, we measured gene expression levels from tissue specimens obtained during endoscopic ultrasound-fine needle aspiration (EUS-FNA) examination using quantitative real-time RT-PCR. Gene expression levels of 14 candidate markers were determined in 20 EUS-FNA samples from patients with PDAC, and 10 EUS-FNA samples from patients with known CP and presumed CFP. Comparing gene expression levels between these two groups, we observed that seven genes (mesothelin, MUC4, CEA, SHH, S100P, FXYD3, and TRIM29) were significantly overexpressed in PDAC compared to CFP (p ! 0.05, two sample t test). Receiver operator characteristic curve analysis showed that the diagnostic accuracy for these seven markers was above 75%. These results suggest that one or more of these seven molecular markers improves the discriminatory power of EUS-FNA to distinguish benign from malignant pancreatic disease. W1279 CEAtTo Amylase Ratio for the Diagnosis of Malignant and Premalignant Cystic Lesions of the Pancreas Michael K. Sanders, Raquel E. Davila, Douglas O. Faigel Introduction: The differentiation of pancreatic cystic lesions between those with significant malignant potential (mucinous cystadenomas, cystadenocarcinomas) from cysts without this potential (serous cystadenomas, pseudocysts) is challenging. EUS-FNA cytology may be non-diagnostic and tumor markers have imperfect sensitivity and specificity. Both cyst fluid CEA and amylase have been advocated as useful markers. Aim: To determine if the ratio of CEA to amylase improves diagnostic accuracy over either marker alone. Methods: A retrospective chart review was performed of all cases of pancreatic cysts evaluated by EUS-FNA from October 2001 to September 2004. The final histology of the cysts was determined by surgical pathology or clinical follow-up with radiographic imaging. Those in whom CEA (ng/ml) and amylase (U/L) levels were measured were included in the study. EUS-FNA was done using the Pentax FG-36UX echoendoscope and WilsonCook 22 gauge needle. Sensitivity and specificity were calculated for each marker and also for the ratio CEA/ln(Amylase). Cut off values were determined by ROC analysis. Results: 25 patients (12M, 13F) had EUS-FNA of pancreatic cysts and final histology determined by surgery and clinical follow-up. 18 patients had both CEA and amylase levels and formed the study cohort. There were 9 males and 9 females, mean age 57yrs (range 28-83). Five had neoplastic cysts (1 cancer, 4 mucinous) determined by surgical pathology, and 13 had benign cysts (11 pseudocysts, 2 serous). 6 of the 13 benign cysts were confirmed surgically and 7 showed resolution on repeat imaging at 6-24 months consistent with benign pseudocysts. See Table. Conclusions: CEAO150 ng/ml was the single best predictor for malignant and premalignant cystic pancreatic lesions. The CEA/ln(Amylase) ratio O 40 may improve specificity without loss of sensitivity.

Background We sought to examine the detection rate of cancer cells in peripheral blood (PBL) and in bone marrow (BM) using an established 7-gene marker panel and evaluated whether there were any definable associations of any individual gene with traditional predictors of prognosis. Methods Patients with T1-T3 primary breast cancer were enrolled into a prospective, multi-institutional cohort study. In this interim analysis 215 PBL and 177 BM samples were analyzed by multimarker, real-time RT-PCR analysis designed to detect circulating and disseminated breast cancer cells. Results At a threshold of three standard deviations from the mean expression level of normal controls, 63% (136/215) of PBL and 11% (19/177) of BM samples were positive for at least one cancer-associated marker. Marker positivity in PBL demonstrated a statistically significant association with grade II-III (vs. grade I; p = 0.0083). Overexpression of the mammaglobin (mam) gene alone had a statistically significant association with high tumor grade (p = 0.0315), and showed a trend towards ER-negative tumors and a high risk category. There was no association between marker positivity in PBL and the pathologic (H&E) and/or molecular (RT-PCR) status of the axillary lymph nodes (ALN). Conclusion This study suggests that molecular detection of circulating cancer cells in PBL detected by RT-PCR is associated with high tumor grade and specifically that overexpression of the mam gene in PBL may be a poor prognostic indicator. There was no statistically significant association between overexpression of cancer-associated genes in PBL and ALN status, supporting the concept of two potentially separate metastatic pathways.