Molecular Markers in Ductal Carcinoma in Situ of the Breast
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362 Vol. 1, 362–375, March 2003 Molecular Cancer Research Molecular Markers in Ductal Carcinoma in Situ of the Breast Dale Porter,1,6 Jaana Lahti-Domenici,1 Aparna Keshaviah,2 Young Kyung Bae,8 Pedram Argani,8 Jeffrey Marks,10 Andrea Richardson,3,6 Amiel Cooper,4 Robert Strausberg,9 Gregory J. Riggins,10 Stuart Schnitt,5 Edward Gabrielson,8 Rebecca Gelman,2,7 and Kornelia Polyak1,6 1Departments of Medical Oncology and 2Biostatistics, Dana-Farber Cancer Institute, Boston, MA; 3Department of Pathology, Brigham and Women’s Hospital, Boston, MA; 4Department of Pathology, Faulkner and Brigham and Women’s Hospital, Boston, MA; 5Department of Pathology, Beth-Israel Deaconess Medical Center, Boston, MA; 6Harvard Medical School and 7Harvard School of Public Health, Boston, MA; 8Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD; 9National Cancer Institute, Bethesda, MD; and 10Department of Pathology, Duke University Medical Center, Durham, NC Abstract DCIS may provide insight into their initiation and progression, Gene expression patterns in ductal carcinoma in situ but very little is known about DCIS at the molecular level. (DCIS), and in invasive, and metastatic breast tumors Current classification of DCIS is based on cytological and were determined using serial analysis of gene architectural features. Some studies have demonstrated a expression (SAGE). We used mRNA in situ hybridization correlation between these features, particularly nuclear to examine gene expression at the cellular level and grade and the presence of comedo necrosis, and clinical immunohistochemistry on tissue microarrays to behavior (1–3). In general, high nuclear grade and comedo determine association between gene expression DCIS are associated with high rate of local recurrence, while patterns and histopathologic characteristics of the low-grade non-comedo tumors have low recurrence rates (4). tumors. We found that that the most dramatic However, classification based on histological features can be transcriptome change occurs at the normal to DCIS determined only with moderate consistency and is complicated transition, while there is no clear universal ‘‘in situ’’ or by intratumoral heterogeneity. Moreover, none of these features ‘‘invasive’’ tumor molecular signature. From the 16,430 is able to predict the risk of progression to invasive disease transcripts analyzed, we identified only 5 and 11 that accurately. Therefore, the molecular characterization of DCIS were preferentially up-regulated in DCIS and invasive with the aim of identifying biologically and potentially tumors, respectively. The majority of invasive cancer clinically meaningful subgroups is of utmost importance. specific SAGE tags correspond to novel genes. The Comprehensive gene expression profiling has proven useful genes we identified may define biologically and clinically for the molecular classification of invasive breast tumors, but meaningful subgroups of DCIS with a high risk of no such extensive study has been performed in DCIS largely progression to invasive disease. due to technical difficulties with obtaining DCIS samples suitable for RNA-based analysis (5, 6). Our laboratory uses Introduction serial analysis of gene expression (SAGE) to identify genes Ductal carcinoma in situ (DCIS) of the breast includes a implicated in breast tumorigenesis (7–9). SAGE requires a heterogeneous group of preinvasive breast tumors with a wide relatively small amount of tissue (50,000 cells or less) for the range of malignant potential. Some DCIS, if untreated, will generation of comprehensive expression profiles without the rapidly progress to invasive cancer, while others will change requirement for RNA/cDNA amplification steps; thus, it is very little in 5–20 years. DCIS now represents a significant particularly well suited for the analysis of small, preinvasive (up to 25%) fraction of newly diagnosed breast cancer cases, tumors (10). Although SAGE allows the quantitative measure- yet the clinical management of DCIS patients is still ment of the mRNA levels of thousands of genes simultaneously controversial. The major challenge is to reliably determine the in one specimen, to establish how frequently an emerging risk of local recurrence and progression to invasive disease, and candidate gene is differentially expressed, it is necessary to to treat patients accordingly. Understanding the pathobiology of examine hundreds of breast specimens. The recently developed tissue microarray technology allows rapid profiling of hundreds of specimens on one slide and is therefore ideally suited for the further evaluation of candidate genes emerging from SAGE Received 12/2/02; revised 2/10/03; accepted 2/13/03. analysis (11, 12). The costs of publication of this article were defrayed in part by the payment of Here we report that based on SAGE analyses of breast page charges. This article must therefore be hereby marked advertisement in accordance with 18 U.S.C. Section 1734 solely to indicate this fact. tumors of different histopathologic stages, we identified several Grant support: National Cancer Institute Cancer Genome Anatomy Project and transcripts that belong to one of the following groups: up- or Specialized Program in Research Excellence in Breast Cancer at Dana-Farber/ down-regulated in breast cancer regardless of stage; preferen- Harvard Cancer Center (CA89393) and Johns Hopkins University (CA88843); Department of Defense Breast Cancer Center of Excellence Grants. tially up-regulated in DCIS; or in invasive carcinomas. The Requests for reprints: Kornelia Polyak, Dana-Farber Cancer Institute, 44 Binney expression of 14 genes was confirmed at the cellular level by St. D740C, Boston, MA 02115. Phone: (617) 632-2106; Fax: (617) 632-4005. E-mail: [email protected] mRNA in situ hybridization using a panel of frozen DCIS and Copyright D 2003 American Association for Cancer Research. invasive breast tumors. Tissue microarrays composed of Downloaded from mcr.aacrjournals.org on September 24, 2021. © 2003 American Association for Cancer Research. Molecular Cancer Research 363 primary breast cancers of different pathological stages were and Methods’’). On the basis of these analyses, we found that used to explore the potential clinical usefulness of 10 genes by the expression of CD74 and a SAGE tag (CTGGGCGCCC) investigating their relationship to histopathologic features of the with no database match were significantly more abundant in tumors and patient outcome. invasive or metastatic tumors than in DCIS (P = 0.02 and P = 0.05, respectively, Table 3). The expression of MGC2328, DCD, and eight other genes was also more likely to occur in Results invasive/metastatic tumors than in DCIS, but none of these Normal and Cancerous Breast Transcriptomes reached statistical significance (Table 3). Similarly, the Genes differentially expressed between normal and cancer- expression of S100A7 and keratin 19 (KRT19) was more ous breast tissues were identified using SAGE. Confirming our frequent and at higher levels in DCIS than in invasive/ previous report using a limited set of SAGE libraries (8), we metastatic tumors, but this was also only marginally statistically found that the most dramatic difference in gene expression significant. In a second statistical analysis, receiver operating patterns occurs at the normal to in situ carcinoma transition and characteristic (ROC) curve analysis was used to choose the it involves the uniform down-regulation of 34 genes (Table 1). ‘‘best’’ cutoff for values that result in the most samples being Because many of these genes encode secreted proteins and correctly classified as DCIS or invasive, weighing both kinds of genes related to epithelial cell differentiation, loss of the misclassification equally (Table 3). Tags that do not include differentiated epithelial phenotype and abnormal autocrine/ 0.50 in the CI might be potentially useful for the differential paracrine interactions appear to play an essential role in the diagnosis of in situ and invasive carcinomas. This includes all initiation of breast tumorigenesis. We also identified 144 genes the tags that had P 0.13 using the higher of two normal up-regulated in a fraction of in situ and invasive or metastatic cutoffs as well as three other high in DCIS tags and three other tumors (Table 2). Nearly one-fourth of these SAGE tags high in invasive tags (Table 3). Using the best cutoff values, currently have no database match, indicating that many several of the SAGE tags correctly classified most of the DCIS transcripts specifically expressed in certain breast carcinomas and invasive SAGE libraries. For example, KRT19 classified remain to be identified. To delineate overall similarities and 75% of the DCIS and 0% of the invasive libraries as DCIS, differences among samples, the 19 SAGE libraries were while MGC23280 identified 78% of the invasive cancer and analyzed by hierarchical clustering (Fig. 1A). A dendogram 0% of the DCIS libraries as invasive. Thus, MGC23280 had created using this program revealed that the two normal 78% sensitivity and 100% specificity to correctly categorize samples (N1 and N2) and primary invasive tumors and lymph breast tumors as DCIS or invasive/metastatic in this data set. node metastases (I1 and LN1, and I2 and LN2) derived from the Next we selected 26 genes for further validation studies that same patients were most similar to each other. In situ and appeared to be the most highly differentially expressed between invasive tumors and metastases