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W Fraser Symmans

Publications and source records attributed to W Fraser Symmans.

At least 37 records · Page 2Linked to original sources

Microtubule-associated protein tau: a marker of paclitaxel sensitivity in breast cancer.

Breast cancers show variable sensitivity to paclitaxel. There is no diagnostic test to identify tumors that are sensitive to this drug. We used U133A chips to identify genes that are associated with pathologic complete response (pCR) to preoperative paclitaxel-containing chemotherapy in stage I-III breast cancer (n = 82). Tau was the most differentially expressed gene. Tumors with pCR had significantly lower (P < 0.3 x 10(-5)) mRNA expression. Tissue arrays from 122 independent but similarly treated patients were used for validation by immunohistochemistry. Seventy-four percent of pCR cases were tau protein negative; the odds ratio for pCR was 3.7 (95% confidence interval, 1.6-8.6; P = 0.0013). In multivariate analysis, nuclear grade (P < 0.01), age <50 (P = 0.03), and tau-negative status (P = 0.04) were independent predictors of pCR. Small interfering RNA experiments were performed to examine whether down-regulation of tau increases sensitivity to chemotherapy in vitro. Down-regulation of tau increased sensitivity of breast cancer cells to paclitaxel but not to epirubicin. Tubulin polymerization assay was used to assess whether tau modulates binding of paclitaxel to tubulin. Preincubation of tubulin with tau resulted in decreased paclitaxel binding and reduced paclitaxel-induced microtubule polymerization. These data suggest that low tau expression renders microtubules more vulnerable to paclitaxel and makes breast cancer cells hypersensitive to this drug. Low tau expression may be used as a marker to select patients for paclitaxel therapy. Inhibition of tau function might be exploited as a therapeutic strategy to increase sensitivity to paclitaxel.

Biomarkers↗

Predictors of invasive breast cancer in patients with an initial diagnosis of ductal carcinoma in situ: a guide to selective use of sentinel lymph node biopsy in management of ductal carcinoma in situ.

BACKGROUND: The role of sentinel lymph node biopsy (SLNB) in patients with an initial diagnosis of ductal carcinoma in situ (DCIS) has not been well defined. The purpose of our study was to determine when the risk of finding invasive disease on final pathology in patients with an initial diagnosis of DCIS was sufficiently high to justify use of SLNB. STUDY DESIGN: The records of 398 consecutive patients from our prospective database with an initial diagnosis of DCIS, treated between July 1999 and December 2002, were analyzed. Associations between clinical and pathologic factors and patient selection for SLNB and outcomes were analyzed for significance using univariate and multivariate analyses. RESULTS: Of the 398 patients, 80 (20%) were found to have invasive disease on final pathology. Multivariate analysis revealed 4 independent predictors of invasive cancer on final pathology: 55 years of age or younger (odds ratio [OR], 2.19; p = 0.024), diagnosis by core-needle biopsy (OR, 3.76; p = 0.006), mammographic DCIS size of at least 4 cm (OR, 2.92; p = 0.001), and high-grade DCIS (OR, 3.06; p = 0.002). A total of 141 patients (35%) underwent SLNB as a component of their initial operation. Multivariate analysis revealed that the presence of comedonecrosis (OR, 2.69; p = 0.007) and larger mammographic DCIS size (OR, 1.18; p = 0.0002) were independent predictors of patients' undergoing SLNB. Of these 141 patients, 103 (73%) were diagnosed by core-needle biopsy, 42 (30%) had invasive disease on final pathology, and 14 (10%) had a positive sentinel lymph node: 12 (86%) by hematoxylin and eosin staining and 2 by immunohistochemistry. The only independent predictor of a positive SLN was the presence of a palpable tumor (OR, 4.28, p = 0.042). Of these 14 patients with a positive sentinel node, only 11 (79%) had invasive cancer on final pathology. CONCLUSIONS: SLNB should not be performed routinely for all patients with an initial diagnosis of DCIS. Risks and benefits of SLNB should be discussed with patients who are younger, are diagnosed by core-needle biopsy, or have large or high-grade DCIS.

Adult↗

Breast cancer biomarkers.

Substantial progress has been made over the past three decades in our understanding of the epidemiology, clinical course and basic biology of breast cancer. This chapter considers the existing ancillary tests and emerging molecular markers in breast cancer prognosis assessment and the prediction of response of breast cancer to treatment of the disease.

Biomarkers, Tumor↗

Comparison of the predictive accuracy of DNA array-based multigene classifiers across cDNA arrays and Affymetrix GeneChips.

We examined how well differentially expressed genes and multigene outcome classifiers retain their class-discriminating values when tested on data generated by different transcriptional profiling platforms. RNA from 33 stage I-III breast cancers was hybridized to both Affymetrix GeneChip and Millennium Pharmaceuticals cDNA arrays. Only 30% of all corresponding gene expression measurements on the two platforms had Pearson correlation coefficient r >or= 0.7 when UniGene was used to match probes. There was substantial variation in correlation between different Affymetrix probe sets matched to the same cDNA probe. When cDNA and Affymetrix probes were matched by basic local alignment tool (BLAST) sequence identity, the correlation increased substantially. We identified 182 genes in the Affymetrix and 45 in the cDNA data (including 17 common genes) that accurately separated 91% of cases in supervised hierarchical clustering in each data set. Cross-platform testing of these informative genes resulted in lower clustering accuracy of 45 and 79%, respectively. Several sets of accurate five-gene classifiers were developed on each platform using linear discriminant analysis. The best 100 classifiers showed average misclassification error rate of 2% on the original data that rose to 19.5% when tested on data from the other platform. Random five-gene classifiers showed misclassification error rate of 33%. We conclude that multigene predictors optimized for one platform lose accuracy when applied to data from another platform due to missing genes and sequence differences in probes that result in differing measurements for the same gene.

Adult↗

Pharmacogenomics and clinical biomarkers in drug discovery and development.

The fields of pathology and clinical pharmacology are in an era of rapid evolution, reflecting continuous technological advancements in molecular diagnostics focused on improving drug efficacy and reducing toxicity. The discovery and refinement of the human genome sequence, further understanding of epigenetic events, and the expansion of proteomics research combined with emerging technologies such as functional imaging, biosensors, and sophisticated computational biology are having an unprecedented impact on the pharmaceutical industry. This review focuses on the discovery and development of DNA-based gene sequence tests and RNA-based gene expression profiles as applied to the prediction of response, resistance, and toxicity of both new and existing anticancer, cardiovascular, and anti-inflammatory drugs. This review will also consider the potential of emerging biomarkers designed to assist in the clinical development of these agents.

Biomarkers↗

Individualized chemotherapy treatment for breast cancer: is it necessary? Is it feasible?

Individualized selection of chemotherapy regimens based on the molecular characteristics of the cancer would be desirable. However, it is not currently feasible. The development of clinically useful predictors of response to chemotherapy has proven to be difficult. Recently, novel analytical tools particularly transcriptional profiling, have shown promise as potential predictive tests in several small exploratory studies. However, many of the practical challenges of clinical pharmacogenomics are the same that have plagued prognostic and predictive marker research for decades. Perhaps, the most important challenge is to prospectively design and conduct validation trials that demonstrate clinical utility by showing improved patient outcomes with the use of a proposed new test.

Antineoplastic Agents↗

Pharmacoproteomic analysis of prechemotherapy and postchemotherapy plasma samples from patients receiving neoadjuvant or adjuvant chemotherapy for breast carcinoma.

BACKGROUND: In this study, proteomic changes were examined in response to paclitaxel chemotherapy or 5-fluorouracil, doxorubicin, and cyclophosphamide (FAC) chemotherapy in plasma from patients with Stage I-III breast carcinoma. The authors also compared the plasma profiles of patients with cancer with the plasma profiles of healthy women to identify breast carcinoma-associated protein markers. METHODS: Sixty-nine patients and 15 healthy volunteers participated in the study. Plasma was sampled on Day 0 before chemotherapy and on Day 3 posttreatment in the 69 patients or 3 days apart in the 15 healthy women. Twenty-nine patients received preoperative chemotherapy, and 40 received postoperative chemotherapy. Surface-enhanced laser desorption/ionization mass spectrometry was used to generate protein mass profiles. RESULTS: Few changes were observed in plasma during treatment. Only 1 protein peak was identified (mass/charge ratio [m/z], 2790) that was induced by paclitaxel and, to a lesser extent, by FAC chemotherapy. This proteomic response was detectable in 80% of patients who were treated preoperatively but also was present with lesser intensity in approximately 40% of patients treated postoperatively. There was no clear correlation between induction of m/z 2790 during a single course of treatment and final tumor response to preoperative chemotherapy. Five other peaks also were identified that discriminated between plasma from patients with breast carcinoma and plasma from normal women. These same peaks also were detectable in a subset of patients who already had undergone surgery to remove their tumors. CONCLUSIONS: A single chemotherapy-inducible SELDI-MS peak and five other peaks that distinguished plasma obtained from patients with breast carcinoma from plasma obtained from normal, healthy women were identified. The (as yet unsequenced) proteins represented by these peaks are candidate markers of micrometastatic disease after surgery.

Adult↗

Change in tumor cellularity of breast carcinoma after neoadjuvant chemotherapy as a variable in the pathologic assessment of response.

BACKGROUND: Complete pathologic response of breast carcinoma to neoadjuvant chemotherapy is a well defined outcome that correlates with prolonged survival. Categorization of incomplete response depends on accurate measurement of residual tumor size but is complicated by the variable histopathologic changes that occur within the tumor bed. In the current study, the authors investigated the contribution of assessing tumor cellularity in the pathologic evaluation of response to chemotherapy. METHODS: The slides from diagnostic core needle biopsy and the subsequent matched resection specimens were examined in 240 patients with breast carcinoma: 120 "treated" patients who received neoadjuvant chemotherapy and 120 "control" patients who received primary surgical management within a few weeks of diagnosis. Clinical response and residual tumor size were evaluated in 108 treated patients who completed a clinical trial with paclitaxel and then received combined 5-fluorouracil, doxorubicin, and cyclophosphamide chemotherapy. Tumor cellularity was assessed from hematoxylin and eosin-stained tissue sections as the percentage of tumor area that contained invasive carcinoma. RESULTS: After neoadjuvant chemotherapy, tumor cellularity decreased from a median of 40% in core needle biopsy to 10% in resection specimens (P<0.01; Wilcoxon signed rank test). The cellularity of core needle biopsy (median, 30%) tended to underestimate the cellularity of resection specimens (median, 40%) in the control group (P<0.01). Changes in cellularity varied within each clinical response category, particularly partial response and minor response. The greatest reduction was observed in the cellularity of residual primary tumors that measured < or =1 cm (pathologic T1a [pT1a] and pT1b tumors), but changes in cellularity varied in the pT1, pT2, and pT3 residual tumor categories. The shape of the distribution of tumor size, expressed as the greatest dimension in cm, was similar in the control group and the treatment group (excluding complete pathologic response); however, when residual tumor size and cellularity were combined, the distribution of pathologic response shifted left (toward complete response) with a steep decline, suggesting that many tumors had a large reduction in cellularity but little change in the tumor size. CONCLUSIONS: Cellularity of the tumor mass was reduced significantly by neoadjuvant chemotherapy, and the change varied widely in different categories of clinical response. Although residual tumors measuring < or =1 cm in greatest dimension had the most reduction in tumor cellularity, there was broad variability for all residual tumor groups (pT1-pT3). The frequency distribution of residual tumor size was altered markedly by the inclusion of tumor cellularity, indicating that the product of pathologic size and tumor cellularity may provide more accurate pathologic response information than tumor size alone.

Antineoplastic Agents, Phytogenic↗

Differential gene and protein expression in primary breast malignancies and their lymph node metastases as revealed by combined cDNA microarray and tissue microarray analysis.

BACKGROUND: Metastatic disease is a major adverse prognostic factor in breast carcinoma. Lymph node metastases often represent the first step in the metastatic process. METHODS: To gain insight into the molecular events that underlie breast carcinoma metastasis, the authors compared gene expression profiles, obtained by cDNA microarray analysis, of nine matched primary tumors and metastases after screening for enrichment of tumor cells. Statistical analysis identified genes that are expressed at elevated or decreased levels in metastases relative to the corresponding primary tumors. Multidimensional scaling analysis indicated that in terms of expression levels, primary tumors were tightly clustered, whereas metastases exhibited a greater spread; this finding points to the more heterogeneous nature of metastases. Among the differentially expressed entities were the invasion- and tissue modeling-related genes IGFBP5, fibronectin, and MMP2; the cell cycle regulatory gene cyclin D1; other genes, such as enolase 2; and an expressed sequence tag similar to angiopoietin 1. To validate and extend these initial findings, the authors constructed a tissue microarray consisting of 100 primary malignancies paired with their lymph node metastases. Antibodies for the IGFBP-5, fibronectin, MMP-2, cyclin D1, and MDM-2 proteins were used to stain tissue array sections. RESULTS: Consistent with microarray data, statistically significant overexpression of IGFBP-5, down-regulation of cyclin D1, and unchanged MDM-2 levels were observed in metastatic tumor cells. Nonetheless, although fibronectin and MMP2 mRNA expression levels were decreased in many metastasis specimens, expression levels of the corresponding proteins in the extracellular matrix were elevated in most metastases. Decreased expression of fibronectin and MMP2 in lymph node metastases was further confirmed by real-time polymerase chain reaction assays performed on five additional specimen pairs. CONCLUSIONS: The results of the current study suggest that extracellular matrix protein expression and nuclear gene expression are associated via a negative-feedback regulatory mechanism. Therefore, gene expression profiling and tissue array validation should be combined to elucidate molecular events associated with the metastatic process.

Breast Neoplasms↗

Optimal fixation conditions for immunocytochemical analysis of estrogen receptor in cytologic specimens of breast carcinoma.

BACKGROUND: The techniques for immunostaining estrogen receptor (ER) in cytologic specimens have varied, as have the detection rates. The authors compared various fixation methods for their effect on ER detection in cytologic smears of breast carcinoma. METHODS: Smears were prepared by gently scraping the cut surfaces of 47 resected breast carcinoma specimens and placing immediately in 1 of the following conditions: 1) a sequence of 10% formalin-methanol-acetone fixatives at -20 degrees C (Abbott method); 2) 10% formalin at room temperature; and 3) Carnoy's fixative at room temperature and then Papanicolaou stained (Carnoy's-Pap). Destaining of Carnoy's-Pap smears (Carnoy's-dPap) was initially attempted before ER staining. One set of smears was also air-dried for 3 minutes before using the Abbott method. Smears and corresponding tissue sections were immunostained with anti-ER antibody 6F11 using a similar protocol except for antigen retrieval, which was not initially applied on cytologic slides. All the ER-negative smears that had been fixed with 10% formalin or Carnoy's-Pap were restained after antigen retrieval. Agreement between cytologic and histologic findings was expressed by both concordance and the kappa coefficient. RESULTS: ER detection in smears processed with the Abbott method correlated best with findings from tissue samples, with an overall correlation of 91.5% (kappa = 0.80). Findings from air-dried smears were less optimal (concordance, 84.4%; kappa = 0.65), followed by Carnoy's-Pap (concordance, 71.4%; kappa = 0.45), formalin (concordance, 31%; kappa = 0.05), and Carnoy's-dPap (concordance, 29.4%; kappa = 0.04). Antigen retrieval converted most of the ER-negative smears to positive (18 of 20 smears in formalin and 6 of 8 smears in Carnoy's-Pap), leading to a final concordance of 93% and kappa = 0.83 for both conditions. Antigen retrieval also led to stronger staining intensity without causing false positivity. CONCLUSIONS: Antigen retrieval was found to greatly improve ER immunodetectability and staining intensity in formalin-fixed and Carnoy's-Pap smears. The former may offer an alternative to the Abbott method because of its easiness and the latter can be reliably used in archival Pap-stained smears for retrospective analysis of ER. Air-drying, destaining Pap smear, and fixation in formalin or Carnoy's-Pap without antigen retrieval are not recommended.

Adenocarcinoma↗

Targeted therapy in breast cancer: the HER-2/neu gene and protein.

The HER-2/neu oncogene, a member of the epidermal growth factor receptor or erb gene family, encodes a transmembrane tyrosine kinase receptor that has been linked to prognosis and response to therapy with the anti-HER-2-humanized monoclonal antibody, trastuzumab (Herceptin, Genentech, South San Francisco, CA) in patients with advanced metastatic breast cancer. HER-2/neu status has also been tested for its ability to predict the response of breast cancer to other therapies including hormonal therapies, topoisomerase inhibitors, and anthracyclines. This review includes an analysis of 80 published studies encompassing more than 25,000 patients designed to consider the relative advantages and disadvantages of the various methods of measuring HER-2/neu in clinical breast cancer specimens. Southern blotting, PCR amplification detection, and fluorescence in situ hybridization assays designed to detect HER-2/neu gene amplification are compared with HER-2/neu protein overexpression assays performed by immunohistochemical techniques applied to frozen and paraffin-embedded tissues and enzyme immunoassays performed on tumor cytosols. The significance of HER-2/neu overexpression in ductal carcinoma in situ and the HER-2/neu status in uncommon female breast conditions and male breast cancer are also considered. The role of HER-2/neu testing for the prediction of response to trastuzumab therapy in breast cancer is reviewed along with the current studies designed to test whether HER-2/neu status can predict the response to standard and newer hormonal therapies, cytotoxic chemotherapy, and radiation. The review will also evaluate the status of serum-based testing for circulating HER-2/neu receptor protein and its ability to predict disease outcome and therapy response.

Antineoplastic Agents↗

Pharmacogenomics.

The discovery of the human genome and subsequent expansion of proteomics research combined with emerging technologies such as functional imaging, biosensors and sophisticated computational biology are producing unprecedented changes in today's healthcare. The expanding knowledge of the molecular basis of cancer has shown that significant differences in gene expression patterns can guide therapy not only for neoplastic conditions, but also for a variety of diseases including inflammatory disorders, cardiovascular disease and neurodegenerative processes. As a result, the fields of pharmacogenetics and pharmacogenomics have emerged as potential new testing platforms for the individualized management of patients. An individual's response to a drug is the complex interaction of both genetic and non-genetic factors. Genetic variants in the drug target itself, disease pathway genes, or drug metabolizing enzymes may all be used as predictors of drug efficacy or toxicity. In oncology, the SNP technology has focused on detecting the predisposition for cancer, predicting of toxic responses to drugs and selecting the best individual and combinations of anti-cancer drugs. Pharmacogenomics involves the application of whole genome technologies (e.g., gene and protein expression data) for the prediction of the sensitivity or resistance of an individual's disease to a single or group of drugs. Genomic microarrays and transcriptional profiling have the ability to generate hundreds of thousands of data points requiring sophisticated and complex information systems necessary for accurate and useful data analysis. This technique has generated a wealth of new information in the fields of leukemia/lymphoma, and solid tumor classification and prediction of metastasis, drug and biomarker target discovery and pharmacogenomic drug efficacy testing.

Drug Resistance, Neoplasm↗

Targeted therapies for cancer 2004.

The regulatory agency approvals in the United States and Europe of imatinib mesylate (Gleevec) for patients with bcr/abl-positive chronic myelogenous leukemia, cetuximab (Erbitux) for patients with epidermal growth factor receptor overexpressing metastatic colorectal cancer, the antiangiogenesis agent bevacizumab (Avastin), and the proteasome inhibitor bortezomib (Velcade)--and the considerable public interest in new anticancer drugs that take advantage of specific genetic defects that render the malignant cells more likely to respond to specific treatment--are driving a new era of integrated diagnostics and therapeutics. The recent discovery of a drug response predicting activating mutation in the epidermal growth factor receptor gene for patients with non-small cell lung cancer treated with gefitinib (Iressa) has intensified this interest. In this review, the history of targeted anticancer therapies is highlighted, with focus on the development of molecular diagnostics for hematologic malignancies and the emergence of trastuzumab (Herceptin), an antibody-based targeted therapy for HER-2/neu overexpressing metastatic breast cancer: The potential of pharmacogenomic strategies and the use of high-density genomic microarrays to classify and select therapy for cancer are briefly considered. This review also considers the widely held view that, in the next 5 to 10 years, the clinical application of molecular diagnostics will further revolutionize the drug discovery and development process; customize the selection, dosing, route of administration of existing and new therapeutic agents; and truly personalize medical care for cancer patients.

Aminoglycosides↗

Breast cancer biomarkers and molecular medicine: part II.

In this second part of the two-part review of breast cancer biomarkers and molecular medicine, the first section will consider additional breast cancer prognostic factors, including oncogenes, tumor suppressor genes, cell adhesion molecules, invasion-associated proteins and proteases, hormone receptor proteins, drug resistance proteins, apoptosis regulators, transcription factors, telomerase, DNA repair and methylation and transcriptional profiling using high-density genomic microarrays. The second section will consider the prediction of therapy response using the techniques of pharmacogenetics and pharmacogenomics.

Biomarkers, Tumor↗

Pathologic changes in breast cancer following neoadjuvant chemotherapy: implications for the assessment of response.

Neoadjuvant chemotherapy (also known as preoperative or primary chemotherapy) is the treatment of choice for patients with locally advanced breast cancer. One of the main advantages of neoadjuvant chemotherapy is that it allows for assessment of pathologic response to treatment. Clinical and radiologic evaluations of response to neoadjuvant chemotherapy are based on change in tumor size, and the correlation with pathologic response is often inaccurate. Pathologic evaluation of tumor size remains the gold standard for evaluation of residual tumor after chemotherapy. Chemotherapy-induced histomorphologic change is commonly observed in posttreatment resection specimens and can contribute to the less-than-perfect correlation between the clinical assessment of tumor size and the pathologic measurement. Therefore, accurate histologic mapping to the macroscopic and radiologic appearance of the tumor bed is necessary. Cytopathologic changes are also common in residual cancer cells after neoadjuvant chemotherapy and have uncertain clinical relevance. There is a role for the development of new histologic approaches to augment the pathologic and clinical assessment and provide information on the differential response, particularly for tumors in which less than pathologic complete response is achieved.

Breast Neoplasms↗

Phase I and II study of exisulind in combination with capecitabine in patients with metastatic breast cancer.

PURPOSE: We studied the safety and clinical activity of exisulind in combination with capecitabine in 35 patients with metastatic breast cancer (MBC). PATIENTS AND METHODS: All patients had received previous anthracycline and taxane chemotherapies. Two dose levels of exisulind were explored, 125 and 250 mg orally bid as continuous daily therapy, concomitant with capecitabine 2,000 mg/m2 for 14 days in 21-day cycles. In the phase I study, the dose-limiting toxicities were hand-foot syndrome and diarrhea. The 125-mg bid dose was selected for phase II testing. RESULTS: The most common nonhematologic grade 2 to 3 adverse events were hand-foot syndrome (57%) and fatigue (48%). The most frequent grade 2 to 3 laboratory abnormality was granulocytopenia. No death, unexpected adverse events, or cumulative toxicity were encountered. One complete and four partial responses were achieved (objective response rate, 16%) in the 31 patients assessable for response. The median duration of response was 31 weeks; three patients experienced stable disease longer than 26 weeks. Overall clinical benefit (complete response, partial response, or stable disease > 26 weeks) was 23%. Fourteen specimens were available for immunohistochemical assessment of phosphodiesterase-5 isoenzyme (PDE-5) and PDE-2 expression, which are the targets of exisulind. Eighty percent of tumors showed some expression of PDE-5 in the invasive cancer cells including 35% that showed moderate or strong staining. PDE-2 showed moderate or strong staining in 78% of tumors. There was no apparent association between tumor response and staining intensity. CONCLUSION: Exisulind (125 mg orally bid) in combination with capecitabine is well tolerated and the combination has anticancer activity similar to that of capecitabine alone in heavily pretreated patients with MBC.

3',5'-Cyclic-GMP Phosphodiesterases↗

Alternative splicing disrupts a nuclear localization signal in spleen tyrosine kinase that is required for invasion suppression in breast cancer.

Spleen tyrosine kinase (Syk) is a candidate tumor (metastasis) suppressor that is highly expressed in mammary epithelial cells. Loss of Syk expression through promoter hypermethylation is associated with increased invasiveness in a subset of breast cancer. Here, we show that in addition to full-length Syk [Syk(L)], an alternatively spliced variant, Syk(S), is frequently expressed in breast cancer cells. Syk(S) is identical to Syk(L), except that it lacks 23 amino acid residues (deletion) within the interdomain B (IDB) of Syk. We also show that the aberrant expression of Syk(S) occurs frequently in primary breast tumors but never in matched normal mammary tissues, suggesting a contribution of Syk(S) to mammary tumor progression. Expression of Syk(L) suppressed breast cancer cell invasiveness. In contrast, Syk(S) expression did not affect the cell invasion potential. This differential phenotypic response is accompanied by their different subcellular localization. Immunocytochemical studies and nuclear and cytoplasmic fractionation experiments indicated that Syk(L) could enter the nucleus, whereas Syk(S) was located exclusively in the cytoplasm. Five basic residues in deletion were found to be critical in determining Syk(L) nuclear transport and invasion suppression activity; mutations completely excluded Syk(L) from the nucleus and blocked Syk(L)-inducible invasion suppression. Moreover, IDB acted as an autonomous nuclear localization signal to facilitate nuclear transport of a heterologous protein. Thus, the IDB of Syk(L) contains a nuclear localization signal that is responsible for Syk(L) nuclear translocation. The correlation of the nuclear localization and invasion suppression function of Syk(L) indicated that nuclear Syk possesses biological activities associated with tumor suppression in mammary epithelial cells.

Alternative Splicing↗

Total RNA yield and microarray gene expression profiles from fine-needle aspiration biopsy and core-needle biopsy samples of breast carcinoma.

BACKGROUND: Gene expression profiling should be applicable to needle biopsy samples if microarray technology is to become practically useful for clinical research or management of breast carcinoma. This study compared gene expression profiles derived from fine-needle aspiration biopsy (FNAB) and from core needle biopsy (CBX). METHODS: Total RNA was extracted from single FNAB and CBX samples. Corresponding pairs of FNAB and CBX were analyzed for similarity of gene expression profiles using cDNA microarrays that contain 30721 human sequences. A subset of genes that distinguished CBX samples from FNAB samples was evaluated in a larger group of needle biopsy samples and in a published genomic database derived from 78 sporadic breast carcinomas with known clinical outcome. RESULTS: Sixty-eight patients with newly diagnosed breast carcinoma were included in the current study. Sixty-five patients underwent FNAB (17 had both FNAB and CBX) and 3 underwent CBX only. Extracted RNA was of suitable quality for hybridization in 46 (71%) FNABs and 15 (75%) CBXs. Total RNA yield in those samples was similar for single-pass FNAB (mean = 3.6 microg and median = 2.2 microg; n = 46) and CBX (mean = 2.8 microg and median = 2.0 microg; n = 15), with 1 microg or more of total RNA in all cases. Transcriptional profiling was performed successfully in all cases when it was attempted, in a total of 50 samples (38 FNABs and 12 CBXs), including matched FNAB and CBX samples from 10 patients. There were differences in gene expression profiles in 10 matched FNAB and CBX sample pairs. Genes that were expressed differently in CBX samples, compared with FNAB samples, were recognized as being predominantly from the endothelium, fibroblasts, myofibroblasts or smooth muscle, and histiocytes. Corresponding microscopic cell counts from FNABs demonstrated means of 80% tumor cells, 15% lymphocytes, and 5% stromal cells, whereas CBXs contained 50% tumor cells, 20% lymphocytes, and 30% stromal cells. Considering that CBXs are approximately six-fold richer in nonlymphoid stromal cells than FNABs and that CBXs differentially express a set of recognized stromal genes, the authors used these biopsies to define a transcriptional profile of breast carcinoma stroma. A set of 120 genes differentially expressed in CBXs was assessed independently in a published breast carcinoma genomic database to classify breast carcinomas based on stromal gene expression. Subgroups of tumors with low or high stromal signal were identified, but there was no correlation with the development of systemic metastases within 5 years. CONCLUSIONS: Both FNAB and CBX yield a similar quality and quantity of total RNA and are suitable for cDNA microarray analyses in approximately 70-75% of single-pass samples. Transcriptional profiles from FNAB and CBX of the same tumor generally are similar and are driven by the tumor cell population. The authors concluded that each technique has relative advantages. The FNABs provide transcriptional profiles that are a purer representation of the tumor cell population, whereas transcriptional profiles from CBXs include more representation from nonlymphoid stromal elements. Selection of the preferred needle biopsy sampling technique for genomic studies of breast carcinomas should depend on whether variable stromal gene expression is desirable in the samples.

Adult↗