Recursive SVM Feature Selection and Sample Classification for Mass-Spectrometry and Microarray Data

Background: Like microarray-based investigations, high-throughput proteomics techniques require machine learning algorithms to identify biomarkers that are informative for biological classification problems. Feature selection and classification algorithms need to be robust to noise and outliers in the data. Results: We developed a recursive support vector machine (R-SVM) algorithm to select important genes/biomarkers for the classification of noisy data. We compared its performance to a similar, state-of-the-art method (SVM recursive feature elimination or SVM-RFE), paying special attention to the ability of recovering the true informative genes/biomarkers and the robustness to outliers in the data. Simulation experiments show that a 5 %-~20 % improvement over SVM-RFE can be achieved regard to these properties. The SVM-based methods are also compared with a conventional univariate method and their respective strengths and weaknesses are discussed. R-SVM was applied to two sets of SELDI-TOF-MS proteomics data, one from a human breast cancer study and the other from a study on rat liver cirrhosis. Important biomarkers found by the algorithm were validated by follow-up biological experiments. Conclusion: The proposed R-SVM method is suitable for analyzing noisy high-throughput proteomics and microarray data and it outperforms SVM-RFE in the robustness to noise and in the ability to recover informative features. The multivariate SVM-based method outperforms the univariate method in the classification performance, but univariate methods can reveal more of the differentially expressed features especially when there are correlations between the features.Statistic

Prognostic Significance of the Proliferation Index in Surgically-Resected Non-Small Cell Lung Cancer

Objective: To determine the utility of measuring the tumor proliferation index as a prognostic marker in patients with non—small-cell lung cancer. Design: Immunostaining for the proliferationassociated antigen Ki-67, quantitated using computerassisted image cytometry, was used to derive the tumor proliferation index for 61 fresh-frozen, banked specimens of non—small-cell lung cancer. DNA ploidy was measured concomitantly for all specimens. A median follow-up of 38 months was achieved for survival analyses. Setting: A large southeastern United States private referral institution and affiliated hospital provided the study environment. Participants: A consecutive, convenience sample of 61 patients was enrolled based on resected tissue preservation and viability over a five-year accruement. Main Outcome Measures: Significant associations between DNA content, proliferation index, established clinicopathological parameters, and outcome were examined. Results: A significant inverse association between patient survival and tumor proliferation index was found that was independent of other established clinicopathological predictors of outcome. Patients whose tumors harbored a proliferation index of less than 3.5 survived significantly longer than patients with tumors demonstrating higher values. No association between DNA content and proliferation index was uncovered. Conclusion: Measurement of the proliferation index, as derived from quantitative Ki-67 immunostaining and analyzed by image cytometry, may provide significant complementary, if not independent, prognostic information for patients with non—small-cell lung cancer

Method of Diagnosing Cancer

A method of diagnosing cancer with antibodies directed to non-cellular components in non-vascular, cellular secretions is disclosed. One such antibody is the monoclonal antibody Lu4B5, which was produced by immunizing mice with a purified, mucin containing fraction prepared from pooled bronchial washings from adenocarcinoma and large cell lung cancer patients. Lu4B5 monoclonal antibody reacts with the bronchial secretions of patients with primary bronchogenic carcinoma significantly more frequently than with secretions from patients without primary lung cancer

Method of Diagnosing Cancer

A method of diagnosing cancer with antibodies directed to non-cellular components in non-vascular, cellular secretions is disclosed. One such antibody is the monoclonal antibody Lu4B5, which was produced by immunizing mice with a purified, mucin containing fraction prepared from pooled bronchial washings from adenocarcinoma and large cell lung cancer patients. Lu4B5 monoclonal antibody reacts with the bronchial secretions of patients with primary bronchogenic carcinoma significantly more frequently than with secretions from patients without primary lung cancer

Prognostic Significance of the Proliferation Index in Surgically-Resected Non-Small Cell Lung Cancer

Objective: To determine the utility of measuring the tumor proliferation index as a prognostic marker in patients with non—small-cell lung cancer. Design: Immunostaining for the proliferationassociated antigen Ki-67, quantitated using computerassisted image cytometry, was used to derive the tumor proliferation index for 61 fresh-frozen, banked specimens of non—small-cell lung cancer. DNA ploidy was measured concomitantly for all specimens. A median follow-up of 38 months was achieved for survival analyses. Setting: A large southeastern United States private referral institution and affiliated hospital provided the study environment. Participants: A consecutive, convenience sample of 61 patients was enrolled based on resected tissue preservation and viability over a five-year accruement. Main Outcome Measures: Significant associations between DNA content, proliferation index, established clinicopathological parameters, and outcome were examined. Results: A significant inverse association between patient survival and tumor proliferation index was found that was independent of other established clinicopathological predictors of outcome. Patients whose tumors harbored a proliferation index of less than 3.5 survived significantly longer than patients with tumors demonstrating higher values. No association between DNA content and proliferation index was uncovered. Conclusion: Measurement of the proliferation index, as derived from quantitative Ki-67 immunostaining and analyzed by image cytometry, may provide significant complementary, if not independent, prognostic information for patients with non—small-cell lung cancer

\u3cem\u3ec-erbB-2\u3c/em\u3e Expression in Breast Cancer Detected by Immunoblotting and Immunohistochemistry

Evidence that the c-erbB-2 proto-oncogene is important in prognosis and oncogenesis in a number of human malignancies is increasing. DNA (Southern) hybridization and immunoblotting (Western) techniques are most commonly utilized to determine the amplification and protein expression of this proto-oncogene, respectively. These extraction techniques are often time consuming, costly, and subject to variability depending on the histological characteristics of the tumor. Immunohistochemistry (IHC), on the other hand, is more often time and cost effective. In addition, IHC may offer enhanced sensitivity over extraction techniques because of the in situ nature of analysis. In data presented here, 71 cases of human mammary carcinoma were concomitantly assessed for c-erbB-2 gene copy number and oncoprotein expression by dilution DNA hybridization and IHC, respectively. In 65 (92%) of 71 cases, high-level expression was associated with gene amplification, whereas moderate or low-level expression was associated with a normal diploid gene copy number. In five of the six discrepant cases, IHC predicted amplification which was not corroborated by Southern analysis. In these cases, tumor mass was limited by the intraductal component of the lesion or by an abundance of stromal elements within the specimen. In 39 of the 71 total cases, Western immunoblotting was compared with IHC in the assessment of oncoprotein expression. Concordance was found in 33 (85%) of 39 cases. In four of the six discrepant cases, high levels of c-erbB-2 expression were demonstrated by IHC but not by immunoblotting. In these cases, intraductal disease and stroma-rich tumors again led to a relative paucity of neoplastic tissue within the specimens. We conclude that IHC offers a favorable alternative to either Southern analysis or Western immunoblotting in the assessment of c-erbB-2 gene copy number and expression levels of oncoprotein in human mammary carcinoma. Furthermore, IHC may prove advantageous to either extraction technique in specimens with limited tumor mass, such as biopsy materials, stroma-rich tumors, or early stage lesions such as intraductal carcinoma

\u3cem\u3ec-erbB-2\u3c/em\u3e Expression in Breast Cancer Detected by Immunoblotting and Immunohistochemistry

Evidence that the c-erbB-2 proto-oncogene is important in prognosis and oncogenesis in a number of human malignancies is increasing. DNA (Southern) hybridization and immunoblotting (Western) techniques are most commonly utilized to determine the amplification and protein expression of this proto-oncogene, respectively. These extraction techniques are often time consuming, costly, and subject to variability depending on the histological characteristics of the tumor. Immunohistochemistry (IHC), on the other hand, is more often time and cost effective. In addition, IHC may offer enhanced sensitivity over extraction techniques because of the in situ nature of analysis. In data presented here, 71 cases of human mammary carcinoma were concomitantly assessed for c-erbB-2 gene copy number and oncoprotein expression by dilution DNA hybridization and IHC, respectively. In 65 (92%) of 71 cases, high-level expression was associated with gene amplification, whereas moderate or low-level expression was associated with a normal diploid gene copy number. In five of the six discrepant cases, IHC predicted amplification which was not corroborated by Southern analysis. In these cases, tumor mass was limited by the intraductal component of the lesion or by an abundance of stromal elements within the specimen. In 39 of the 71 total cases, Western immunoblotting was compared with IHC in the assessment of oncoprotein expression. Concordance was found in 33 (85%) of 39 cases. In four of the six discrepant cases, high levels of c-erbB-2 expression were demonstrated by IHC but not by immunoblotting. In these cases, intraductal disease and stroma-rich tumors again led to a relative paucity of neoplastic tissue within the specimens. We conclude that IHC offers a favorable alternative to either Southern analysis or Western immunoblotting in the assessment of c-erbB-2 gene copy number and expression levels of oncoprotein in human mammary carcinoma. Furthermore, IHC may prove advantageous to either extraction technique in specimens with limited tumor mass, such as biopsy materials, stroma-rich tumors, or early stage lesions such as intraductal carcinoma

Expression of p53 in Human Neuroblastoma- and Neuroepithelioma-Derived Cell Lines

Overexpression of the nuclear phosphoprotein p53 has been detected in many different transformed human cell lines and primary adult tumors. Elevated steady-state levels of p53 appear to be the result of an increase in the stability of the protein and, in adult cancers, high levels of the protein are associated with mutation of the p53 gene. In this study, overexpression of p53 was detected in 4 out of 5 human neuroblastoma-derived cell lines. The protein expressed by each of these four lines had a significantly prolonged half-life relative to the p53 protein in immortalized rodent fibroblasts and normal bovine adrenal medullary cells. However, no mutations were detected in the highly conserved regions of the p53 gene in these four neuroblastoma lines and the protein being expressed was not recognized by the mutant-specific anti-p53 monoclonal antibody, PAb 240. Upon retinoic acid-induced differentiation of the LA-N-5 neuroblastoma cell line, the level of p53 protein declined, as did the level of p53 mRNA, but the half-life of the protein remained unchanged. The high level of protein observed in the undifferentiated cell lines appears to result from expression of a stable wild-type p53 protein and increased transcription. In contrast, p53 protein was undetectable in two neuroepithelioma-derived cell lines; the p53 gene in one of these lines contained a nonsense mutation, while the other transcribed truncated p53 mRNA