Analysis of breast cancer progression using principal component analysis and clustering

We develop a new technique to analyse microarray data which uses a combination of principal components analysis and consensus ensemble k-clustering to find robust clusters and gene markers in the data. We apply our method to a public microarray breast cancer dataset which has expression levels of genes in normal samples as well as in three pathological stages of disease; namely, atypical ductal hyperplasia or ADH, ductal carcinoma in situ or DCIS and invasive ductal carcinoma or IDC. Our method averages over clustering techniques and data perturbation to find stable, robust clusters and gene markers. We identify the clusters and their pathways with distinct subtypes of breast cancer (Luminal,Basal and Her2+). We confirm that the cancer phenotype develops early (in early hyperplasia or ADH stage) and find from our analysis that each subtype progresses from ADH to DCIS to IDC along its own specific pathway, as if each was a distinct disease.     

GeoPCA: a new tool for multivariate analysis of dihedral angles based on principal component geodesics

The GeoPCA package is the first tool developed for multivariate analysis of dihedral angles based on principal component geodesics. Principal component geodesic analysis provides a natural generalization of principal component analysis for data distributed in non-Euclidean space, as in the case of angular data. GeoPCA presents projection of angular data on a sphere composed of the first two principal component geodesics, allowing clustering based on dihedral angles as opposed to Cartesian coordinates. It also provides a measure of the similarity between input structures based on only dihedral angles, in analogy to the root-mean-square deviation of atoms based on Cartesian coordinates. The principal component geodesic approach is shown herein to reproduce clusters of nucleotides observed in an η-θ plot. GeoPCA can be accessed via http://pca.limlab.ibms.sinica.edu.tw.     

Eicosanoids in breast cancer patients before and after mastectomy.

In 19 patients with a malignant breast tumor, tumor tissue and blood were taken to determine the eicosanoid profile and platelet aggregation. Values were compared with those of patients with benign tumors (n = 4), or undergoing a mammary reduction (n = 7). Postoperatively, blood was taken as well in order to compare pre- and postoperative values. Eicosanoids were measured in peripheral blood monocytes and mammary tissue by means of HPLC; furthermore, TXA2, 6-keto-PGF1 alpha, and PGE2 were determined by RIA. Differences in pre- and postoperative values of cancer patients were seen in plasma RIA values: PGE2 and 6-k-PGF1 alpha were significantly higher preoperatively when compared with postoperatively, however, such differences were seen in the control groups as well. Compared to benign tumor or mammary reduction test material the eicosanoid profile of tissue obtained from malignant mammary tumors showed important differences. Except for PGF2 alpha, HHT and 15-HETE no detectable quantities of eicosanoids were found in the non-tumor material, whereas in the malignant tumor material substantial quantities of a number of eicosanoid metabolites were present. Statistically significant correlations could be established between patient/histopathology data and the results of the platelet aggregation assays, e.g. between menopausal status and ADP aggregation; oestrogen receptor (+/-) and collagen and arachidonic acid aggregation, inflammatory cell infiltration score and arachidonic acid aggregation and fibrosis score and ADP aggregation. The results show that eicosanoid synthesis in material from mammary cancer patients is different from that in benign mammary tissue. The implications, in particular, in relation to future prognosis of the patient, remain obscure.     

A web-based tool for principal component and significance analysis of microarray data

We have developed a program for microarray data analysis, which features the false discovery rate for testing statistical significance and the principal component analysis using the singular value decomposition method for detecting the global trends of gene-expression patterns. Additional features include analysis of variance with multiple methods for error variance adjustment, correction of cross-channel correlation for two-color microarrays, identification of genes specific to each cluster of tissue samples, biplot of tissues and corresponding tissue-specific genes, clustering of genes that are correlated with each principal component (PC), three-dimensional graphics based on virtual reality modeling language and sharing of PC between different experiments. The software also supports parameter adjustment, gene search and graphical output of results. The software is implemented as a web tool and thus the speed of analysis does not depend on the power of a client computer. AVAILABILITY: The tool can be used on-line or downloaded at http://lgsun.grc.nia.nih.gov/ANOVA/     

Quantitative image analysis of estrogen and progesterone receptors as a prognostic tool for selecting breast cancer patients for therapy

OBJECTIVE: To assess estrogen and progesterone receptor presence in human breast tumors using immunocytochemical analysis. STUDY DESIGN: For both estrogen (ER) and progesterone (PR) receptor assay, percent of stained cells and intensity of staining were estimated on a series of 251 consecutive breast cancer cases from the M. Ascoli Cancer Hospital Center in Palermo using the CAS 200 image analysis system. RESULTS: Cytochemical assay revealed a differential distribution of both ER and PR, by menopausal status of the patients; premenopause (PreM) was mostly ER negative (63%), and postmenopause (PostM) > 10 years was mostly ER and PR positive (64%). The percent of cells stained for ER was significantly different between PreM and PostM patients when they were considered as a whole. By contrast, no difference emerged for PR staining among menopausal groups. Overall, patients whose tumors were PR positive showed a significantly (P < .03) longer interval free of relapse. CONCLUSION: The present results suggest that PRs behave as better indicators than ERs of early relapse in breast cancer patients. Further studies, with longer follow-up, are needed, however, to validate this concept.     

Mammary skin oedema: a new prognostic indicator for breast cancer.

Mammary skin thickening shown on the mammogram was measured in 220 patients with non-inflammatory breast cancer, and the mean skin oedema was derived by taking the mean of five measurements from separate sites on the breast (upper part, lower part, medial part, lateral part, and areola) after subtracting the corresponding figures from the opposite (normal) breast. The prevalence of appreciable oedema (greater than 0.25 mm) was 70% for tumours less than 1 cm and 100% for tumours more than 3 cm in diameter. This measure of oedema correlated positively and significantly with tumour size and lymph node status. In a minimum of 60 months'' follow up patients developing recurrence had significantly higher oedema values. The amount of oedema also predicted recurrence better than lymph node status, tumour size, or tumour stage. Oedema and tumour size, information available preoperatively, provide a simple means of assessing prognosis before definitive treatment.     

SHCBP1:乳腺癌治疗候选靶点和潜在预后标志物

探讨SHCBP1在乳腺癌及其不同亚型中的表达特征和预后价值。利用Oncomine, bc-GenExMiner v4.2, Kaplan-Meier plotter, GSE41994及STRING数据库分析乳腺癌病人SHCBP1的mRNA表达水平及其与乳腺癌患者生存率的相关性等。结果:(1)乳腺癌组织中SHCBP1的mRNA水平明显高于正常组织样本,但不同分子亚型的乳腺癌患者中SHCBP1的表达水平不同;(2)SHCBP1表达升高可导致Luminal A亚型更短的无转移生存期(Distant metastasis-free survival,DMFS)和无病生存期(Disease-free survival, DFS);(3)在雌激素受体阳性(ER+)、孕酮受体阳性(PR+)亚型、仅接受辅助化疗、仅接受辅助化疗的ER(+)与接受包括或排除内分泌治疗乳腺癌患者中,SHCBP1表达升高则无复发生存率(Relapse-free survival,RFS)显著缩短;(4)SHCBP1和CDC45 mRNA表达水平之间呈正相关,并可能与KIF23等10种蛋白相互作用。结论:SHCBP1是一种很有前景的乳腺癌预后指标和潜在的治疗靶点。     

A new approach for heparin standardization: combination of scanning UV spectroscopy, nuclear magnetic resonance and principal component analysis

The year 2007 was marked by widespread adverse clinical responses to heparin use, leading to a global recall of potentially affected heparin batches in 2008. Several analytical methods have since been developed to detect impurities in heparin preparations; however, many are costly and dependent on instrumentation with only limited accessibility. A method based on a simple UV-scanning assay, combined with principal component analysis (PCA), was developed to detect impurities, such as glycosaminoglycans, other complex polysaccharides and aromatic compounds, in heparin preparations. Results were confirmed by NMR spectroscopy. This approach provides an additional, sensitive tool to determine heparin purity and safety, even when NMR spectroscopy failed, requiring only standard laboratory equipment and computing facilities.     

Clinical breast cancer, new developments in selection and endocrine treatment of patients.

Breast cancer is the most common malignant tumor among women, comprising an estimated 24% of all cancer cases and 18% of all cancer deaths. At least half of the patients with primary breast cancer will ultimately die by metastatic disease. The tumor characteristics, the natural course of the disease and the response to therapy vary strongly. A number of recently detected cell biological parameters such as oncogenes/suppressor genes, growth factors and secretory proteins are more or less important prognostic factors, because they influence the characteristics and behavior of a tumor with respect to metastatic pattern, extent of cellular differentiation, growth rate and response to treatment. However, there is no clear consensus how best to identify patients at high or low risk. In our experience c-myc amplification and pS2 protein are strong prognosticators for relapse rate, while in advanced disease (apart from a negative estrogen/progesterone receptor/pS2 status) amplification of HER2/neu is a good prognosticator for failure to endocrine therapy. In the diagnosis of breast cancer, in vivo imaging of tumors by labeled hormones or other factors also forms a new development which might have implications for treatment too. With respect to treatment both endocrine and chemotherapy can cure a minority of patients with micrometastases, but in patients with advanced disease only a prolongation of (progression-free) survival can be reached. Response rates decrease with increasing tumor load. In the past decade a number of interesting new endocrine agents has been developed such as new (pure) (anti)steroidal agents, vitamins, aromatase inhibitors, analogs of peptide hormones, prolactin inhibitors and growth factor antagonists. However, less is known on the (potential) interaction between hormones, chemotherapeutic agents, retinoids, cytokins, growth factor antagonists and irradiation. Rapid detection of new powerful combination therapies are needed to improve treatment results during the nineties.     

Complications after breast reconstruction with alloplastic material in breast cancer patients submitted or not to post mastectomy radiotherapy

Background and purposeBreast reconstruction following mastectomy is a relevant element of breast cancer treatment. The purpose of this study was to evaluate the influence of radiotherapy (RT) on local complications in patients with breast cancer that had undergone breast reconstruction with alloplastic material.Materials and methodsRetrospective study of breast cancer patients submitted to mastectomy and breast reconstruction from 2009 to 2013. Clinical and treatment variables were correlated with early and late complications.Results251 patients were included; mean age was 49.7 (25 to 78) years. Reconstruction was immediate in 94% of the patients, with 88% performed with a temporary tissue expander. Postoperative radiotherapy (RT) was delivered to 167 patients (66.5%). Early complications were present in 26.3% of the patients. Irradiated patients presented 5.4% incidence of late complications versus 2.4% for non-irradiated patients (p = 0.327). Diabetes (OR = 3.41 95% CI: 1.23–9.45, p = 0.018) and high body mass index (BMI) (OR = 2.65; 95% CI: 1.60–4.37, p < 0.0001) were the main risk factors. The overall incidence of late complications was 4.4%, with predominance of severe capsular contracture (8/11). Arterial hypertension (OR = 4.78; 95% CI: 1.97–11.63, p = 0.001), BMI (OR = 0.170; 95% CI: 0.048–0.607, p = 0.006) and implant placement (OR = 3.55; 95% CI: 1.26–9.99, p = 0.016) were related to late complications.ConclusionsThe overall rate of complications was low in this population. Radiotherapy delivery translated into a higher but not statistically significant risk of late complications when compared with the non-irradiated patients. Already well-known clinical risk factors for complications after breast reconstruction were identified.     

Paget's disease of the breast after subcutaneous mastectomy and reconstruction with a silicone prosthesis

Eight years after subcutaneous mastectomy for extensive fibrocystic disease, a patient developed Paget's disease of the breast associated with an underlying infiltrating duct cell adenocarcinoma. We emphasize the need for meticulous examination of the subcutaneous mastectomy specimen and long-term follow-up examination of the breasts in patients treated with subcutaneous mastectomy.     

Correlation between qualitatively distributed predicting variables and chemical terms in acridine derivatives using principal component analysis

When biological variables are not continuously distributed, the multiple and multivariate regression analysis cannot be used to correlate these variables against chemical regressors. As the employment of discriminant analysis requires the homogeneity of dispersion matrices and, that n_hp where n_h= degree of freedom of hypothesis, p =number of chemical terms, the reliability and validity of this method is highly questionable here. An alternative method is based on the principal component analysis where multicategory variables of drug responses can be classified into measures of inactive, slightly active, sufficiently active, and highly active drugs, for instance. The rules for classification are based on biological sources that can be expressed by chemical terms, too. An example adapted from antitumor action of acridine derivatives shows the working technique.     

Harmonicity and anharmonicity in protein dynamics: A normal mode analysis and principal component analysis

A comparison of a normal mode analysis and principal component analysis of a 200-ps molecular dynamics trajectory of bovine pancreatic trypsin inhibitor in vacuum has been made in order to further elucidate the harmonic and anharmonic aspects in the dynamics of proteins. An anharmonicity factor is defined which measures the degree of anharmonicity in the modes, be they principal modes or normal modes, and it is shown that the principal mode system naturally divides into anharmonic modes with peak frequencies below 80 cm^?1, and harmonic modes with frequencies above this value. In general the larger the mean-square fluctuation of a principal mode, the greater the degree of anharmonicity in its motion. The anharmonic modes represent only 12% of the total number of variables, but account for 98% of the total mean-square fluctuation. The transitional nature of the anharmonic motion is demonstrated. The results strongly suggest that in a large subspace, the free energy surface, as probed by the simulation, is approximated by a multi-dimensional parabola which is just a resealed version of the parabola corresponding to the harmonic approximation to the conformational energy surface at a single minimum. After 200 ps, the resealing factor, termed the “normal mode resealing factor,” has apparently converged to a value whereby the mean-square fluctuation within the subspace is about twice that predicted by the normal mode analysis. © 1995 Wiley-Liss, Inc.     

A new semiempirical codon substitution model based on principal component analysis of mammalian sequences

Codon substitution models have traditionally been parametric Markov models, but recently, empirical and semiempirical models also have been proposed. Parametric codon models are typically based on 61×61 rate matrices that are derived from a small number of parameters. These parameters are rooted in experience and theoretical considerations and generally show good performance but are still relatively arbitrary. We have previously used principal component analysis (PCA) on data obtained from mammalian sequence alignments to empirically identify the most relevant parameters for codon substitution models, thereby confirming some commonly used parameters but also suggesting new ones. Here, we present a new semiempirical codon substitution model that is directly based on those PCA results. The substitution rate matrix is constructed from linear combinations of the first few (the most important) principal components with the coefficients being free model parameters. Thus, the model is not only based on empirical rates but also uses the empirically determined most relevant parameters for a codon model to adjust to the particularities of individual data sets. In comparisons against established parametric and semiempirical models, the new model consistently achieves the highest likelihood values when applied to sequences of vertebrates, which include the taxonomic class where the model was trained on.     

The immunological status of breast cancer patients during treatment with a new antiestrogen,toremifene

Summary The immune status of breast cancer patients was followed during antiestrogen treatment for at least 1 year or until progression of the disease. Twelve postmenopausal women with advanced estrogen-receptor-positive breast cancer were treated with a novel antiestrogen, toremifene. Immune functions were determined before the start of the treatment and at 3, 6, and 12 months. For NK cell cytotoxicity testing there were 74 healthy controls and for T cell subset measurements 28 healthy controls. No statistically significant changes in the T cell subsets or NK cell cytotoxicity were observed during treatment. However, throughout toremifene treatment patients had fewer CD4 cells (T helper lymphocytes) than did the controls. Cancer patients had higher pretreatment B cell values than the controls,P = 0.01, but during the first months of toremifene treatment B cell values decreased and remained within the normal range thereafter. A positive effect on mitogen-stimulation tests with phytohemagglutinin (PHA) and concanavalin A (ConA) was observed during the first months of treatment (P = 0.01 for PHA and 0.03 for log [ConA] and a stabilization at the higher level thereafter. These results indicate that toremifene has a stimulatory effect on cell-mediated immunity in breast cancer patients.     

Nitroblue tetrazolium test in patients with breast cancer undergoing mastectomy and radiotherapy

The reduction of nitrotetrazolium blue with stimulated and unstimulated granulocytes was performed in 40 patients with breast cancer. Blood was collected from peripheral vein before surgical intervention, during surgery from vein draining of tumor, two weeks after surgery and three months after surgery when radiotherapy was finished. In parallel experiments the NBT test was made in the peripheral blood of 20 healthy individuals. We have observed decreased reduction of nitrotetrazolium blue in stimulated granulocytes, which may indicate that granulocytes from these patients are unable for efficient stimulation. No evident effect concerning the advancement of disease and applied therapy could be found. The importance of determining the NBT test in cancer patients is briefly discussed.     

Breast-conservation treatment for early invasive breast cancer: prognostic factors for survival after salvage treatment of local recurrence

The aim of the study was to investigate prognosis of patients who develop an isolated local recurrence (ILR) after conservative surgery (CS) for early-stage invasive breast cancer. Between 1983 and 1987, 415 patients with stage I-II breast cancer were treated with CS. Of these patients, 68 developed an ILR. The mean follow-up time after ILR was 167 months. Cox models taking potential prognostic factors into account were used to estimate the risk of death. On univariate analysis, age (< or =40 vs. >40 years) at first treatment, time to ILR (< or =24 vs. >24 months), type of recurrence (true vs. new primary tumor, NP), and extent of recurrence (operable vs. inoperable) were, but initial tumor stage (pT1 vs. pT2), initial lymph node stage (pN-negative vs. -positive), adjuvant radiotherapy (yes vs. no), type of salvage surgery (wide excision vs. mastectomy), and recurrent tumor grade (1-2 vs. 3) were not significant predictors of post-recurrence survival. On multivariate analysis only time to ILR proved independent predictor of survival (relative risk: 3.2; 95% confidence interval: 1.4-7.3; p = 0.0051), and the age of the patients showed borderline significance (p = 0.0659). The 15-year actuarial rate of cause-specific survival after ILR was 58% for all patients, 60% and 0% for patients with operable or inoperable recurrence, 30% and 71% for patients with age < or =40 or >40 years, 25% and 72% for patients with time to ILR < or =24 or >24 months, 54% and 88% for patients with true recurrence or NP, and 92% for patients with age >40 years with NP, respectively. The rate of second local recurrence after salvage mastectomy or repeated wide excision was 16% and 28%, respectively (p = 0.2265). As a conclusion, many patients with ILR have good prognosis, particularly those with operable recurrence with prolonged time to ILR, or with NP. Salvage mastectomy is not mandatory for all CS patients.