Predicting the HER2 status of breast cancer from basic histopathology data: an analysis of 1500 breast cancers as part of the HER2000 International Study

The tests that are currently available for the measurement of overexpression of the human epidermal growth factor-2 (HER2) in breast cancer have shown considerable problems in accuracy and interlaboratory reproducibility. Although these problems are partly alleviated by the use of validated, standardised 'kits', there may be considerable cost involved in their use. Prior to testing it may therefore be an advantage to be able to predict from basic pathology data whether a cancer is likely to overexpress HER2. In this study, we have correlated pathology features of cancers with the frequency of HER2 overexpression assessed by immunohistochemistry (IHC) using HercepTest (Dako). In addition, fluorescence in situ hybridisation (FISH) has been used to re-test the equivocal cancers and interobserver variation in assessing HER2 overexpression has been examined by a slide circulation scheme. Of the 1536 cancers, 1144 (74.5%) did not overexpress HER2. Unequivocal overexpression (3+ by IHC) was seen in 186 cancers (12%) and an equivocal result (2+ by IHC) was seen in 206 cancers (13%). Of the 156 IHC 3+ cancers for which complete data was available, 149 (95.5%) were ductal NST and 152 (97%) were histological grade 2 or 3. Only 1 of 124 infiltrating lobular carcinomas (0.8%) showed HER2 overexpression. None of the 49 'special types' of carcinoma showed HER2 overexpression. Re-testing by FISH of a proportion of the IHC 2+ cancers showed that only 25 (23%) of those assessable exhibited HER2 gene amplification, but 46 of the 47 IHC 3+ cancers (98%) were confirmed as showing gene amplification. Circulating slides for the assessment of HER2 score showed a moderate level of agreement between pathologists (kappa 0.4). As a result of this study we would advocate consideration of a triage approach to HER-2 testing. Infiltrating lobular and special types of carcinoma may not need to be routinely tested at presentation nor may grade 1 NST carcinomas in which only 1.4% have been shown to overexpress HER2. Testing of these carcinomas may be performed when HER2 status is required to assist in therapeutic or other clinical/prognostic decision-making. The highest yield of HER2 overexpressing carcinomas is seen in the grade 3 NST subgroup in which 24% are positive by IHC. (C) 2003 Elsevier Science Ltd. All rights reserved.

Model-based clustering in gene expression microarrays: An application to breast cancer data

In microarray studies, the application of clustering techniques is often used to derive meaningful insights into the data. In the past, hierarchical methods have been the primary clustering tool employed to perform this task. The hierarchical algorithms have been mainly applied heuristically to these cluster analysis problems. Further, a major limitation of these methods is their inability to determine the number of clusters. Thus there is a need for a model-based approach to these. clustering problems. To this end, McLachlan et al. [7] developed a mixture model-based algorithm (EMMIX-GENE) for the clustering of tissue samples. To further investigate the EMMIX-GENE procedure as a model-based -approach, we present a case study involving the application of EMMIX-GENE to the breast cancer data as studied recently in van 't Veer et al. [10]. Our analysis considers the problem of clustering the tissue samples on the basis of the genes which is a non-standard problem because the number of genes greatly exceed the number of tissue samples. We demonstrate how EMMIX-GENE can be useful in reducing the initial set of genes down to a more computationally manageable size. The results from this analysis also emphasise the difficulty associated with the task of separating two tissue groups on the basis of a particular subset of genes. These results also shed light on why supervised methods have such a high misallocation error rate for the breast cancer data.

Nerve growth factor overexpression and autocrine loop in breast cancer cells

We show here that nerve growth factor (NGF), the canonical neurotrophic factor, is synthesized and released by breast cancer cells. High levels of NGF transcript and protein were detected in breast cancer cells by reverse transcription-PCR, Western blotting, ELISA assay and immunohistochemistry. Conversely, NGF production could not be detected in normal breast epithelial cells at either the transcriptional or protein level. Confocal analysis indicated the presence of NGF within classical secretion vesicles. Breast cancer cell-produced NGF was biologically active, as demonstrated by its ability to induce the neuronal differentiation of embryonic neural precursor cells. Importantly, the constitutive growth of breast cancer cells was strongly inhibited by either NGF-neutralizing antibodies or K-252a, a pharmacological inhibitor of NGF receptor TrkA, indicating the existence of an NGF autocrine loop. Together, our data demonstrate the physiological relevance of NGF in breast cancer and its potential interest as a marker and therapeutic target.

Genetic variation in foliar carbon isotope composition in relation to tree growth and foliar nitrogen concentration in clones of the F-1 hybrid between slash pine and Caribbean pine

The objectives of this study were: (1) to quantify the genetic variation in foliar carbon isotope composition (delta(13)C) of 122 clones of ca. 4-year-old F-1 hybrids between slash pine (Pinus elliottii Engelm var. elliottii) and Caribbean pine (Pinus caribaea var. hondurensis Barr.,et Golf.) grown at two field experimental sites with different water and nitrogen availability in southeast Queensland, Australia, in relation to tree growth and foliar nitrogen concentration (N-mass); and (2) to assess the potential of using delta(13)C measurements, in the foliage materials collected from the clone hedges at nursery and the 4-year-old tree canopies in the field, as an indirect index of tree water use efficiency for selecting elite F-1 hybrid pine clones with improved tree growth. There were significant differences in foliar delta(13)C between the nursery hedges and the 4-year-old tree canopies in the field, between the summer and winter seasons, between the two experimental sites, and between the upper outer and lower outer canopy positions sampled. This indicates that delta(13)C measurements in the foliage materials are significantly influenced by the sampling techniques and environmental conditions. Significant differences in foliar delta(13)C, at the upper outer canopy in both field experiments in summer and winter, were detected between the clones, and between the female parents of the clones. Clone means of tree height at age ca. 3 years were positively related to those of the upper outer canopy delta(13)C at both experimental sites in winter, but only for the wetter site in summer. There were positive, linear relationships between clone means of canopy delta(13)C and those of canopy N-mass, indicating that canopy photosynthetic capacity might be an important factor regulating the clonal variation in canopy delta(13)C. Significant correlations were found between clone means of canopy delta(13)C at both experimental sites in summer and winter, and between those at the upper outer and lower outer canopy positions. Mean clone delta(13)C for the nursery hedges was only positively related to mean clone stem diameter at 1.3 m height at age 3 years on the wetter site. The clone by site interaction for foliar delta(13)C at the upper outer canopy was significant only in summer. Overall, the relatively high genetic variance components for foliar delta(13)C and significant, positive correlations between clone means of foliar delta(13)C and tree growth have highlighted the potential of using foliar delta(13)C measurements for assisting in selection of the elite F-1 hybrid pine clones with improved tree growth. (C) 2002 Elsevier Science B.V. All rights reserved.

Part 2. Carcass composition and fatty acid profiles of adipose tissue of male goats: effects of genotype and liveweight at slaughter

The dissected carcass composition and fatty acid profiles of intermuscular fat from 110 male goat kids from six genotypes i.e. Boer x Angora (BA), Boer x Feral (BF), Boer x Saanen (BS), Feral x Feral (1717), Saanen x Angora (SA) and Saanen x Feral (SF) and two slaughter weight groups i.e. Capretto and Chevon (liveweight at slaughter 14-22 and 30-35 kg, respectively) were compared. Carcass tissue distribution for various genotypes was: muscle (63-66%), fat (10-13%) and bone (21-24%). Genotype significantly (P < 0.05) influenced the carcass composition; BA and FF carcasses had significantly higher muscle to bone ratio, while carcasses from BS kids were leaner compared to other genotypes. However, the two slaughter weight groups did not differ significantly (P > 0.05) in terms of carcass composition, when compared at the same carcass weight. In the present study, significant (P < 0.01) correlations were observed between percentage of muscle, fat and bone in most of the primal cuts and that in the carcass side. The main saturated fatty acids (SFAs) identified were palmitic (16:0) and stearic acid (18:0), while oleic acid (18: 1, omega9) was the main unsaturated fatty acid (UFA) in the intermuscular fat from goat kids. There were significant (P < 0.05) differences between genotypes in the proportions of individual fatty acids. Adipose tissue from BS kids had significantly higher UFAs (mainly oleic acid) and thus had a significantly lower melting point compared to other genotypes. There were significantly higher proportions of palmitic acid (35%) in the adipose tissue from Capretto kids compared to that from Chevon kids (22%). The concentration of UFAs increased in the adipose tissue from Capretto to Chevon carcasses. (C) 2003 Elsevier Science B.V. All rights reserved.

Suppressor of cytokine signalling gene expression is elevated in breast carcinoma

Cytokines are important for breast cell function, both as trophic hormones and as mediators of host defense mechanisms against breast cancer. Recently, inducible feedback suppressors of cytokine signalling (SOCS/JAB/SSI) have been identified, which decrease cell sensitivity to cytokines. We examined the expression of SOCS genes in 17 breast carcinomas and 10 breast cancer lines, in comparison with normal tissue and breast lines. We report elevated expression of SOCS-1-3 and CIS immunoreactive proteins within in situ ductal carcinomas and infiltrating ductal carcinomas relative to normal breast tissue. Significantly increased expression of SOCS-1-3 and CIS transcripts was also shown by quantitative in situ hybridisation within both tumour tissue and reactive stroma. CIS transcript expression was elevated in all 10 cancer lines, but not in control lines. However, there was no consistent elevation of other SOCS transcripts. CIS protein was shown by immunoblot to be present in all cancer lines at increased levels, mainly as the 47 kDa ubiquitinylated form. A potential proliferative role for CIS overexpression is supported by reports that CIS activates ERK kinases, and by strong induction in transient reporter assays with an ERK-responsive promoter. The in vivo elevation of SOCS gene expression may be part of the host/tumour response or a response to autocrine/paracrine GH and prolactin. However, increased CIS expression in breast cancer lines appears to be a specific lesion, and could simultaneously shut down STAT 5 signalling by trophic hormones, confer resistance to host cytokines and increase proliferation through ERK kinases.

Dietary interactions influence the effects of bovine folate-binding protein on the bioavailability of tetrahydrofolates in rats

The newborns of mammals have a high folate demand, yet obtain adequate folate nutrition solely from their mothers' milk despite its low folate content. Milk folate is entirely bound by an excess of folate-binding protein (FBP), prompting speculation that FBP may affect the bioavailability of the limited folate supply. Previous research has shown that FBP-bound folic acid is more gradually absorbed, thereby reducing the peak plasma folate concentration and preventing loss into the urine. Natural folates are reduced derivatives of folic acid, with milk predominantly containing 5-methyltetrahydrofolate, yet little research has been carried out to determine the role of FBP in the bioavailability of reduced folates. We studied the effect of FBP on folate nutrition of rats in both single-dose and 4-wk feeding experiments. The effect of FBP was influenced by the presence of other milk components. FBP increased bioavailability of dietary folate when it was consumed with other whey proteins or with soluble casein. However, in the presence of acid-precipitated casein or a whey preparation enriched in lipids, bioavailability was decreased. These results highlight the difficulties of extrapolating from experimental results obtained using purified diets alone and of studying interactions among dietary components. They suggest that the addition of FBP-rich foods to folate-rich foods could enhance the bioavailability of natural folates, but that the outcome of such a combination would depend on interactions with other components of the diet.

Heat-induced changes in UHT milks - Part 1

Raw milk was stored for 0, 2 and 4 days and processed in a UHT pilot plant by either direct or indirect heating. The unstored raw milk was also pasteurised. The thermally induced changes resulting from these treatments were investigated by examining a number of indices of heat damage. Lactulose, furosine, total and free hydroxymethylfurfural (HMF) and acid-soluble beta-lactoglobulin were analysed by high performance liquid chromatography (HPLC) while soluble tryptophan was examined by fluorescence spectroscopy. The directly heated UHT milk showed less heat damage than the indirectly heated milk, while the pasteurised milk displayed the least heat damage. During storage of the UHT milk for 12 weeks at similar to20degreesC, the levels of lactulose remained constant, while the furosine concentration increased. Both the total HMF and undenatured beta-lactoglobulin contents showed a general decrease during storage; however free HMF values initially rose but then decreased after four weeks' storage. As the age of the milk at the time of UHT processing increased, the levels of some of the indicators decreased. It is concluded that lactulose is the most reliable index of heat treatment, as it is virtually unaffected by refrigerated storage of the milk before or ambient storage after UHT processing. Reliance on other indicators may give misleading information on the heat load that UHT milk has received during processing.

Diagnosing the cause of proteolysis in UHT milk

Proteolysis of UHT milk during storage at room temperature is a major factor limiting its shelf-life through changes in its flavour and texture. The latter is characterised by increases in viscosity leading in some cases to gel formation. The enzymes responsible for the proteolysis are the native milk alkaline proteinase, plasmin, and heat-stable, extracellular bacterial proteinases produced by psychrotrophic bacterial contaminants in the milk prior to heat processing. These proteinases react differently with the milk proteins and produce different peptides in the UHT milk. In order to differentiate these peptide products, reversed-phase HPLC and the fluorescamine method were used to analyse the peptides soluble in 12% trichloroacetic acid (TCA) and those soluble at pH 4.6. The TCA filtrate showed substantial peptide peaks only if the milk was contaminated by bacterial proteinase, while the pH 4.6 filtrate showed peptide peaks when either or both bacterial and native milk proteinases caused the proteolysis. Results from the fluorescamine test were in accordance with the HPLC results whereby the TCA filtrate exhibited significant proteolysis values only when bacterial proteinases were present, but the pH 4.6 filtrates showed significant values when the milk contained either or both types of proteinase. A procedure based on these analyses is proposed as a diagnostic test for determining which type of proteinase-milk plasmin, bacterial proteinase, or both-is responsible for proteolysis in UHT milk. (C) 2003 Swiss Society of Food Science and Technology. Published by Elsevier Science Ltd. All rights reserved.

Yogurt from UHT milk: a review

Continuous heat treatment by UHT processing has attracted interest as an alternative to the batch-heating method conventionally used in the production of yogurt. Several studies have been conducted on the manufacture of yogurt from milk heated by UHT processes and have compared it with the conventional method. This paper reviews the characteristics of yogurt made from UHT milk, including its apparent viscosity, gel strength, microstructure, syneresis (water-holding capacity) and flavour, as well as the behaviour of yogurt cultures in the UHT-treated pre-mix.

Production of proteinases by psychrotrophic bacteria in raw milk stored at low temperature

Raw milk samples from two different sources were stored at 2degreesC, 4degreesC and 7degreesC for 10 days and the growth of psychrotrophic bacteria, production of proteinase and proteolysis in the milks were measured during storage. Peptide analyses by the fluorescamine method and RP-HPLC were used in determination of proteolysis and proteinase activity. The average times taken for the psychrotroph counts to reach 10(7) cfu/mL at 2degreesC, 4degreesC and 7degreesC were approximately 9, 7 and 4 days, although there was considerable variation in growth rates in the different milks. There was little correlation between psychrotroph counts and either proteolysis or proteinase activity levels. At 2degreesC, no milk stored showed significant proteolysis by the fluorescamine method after 10 days' storage, but significant proteinase activity could be measured in some of these milks at 8 and 10 days. RP-HPLC analysis was a more sensitive means of detecting peptides than the fluorescamine method.

Dietary influences on survival after ovarian cancer

We evaluated the effects of various food groups and micronutrients in the diet on survival among women who originally participated in a population-based case-control study of ovarian cancer conducted across 3 Australian states between 1990 and 1993. This analysis included 609 women with invasive epithelial ovarian cancer, primarily because there was negligible mortality in women with borderline tumors. The women's usual diet was assessed using a validated food frequency questionnaire. Deaths in the cohort were identified using state-based cancer registries and the Australian National Death Index (NDI). Crude 5-year survival probabilities were estimated using the Kaplan-Meier technique, and adjusted hazard ratios (HRs) and 95% confidence intervals (CIs) were obtained from Cox regression models. After adjusting for important confounding factors, a survival advantage was observed for those who reported higher intake of vegetables in general (HR = 0.75, 95% CI = 0.57-0.99, p-value trend 0.01 for the highest third, compared to the lowest third), and cruciferous vegetables in particular (HR = 0.75, 95% CI = 0.57-0.98, p-value trend 0.03), and among women in the upper third of intake of vitamin E (HR = 0.76, 95% CI = 0.58-1.01, p-value trend 0.04). Inverse associations were also seen with protein (p-value trend 0.09), red meat (p-value trend 0.06) and white meat (p-value trend 0.07), and modest positive trends (maximum 30% excess) with lactose (p-value trend 0.04), calcium and dairy products. Although much remains to be learned about the influence of nutritional factors after a diagnosis of ovarian cancer, our study suggests the possibility that a diet high in vegetable intake may help improve survival. (C) 2003 Wiley-Liss, Inc.

A low concentration of ouabain (0.18 µg/kg) enhances hypertension in spontaneously hypertensive rats by inhibiting the Na+ pump and activating the renin-angiotensin system

We investigated the effects of low ouabain concentrations on systolic (SAP) and diastolic (DAP) arterial pressures and on pressor reactivity in 3-month-old male spontaneously hypertensive rats (SHR). Arterial blood pressure (BP) and pressor reactivity to phenylephrine (PHE) were investigated before and after 0.18 μg/kg ouabain administration (N = 6). The influence of hexamethonium (N = 6), canrenone (N = 6), enalapril (N = 6), and losartan (N = 6) on ouabain actions was evaluated. Ouabain increased BP (SAP: 137 ± 5.1 to 150 ± 4.7; DAP: 93.7 ± 7.7 to 116 ± 3.5 mmHg; P < 0.05) but did not change PHE pressor reactivity. Hexamethonium reduced basal BP in control but not in ouabain-treated rats. However, hexamethonium + ouabain increased DAP sensitivity to PHE. Canrenone did not affect basal BP but blocked ouabain effects on SAP. However, after canrenone + ouabain administration, DAP pressor reactivity to PHE still increased. Enalapril and losartan reduced BP and abolished SAP and DAP responses to ouabain. Enalapril + ouabain reduced DAP reactivity to PHE, while losartan + ouabain reduced SAP and DAP reactivity to PHE. In conclusion, a small dose of ouabain administered to SHR increased BP without altering PHE pressor reactivity. Although the renin-angiotensin system (RAS), Na+ pump and autonomic reflexes are involved in the effects of ouabain on PHE reactivity, central mechanisms might blunt the actions of ouabain on PHE pressor reactivity. The effect of ouabain on SAP seems to depend on the inhibition of both Na+ pump and RAS, whereas the effect on DAP seems to depend only on RAS.