BCIRG 001 molecular analysis: Identification of prognostic factors in patients (pts) receiving adjuvant therapy for node- positive (N+) breast cancer (BC)

525

Background: BCIRG 001 (1,491 pts) demonstrated significant superiority of docetaxel/doxorubicin/cyclophosphamide (TAC) over fluorouracil/doxorubicin/cyclophosphamide (FAC) given as adjuvant therapy for N+ operable BC in terms of disease-free survival (DFS) and overall survival (OS) (Martin et al, N Eng J Med, 2005). This ancillary study was aimed to identify tumor-associated factors related to DFS and OS. Methods: Formalin-fixed primary tumors from pts in BCIRG 001 were analysed by immunohistochemistry. Protocol- specified assessment of histological grade (GR), tumor size (TS), estrogen (ER) and progesterone receptors (PR), lymph node status (LN), HER2, MUC1, Mib, p53, Bcl-2, Bax, Bcl-X, Bag-1, tubulin β isotypes II, III and IV, tau protein and detyrosinated a tubulin was performed. Parameters were scored as the percentage of positive cells and analysed as lower or greater than median values. The samples were randomly split into training (2/3) and validation (1/3) sets. Associations between selected parameters and DFS or OS were tested through univariate analyses using the Kaplan Meier method (log-rank test) on the training set. A backward stepwise Cox regression analysis was performed to identify the final model of prognostic factors on the training set. Multivariate analyses were applied to the validation set. Results: 1,350 samples were split into a training (n=906) and a validation (n=444) set. In univariate GR, TS, LN, ER and PR, Mib, tau protein and HER2 were correlated with DFS in both sets. In multivariate ER, PR, TS, LN, Mib (all p<0.01) and tau (p=0.043) were significantly associated with DFS in the training set. In univariate GR, TS, LN, ER and PR, Mib, MUC1, Bcl-2, tubulin III and IV and tau were correlated with OS in both sets, with a trend for p53. In multivariate ER, TS, LN, Mib, p53 (all p<0.01) and PR (p=0.028) were independently correlated with OS in the training set. Conclusions: These data suggest that tau and p53 are independent markers of DFS and OS, respectively, while Mib is correlated with both DFS and OS in pts receiving these forms of adjuvant chemotherapy for N+ BC. Complementary analyses will be presented.

No significant financial relationships to disclose.

The (in)dependence of alternative splicing and gene duplication

Alternative splicing (AS) and gene duplication (GD) both are processes that diversify the protein repertoire. Recent examples have shown that sequence changes introduced by AS may be comparable to those introduced by GD. In addition, the two processes are inversely correlated at the genomic scale: large gene families are depleted in splice variants and vice versa. All together, these data strongly suggest that both phenomena result in interchangeability between their effects. Here, we tested the extent to which this applies with respect to various protein characteristics. The amounts of AS and GD per gene are anticorrelated even when accounting for different gene functions or degrees of sequence divergence. In contrast, the two processes appear to be independent in their influence on variation in mRNA expression. Further, we conducted a detailed comparison of the effect of sequence changes in both alternative splice variants and gene duplicates on protein structure, in particular the size, location, and types of sequence substitutions and insertions/deletions. We find that, in general, alternative splicing affects protein sequence and structure in a more drastic way than gene duplication and subsequent divergence. Our results reveal an interesting paradox between the anticorrelation of AS and GD at the genomic level, and their impact at the protein level, which shows little or no equivalence in terms of effects on protein sequence, structure, and function. We discuss possible explanations that relate to the order of appearance of AS and GD in a gene family, and to the selection pressure imposed by the environment.

Determination of Charge and Molecular Weight of Rigid-Rod Polyelectrolytes

Rod-like polyelectrolytes are an interesting model system because their persistence length is independent of the ionic strength and pH of the surrounding medium and they permit the investigation of polyelectrolytes in the absence of conformational degrees of freedom. In this work, rigid-rod poly(aramide) polyelectrolytes were synthesized by the Higashi method. Electrophoresis NMR spectroscopy in conjunction with diffusion NMR spectroscopy has been applied to determine the effective charge of the polymer. The charge was determined from the balance between the force in the electric field and the hydrodynamic friction in the steady-state electrophoretic motion. Because only organic counterions were present, and were identified in the proton NMR spectra, the counterions were investigated as well, and the fraction of condensed counterions was determined directly. From the effective charge per molecule and the knowledge of the fraction of condensed counterions, the total charge per molecule was determined. Finally, from the total charge, the number of repeat units and thus the molecular weight were inferred.

[A rare case of secondary hypertension]

Die Patientin wurde mit einer therapieresistenten Hypertonie unter einer Trippeltherapie zugewiesen; auch ein Ausbau der medikamentösen Therapie zeigte keinen Erfolg. Laborchemisch zeigte sich ein primärer Hyperparathyreoidismus. Die weiteren Resultate der Diagnostik ergaben keine Hinweise auf eine andere Ursache der Hypertonie. In der Literatur sind Fälle mit therapieresistenter Hypertonie und primärem Hyperparathyreoidismus beschrieben. Die Patientin wurde total thyreoidektomiert, ein halbes Jahr später zeigt sich eine gut eingestellte Hypertonie unter einer Zweiertherapie, die Nervosität, Ängstlichkeit, Durstgefühle und die Muskelschmerzen waren nicht mehr vorhanden.

Prevalence of yeasts in beach sand at three bathing beaches in South Florida

The abundance and types of yeasts in the wet and dry sand of three recreational beaches in South Florida were determined. Samples were collected on 17 occasions between August 2001 and July 2002. After analyzing 102 sand samples, a total of 21 yeast species were identified by molecular methods. These isolates comprised four Basidiomycetes and 17 Ascomycetes and included eight species that had previously been reported from humans. The most frequently encountered yeasts were Candida tropicalis and Rhodotorula mucilaginosa. A greater diversity of species (16 species) was found in the dry sand above the high tide mark compared with the wet sand in the intertidal zone (11 species). Densities were also highest in the dry sand relative to wet sand (20-fold higher at Hobie beach, 6-fold higher at Fort Lauderdale Beach and 1.3-fold higher at Hollywood beach). There were no clear temporal patterns in the data and overall densities were greatest at the busiest bathing beach (Hobie Beach) where total yeasts averaged 37,720 cfu 100g(-1) dry sand and 1852 cfu 100 g(-1) in the wet sand. This concentration of yeast was significantly higher than populations at the less populated beaches. Fort Lauderdale beach had a mean count of 4130 cfu 100 g(-1) dry sand and 705 cfu 100g(-1) in the wet sand while the least populated beach, Hollywood Beach averaged 1945 cfu 100g(-1) dry sand and 1483 cfu 100g(-1) wet sand. While definitive statements cannot be made, high levels of yeasts may have a deleterious bearing on human health and the presence of such a diverse aggregation of species suggests that yeasts could have a role as indicators of beach health.

Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation

We report a method for large-scale absolute protein expression measurements (APEX) and apply it to estimate the relative contributions of transcriptional- and translational-level gene regulation in the yeast and Escherichia coli proteomes. APEX relies upon correcting each protein's mass spectrometry sampling depth (observed peptide count) by learned probabilities for identifying the peptides. APEX abundances agree with measurements from controls, western blotting, flow cytometry and two-dimensional gels, as well as known correlations with mRNA abundances and codon bias, providing absolute protein concentrations across approximately three to four orders of magnitude. Using APEX, we demonstrate that 73% of the variance in yeast protein abundance (47% in E. coli) is explained by mRNA abundance, with the number of proteins per mRNA log-normally distributed about approximately 5,600 ( approximately 540 in E. coli) protein molecules/mRNA. Therefore, levels of both eukaryotic and prokaryotic proteins are set per mRNA molecule and independently of overall protein concentration, with >70% of yeast gene expression regulation occurring through mRNA-directed mechanisms.

The SUPERFAMILY database in 2007: families and functions

The SUPERFAMILY database provides protein domain assignments, at the SCOP 'superfamily' level, for the predicted protein sequences in over 400 completed genomes. A superfamily groups together domains of different families which have a common evolutionary ancestor based on structural, functional and sequence data. SUPERFAMILY domain assignments are generated using an expert curated set of profile hidden Markov models. All models and structural assignments are available for browsing and download from http://supfam.org. The web interface includes services such as domain architectures and alignment details for all protein assignments, searchable domain combinations, domain occurrence network visualization, detection of over- or under-represented superfamilies for a given genome by comparison with other genomes, assignment of manually submitted sequences and keyword searches. In this update we describe the SUPERFAMILY database and outline two major developments: (i) incorporation of family level assignments and (ii) a superfamily-level functional annotation. The SUPERFAMILY database can be used for general protein evolution and superfamily-specific studies, genomic annotation, and structural genomics target suggestion and assessment.

[Dieulafoy's lesion of the right hemicolon]

Dieulafoy's lesion was described in 1896 by the French pathologist Georges D. Dieulafoy as a vascular malformation in the stomach. Although usually found in the stomach, the lesion may occur anywhere within the gastrointestinal tract and can cause severe hemorrhage. There is no sex or age predilection. The diagnosis is established endoscopically, and the current therapy of choice is endoscopic hemoclipping. Only rarely is the diagnosis confirmed histologically. We report the case of an elderly female patient who, while hospitalised for a slipped intervertebral disc, presented with lower gastrointestinal bleeding. The source of the bleeding was suspected to be in the right colon by endoscopy. Renewed massive bleeding necessitated surgical treatment with resection of the right hemicolon. The histological work-up of the resected specimen identified a 350-micron large tortuous submucosal artery that had eroded.

Second consensus on medical treatment of metastatic breast cancer

The present consensus manuscript defines evidence-based recommendations for state-of-the-art treatment of metastatic breast cancer depending on disease-associated and biologic variables.

Updated results of a multicenter phase II trial of neoadjuvant docetaxel, carboplatin and capecitabine for inflammatory and locally advanced breast cancer (LABC)

10685

Background: Neoadjuvant chemotherapy for the treatment of LABC has become the standard of care but the best combination is not established. The combination of docetaxel and capecitabine demonstrates synergism in patients(pts) with metastatic breast cancer (MBC). Recent studies support the value of platinum salts in LABC and MBC. Methods: pts with stage IIA-IIIC or inflammatory BC, EGOG PS 0–1, are eligible.We are evaluating the combination of weekly docetaxel 30mg/m2, carboplatin AUC2 on D1, 8,15 of a 4-week cycle plus capecitabine 625 mg/m2 BID given on days 5–18 (based on the upregulation of thymidine phosphorylase) for 4 cycles prior to surgery. The primary objective of this phase II trial is pCR rate in breast. Results: 39 of 48 pts have been enrolled from 7 centers. Median age 46 (range 26–75), stage II 41%, stage III 59%. Median baseline tumor is 5.4cm (range 2.1–15); 1pt inflammatory BC; 10 pts N2 disease (36%); 12 tumors were ER+, 20 ER-, and 5 Her-2+. To date, 2,377 doses (including daily capecitabine doses) were administered out of a total of 2,560 (93% of intended doses) with only 10 dose delays and 8 dose reductions. 37 pts are evaluable for toxicities. No grade IV toxicities were seen, grade III neutropenia was seen in 3/37(8%) and grade III fatigue in 1/37(3%). There were no episodes of neutropenic fever.The most common grade I/II toxicities were nausea in 57%, diarrhea 38%, fatigue 43%, epiphora 24%, mucositis 24% and hand-foot syndrome 3%. No death related treatments have been reported. 32 pts have completed definitive surgery. Objective clinical response is 94% with 53% cCR. 5 patients had pCRs in breast(16%) and 5 pCR in breast and axilla(16%). 9 pts (28%) have microscopic residual disease in the breast (<3mm). 14 pts had complete axillary clearance (44%). Conclusions: The preoperative combination of docetaxel, carboplatin and capecitabine is feasible with very good response rate and a very acceptable toxicity profile. Accrual is ongoing.

No significant financial relationships to disclose.

Protein family expansions and biological complexity

During the course of evolution, new proteins are produced very largely as the result of gene duplication, divergence and, in many cases, combination. This means that proteins or protein domains belong to families or, in cases where their relationships can only be recognised on the basis of structure, superfamilies whose members descended from a common ancestor. The size of superfamilies can vary greatly. Also, during the course of evolution organisms of increasing complexity have arisen. In this paper we determine the identity of those superfamilies whose relative sizes in different organisms are highly correlated to the complexity of the organisms. As a measure of the complexity of 38 uni- and multicellular eukaryotes we took the number of different cell types of which they are composed. Of 1,219 superfamilies, there are 194 whose sizes in the 38 organisms are strongly correlated with the number of cell types in the organisms. We give outline descriptions of these superfamilies. Half are involved in extracellular processes or regulation and smaller proportions in other types of activity. Half of all superfamilies have no significant correlation with complexity. We also determined whether the expansions of large superfamilies correlate with each other. We found three large clusters of correlated expansions: one involves expansions in both vertebrates and plants, one just in vertebrates, and one just in plants. Our work identifies important protein families and provides one explanation of the discrepancy between the total number of genes and the apparent physiological complexity of eukaryotic organisms.

One of the main goals in biology is to understand how complex organisms have evolved. Much of an organism's physiology, and hence complexity, is determined by its protein repertoire. The repertoire has been largely formed by the duplication, divergence, and combination of genes. This means that proteins can be grouped into families whose members are descended from a common ancestor. The authors have examined the sizes of 1,219 protein families in 38 eukaryotes of different complexity. Only a small fraction of protein families have expansions that are correlated with the number of cell types in the organisms. Half of these families are involved in regulation or extracellular processes. Other families do have expansions but in a lineage-specific manner. Thus, certain protein family expansions are “progressive” in that they lead to increases in biological complexity; other expansions are “conservative” in that they help an organism to adapt better to its environment, but do not increase its complexity. This means that there is no simple correlation between an organism's complexity and the number of its genes.

Double-hadron leptoproduction in the nuclear medium

The first measurements of double-hadron production in deep-inelastic scattering within the nuclear medium were made with the HERMES spectrometer at DESY HERA using a 27.6 GeV positron beam. By comparing data for deuterium, nitrogen, krypton, and xenon nuclei, the influence of the nuclear medium on the ratio of double-hadron to single-hadron yields was investigated. Nuclear effects on the additional hadron are clearly observed, but with little or no difference among nitrogen, krypton, or xenon, and with smaller magnitude than effects seen on previously measured single-hadron multiplicities. The data are compared with models based on partonic energy loss or prehadronic scattering and with a model based on a purely absorptive treatment of the final-state interactions. Thus, the double-hadron ratio provides an additional tool for studying modifications of hadronization in nuclear matter.

Pyloric gland adenoma-- how to diagnose?

The term "pyloric gland adenoma" reflects its etiogenesis from deep mucoid glands in the stomach. The diagnosis can be confirmed by immunohistochemistry. Typically, pyloric gland adenomas are strongly positive for Mucin 6 (deep mucoid gastric glands). These lesions express Mucin 6 over the whole lesion up to the surface often only with a small layer of columnar epithelium expressing Apomucin 5AC. The amount of mucin 5AC which is expressed on normal within the apical foveolar epithelium might vary from case to case. Combination or transdifferentiation with ordinary tubular (intestinal differentiation) adenoma can be observed. The gastric corpus mucosa of elderly female patients with autoimmune gastritis is highly affected. The frequency of pyloric gland adenoma is given in the literature being 2.7% of all gastric polyps. Therefore pyloric gland adenomas are not that rare that one might assume. Only a few publications are available which makes one think that these lesions are frequently misinterpreted. Pyloric gland adenomas can arise in gastric heterotopia and gastric metaplasia in the whole gastrointestinal tract. The clinical significance is given by a 30% rate of malignant transformation. These cases represent for the most well differentiated early adenocarcinomas which are known to have an excellent prognosis after complete polypectomy and limitation to the mucosal layer.

Duplication, divergence and formation of novel protein topologies

The rearrangement or permutation of protein substructures is an important mode of divergence. Recent work explored one possible underlying mechanism called permutation-by-duplication, which produces special forms of motif rearrangements called circular permutations. Permutation-by-duplication, involving gene duplication, fusion and truncation, can produce fully functional intermediate proteins and thus represents a feasible mechanism of protein evolution. In spite of this, circular permutations are relatively rare and we discuss possible reasons for their existence.

Measurement of the tensor structure function b1 of the deuteron

The Hermes experiment has investigated the tensor spin structure of the deuteron using the 27.6 GeV/c positron beam of DESY HERA. The use of a tensor-polarized deuteron gas target with only a negligible residual vector polarization enabled the first measurement of the tensor asymmetry A(d)zz and the tensor structure function b(d)1 for average values of the Bjorken variable 0.01< <x> <0.45 and of the negative of the squared four-momentum transfer 0.5 GeV2 < <Q2> <5 GeV2. The quantities A(d)zz and b(d)1 are found to be nonzero. The rise of b(d)1 for decreasing values of x can be interpreted to originate from the same mechanism that leads to nuclear shadowing in unpolarized scattering.

The effects of joint misclassification of exposure and disease on the attributable risk

While there is extensive methodological literature analysing the effects of misclassification on the relative risk under various misclassification scenarios, for the attributable risk only the effects of non-differential misclassification either of exposure or disease, and the effects of non-differential independent misclassification of exposure and disease have been discussed for the 2 x 2-situation. The paper investigates the effects of non-differential correlated misclassification of exposure and disease on the attributable risk taking possible correlations of both types of misclassification into account. Furthermore, a comparison with the corresponding effects on the relative risk is drawn. We propose a matrix-based approach to describe the underlying structure of non-differential misclassification. The bias arising from non-differential misclassification in the attributable risk and relative risk is evaluated in four examples assuming under- or overreporting of exposure and disease. In each of the four examples we found scenarios where pronounced differences in degree and, more importantly, in direction of bias occurred. Our results clearly demonstrate the danger lying in the stereotype transfer of findings regarding misclassification effects on the relative risk to other epidemiologic risk measures and underline the necessity of specific analyses of the effects of misclassification on the attributable risk.

Value of morphological parameters for grading of brain swelling

This study investigated the value of both gross features and histological findings for grading of brain swelling. For this purpose, the grooving of the temporal gyri (unci) as well as the extension of the cones at the basal part of the cerebellum were measured in 42 brains obtained at autopsy. Furthermore, the distension of perivascular spaces in tissue samples from seven different regions of the brains was evaluated histologically, assisted by an automatic image processing and analysis system. In each individual, the normal range of brain weight was calculated on the basis of the body height, using the formulae by Röthig and Schaarschmidt. The difference between this calculated (normal) value and the brain weight evaluated at autopsy was considered as a reliable criterion for the grade of brain swelling. There was no statistical evidence of a positive correlation between the various parameters. Hence, it can be concluded that both gross section and histological findings are of minimal significance for grading of brain swelling.

Single-spin asymmetries in semi-inclusive deep-inelastic scattering on a transversely polarized hydrogen target

Single-spin asymmetries for semi-inclusive electroproduction of charged pions in deep-inelastic scattering of positrons are measured for the first time with transverse target polarization. The asymmetry depends on the azimuthal angles of both the pion (phi) and the target spin axis (phi(S)) about the virtual-photon direction and relative to the lepton scattering plane. The extracted Fourier component sin((phi+phi(S))(pi)(UT) is a signal of the previously unmeasured quark transversity distribution, in conjunction with the Collins fragmentation function, also unknown. The component sin((phi-phi(S)(pi)(UT) arises from a correlation between the transverse polarization of the target nucleon and the intrinsic transverse momentum of quarks, as represented by the previously unmeasured Sivers distribution function. Evidence for both signals is observed, but the Sivers asymmetry may be affected by exclusive vector meson production.

The relationship between domain duplication and recombination

Protein domains represent the basic evolutionary units that form proteins. Domain duplication and shuffling by recombination are probably the most important forces driving protein evolution and hence the complexity of the proteome. While the duplication of whole genes as well as domain-encoding exons increases the abundance of domains in the proteome, domain shuffling increases versatility, i.e. the number of distinct contexts in which a domain can occur. Here, we describe a comprehensive, genome-wide analysis of the relationship between these two processes. We observe a strong and robust correlation between domain versatility and abundance: domains that occur more often also have many different combination partners. This supports the view that domain recombination occurs in a random way. However, we do not observe all the different combinations that are expected from a simple random recombination scenario, and this is due to frequent duplication of specific domain combinations. When we simulate the evolution of the protein repertoire considering stochastic recombination of domains followed by extensive duplication of the combinations, we approximate the observed data well. Our analyses are consistent with a stochastic process that governs domain recombination and thus protein divergence with respect to domains within a polypeptide chain. At the same time, they support a scenario in which domain combinations are formed only once during the evolution of the protein repertoire, and are then duplicated to various extents. The extent of duplication of different combinations varies widely and, in nature, will depend on selection for the domain combination based on its function. Some of the pair-wise domain combinations that are highly duplicated also recur frequently with other partner domains, and thus represent evolutionary units larger than single protein domains, which we term "supra-domains".

Glucosinolate biosynthesis: demonstration and characterization of the condensing enzyme of the chain elongation cycle in Eruca sativa

Glucosinolates are a group of sulfur-rich thioglucoside natural products common in the Brassicaceae and related plant families. The first phase in the formation of many glucosinolates involves the chain extension of the amino acid methionine. Additional methylene groups are inserted into the side chain of methionine by a three-step elongation cycle involving 2-oxo acid intermediates. This investigation demonstrated the first step of this chain elongation cycle in a partially-purified preparation from arugula (Eruca sativa). The 2-oxo acid derived from methionine, 4-methylthio-2-oxobutanoic acid, was shown to condense with acetyl-CoA to form 2-(2'-methylthioethyl)malate. The catalyst, designated as a 2-(omega-methylthioalkyl)malate synthase, belongs to a family of enzymes that mediate the condensation of acyl-CoAs with 2-oxo acids, including citrate synthase of the citric acid cycle, and 2-isopropylmalate synthase of leucine biosynthesis. The 2-(omega-methylthioalkyl)malate synthase studied here shares properties with other enzymes of this class, but appears chromatographically distinct and is found only in extracts of plant species producing glucosinolates from chain-elongated methionine derivatives. Although the principal glucosinolates of arugula are formed from methionine that has undergone two rounds of chain elongation to form dihomomethionine, studies with substrates and substrate analogs of different chain lengths showed that the isolated enzyme is responsible only for the condensation step of the first round of elongation.

Structure, function and evolution of multidomain proteins

Proteins are composed of evolutionary units called domains; the majority of proteins consist of at least two domains. These domains and nature of their interactions determine the function of the protein. The roles that combinations of domains play in the formation of the protein repertoire have been found by analysis of domain assignments to genome sequences. Additional findings on the geometry of domains have been gained from examination of three-dimensional protein structures. Future work will require a domain-centric functional classification scheme and efforts to determine structures of domain combinations.