Pharmacogenomic analysis of needle biopsies obtained before preoperative docetaxel/capecitabine/FEC (TX/FEC) chemotherapy for breast cancer

10595

Background: Our goal was to evaluate the feasibility of obtaining fine needle biopsies, for pharmacogenomic analysis, in community based oncology practices and develop gene expression-based predictors of pathologic complete response (pCR) to preoperative sequential docetaxel/capecitabine and 5-fluorouracil, epirubicin, cyclophosphamide chemotherapy. Methods: One hundred seventy-five patients were accrued at 29 sites in the US Oncology Research network. FNA specimens were mailed to a central laboratory (MDACC) and gene expression profiling was performed on Affymetrix U133A chips. Results: RNA extraction was started on 140 specimens, 112 of these (80%) yielded ≥1 μg total RNA, 69 were hybridized and 65 (94%) gene expression profiles have passed quality control as of abstract submission date. The analysis plan is to develop a multigene predictor of pCR from the first 80 cases and test its performance independently in the remaining cases. Conclusions: Collection of mandatory research FNA biopsies for pharmacogenomic research is feasible in community practice. Approximately 80% of biopsies yield sufficient RNA for gene expression profiling. In 20% of patients, either technical factors, which can be addressed, or tumor biology (necrotic, rapidly growing tumors) were limiting. Supported by Roche Laboratories, Inc., Nutley, NJ; Pfizer, New York, NY; and Precision Therapeutics, Pittsburgh, PA.

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Pharmacogenomic analysis of HER2 amplified breast cancer treated with preoperative trastuzumab and paclitaxel, 5-fluorouracil, epirubicin, cyclophosphamide (T/FEC) chemotherapy

545

Background: We performed gene expression analysis to identify molecular predictors of resistance to preoperative concomitant trastuzumab and T/FEC chemotherapy. Methods: Pretreatment fine needle aspirations from 21 patients with HER2 amplified, stages II-III breast cancer were available for transcriptional profiling with Affymetrix U133 A chips. Results: Overall pathologic complete response (pCR) rate was 71%. Age, nuclear grade, tumor size, nodal status or quantitative estrogen and HER2 receptor mRNA expression showed no association with response in univariate and multivariate logistic regression. We tested the accuracy of a 30-gene pCR predictor that was previously developed from patients who received T/FEC only preoperative chemotherapy. This predictor was accurate in validation in T/FEC treated patients (n=51) but showed low sensitivity in patients who also received trastuzumab (sensitivity 53% versus 92%). We could not identify any differentially expressed genes between pCR (n=15) and residual disease (RD, n=6) at a false discovery rate (FDR) <90% in the HER2 amplified trastuzumab-treated cases. Hierarchical clustering using the “Perou intrinsic gene set” also failed to separate pCR from RD. Gene Set Enrichment Analysis with 22 genes from trastuzumab-resistant cell lines showed a modest association with RD (FDR=9%). Conclusions: Clinical variables and pharmacogenomic predictors that predict pCR in the absence of trastuzumab are no longer accurate when trastuzumab is included in the treatment. Trastuzumab-resistance associated genes identified in vitro are also associated with resistance in vivo. Support: Ellence Foundation.

No significant financial relationships to disclose.

Role of lateral alkyl chains in modulation of molecular structures on metal surfaces

We use low energy electron diffraction, scanning tunneling microscopy, first-principles density-functional theory, and molecular mechanics calculations to analyze the adsorption and growth of quinacridone derivatives (QA) with alkyl chains of 4 and 16 carbon atoms on a Ag(110) substrate. Surprisingly, we find that the alkyl chains determine the orientation of the molecular overlayers. While the interaction of QA and the Ag substrate is primarily due to chemical bonding of oxygen to the silver substrate, determining the molecular orientation and preferred adsorption site, the intermolecular arrangement can be adjusted via the length of alkyl chains. We are thus able to fabricate uniform QA films with very well controlled physical properties.

RAPD analysis of genetic diversity and population genetic structure of Stipa krylovii Reshov. in Inner Mongolia steppe

Random amplified polymorphic DNA (RAPD) analysis was used to characterize the genetic diversity and population genetic structure of Stipa krylovii populations in Inner Mongolia steppe of North China. Thirteen 10 bp oligonucleotide primers, which generated 237 RAPD bands, were used to analyze 90 plants of five populations from three regions, meadow steppe, typical steppe and desert steppe, from the east to the west. The genetic diversity of Stipa krylovii that was revealed by observed number of alleles (na), expected number of alleles (ne), Nei's diversity index (h), Shannon's diversity index (H), amplificated loci, polymorphic loci and the percentage of polymorphic loci (PPB) increased from the east to the west. The Pearson's correlation analysis between genetic diversity parameters and ecological parameters indicated that the genetic diversity of Stipa krylovii was associated with precipitation and cumulative temperature variations along the longitude (humidity were calculated by precipitation and cumulative temperature). Dendrogram based on Jaccard's genetic distance showed that the individuals from the same population formed a single sub-group. Although most variation (56.85%) was within populations, there was high genetic differentiation among populations of Stipa krylovii, high differentiation within and between regions by AMOVA analysis. Either Nei's unbiased genetic distance (G(ST)) or gene flow (Nm) among pairwise populations was not correlated with geographical distance by Mantel's test (P > 0.05), suggesting that there was no consistency with the isolation by distance model in these populations. Natural selection may have played a role in affecting the genetic diversity and population structure, but habitat destruction and degradation in northern grassland in China may be the main factor responsible for high genetic differentiation among populations, within and among regions.

Sustained augmentation of cardiac alpha1A-adrenergic drive results in pathological remodeling with contractile dysfunction, progressive fibrosis and reactivation of matricellular protein genes

We previously reported that transgenic (TG) mice with cardiac-restricted alpha(1A)-adrenergic receptor (alpha(1A)-AR)-overexpression showed enhanced contractility, but no hypertrophy. Since chronic inotropic enhancement may be deleterious, we investigated if long-term, cardiac function and longevity are compromised. alpha(1A)-TG mice, but not their non-TG littermates (NTLs), showed progressive loss of left ventricular (LV) hypercontractility (dP/dt(max): 14,567+/-603 to 11,610+/-915 mmHg/s, P<0.05, A1A1 line: 170-fold overexpression; and 13,625+/-826 to 8322+/-682 mmHg/s, respectively, P<0.05, A1A4 line: 112-fold overexpression, at 2 and 6 months, respectively). Both TG lines developed LV fibrosis, but not LV dilatation or hypertrophy, despite activation of hypertrophic signaling pathways. Microarray and real time RT-PCR analyses revealed activation of matricellular protein genes, including those for thrombospondin 1, connective tissue growth factor and tenascin C, but not transforming growth factor beta1. Life-span was markedly shortened (mean age at death: 155 days, A1A1 line; 224 days, A1A4 line compared with NTLs: >300 days). Telemetric electrocardiography revealed that death in the alpha(1A)-AR TG mice was due to cardiac standstill preceded by a progressive diminution in QRS amplitude, but not by arrhythmias. The QRS changes and sudden death could be mimicked by alpha(1)-AR activation, and reversed preterminally by alpha(1)-AR blockade, suggesting a relationship to stress- or activity-associated catecholamine release. Thus, long-term augmentation of cardiac alpha(1A)-adrenergic drive leads to premature death and progressive LV fibrosis with reactivation of matricellular protein genes. To our knowledge this is the first evidence in vivo for a role of the alpha(1A)-AR in ventricular fibrosis and in pathological cardiac remodeling.

Mapping QTL associated with resistance to Fusarium head blight in the Nanda2419 x Wangshuibai population. II: type I resistance

Fusarium head blight (FHB) is a serious disease in wheat and barley affecting both yield and quality. To identify genes for resistance to infection, the RIL population derived from 'Nanda2419' x 'Wangshuibai' and the parents were evaluated for percentage of infected spikes (PIS) in four different environments. Using a 2,960 cM marker framework map constructed for this population, ten chromosome regions were detected for their association with type I resistance through interval mapping with Mapmaker/QTL, among which QTLs mapped in the intervals of Xwmc349--Xgwm149 on chromosome 4B, of Xwmc96--Xgwm304 on chromosome 5A and of Xgwm408--Xbarc140 on chromosome 5B were revealed in at least three environments and have Wangshuibai as the source of resistance alleles. Qfhi.nau-4B and Qfhi.nau-5A had larger effects and explained up to 17.5 and 27.0% of the phenotypic variance, respectively. To detect epistasis QTLs, two-locus interactions were examined by whole genome scan. Interactions of five locus pairs were found to have significant effects on type I resistance with the LOD score ranging 3.8-6.5 and four of them conferred resistance in parental phase. The one with the most significant effect was Xcfd42--Xgwm469 (6D)/Xwmc390-2--Xbd04 (2A) pair. No QTL x E interaction was detected for PIS. It was found that flowering time did not have significant effects on PIS in this population. Our studies indicated that Wangshuibai is useful for breeding for both type I and type II scab resistance and the markers associated with the QTLs could be used in marker-assisted selection and isolation of scab-resistance QTLs.

Mapping QTL associated with resistance to Fusarium head blight in the Nanda2419 x Wangshuibai population. II: type I resistance

Fusarium head blight (FHB) is a serious disease in wheat and barley affecting both yield and quality. To identify genes for resistance to infection, the RIL population derived from 'Nanda2419' x 'Wangshuibai' and the parents were evaluated for percentage of infected spikes (PIS) in four different environments. Using a 2,960 cM marker framework map constructed for this population, ten chromosome regions were detected for their association with type I resistance through interval mapping with Mapmaker/QTL, among which QTLs mapped in the intervals of Xwmc349--Xgwm149 on chromosome 4B, of Xwmc96--Xgwm304 on chromosome 5A and of Xgwm408--Xbarc140 on chromosome 5B were revealed in at least three environments and have Wangshuibai as the source of resistance alleles. Qfhi.nau-4B and Qfhi.nau-5A had larger effects and explained up to 17.5 and 27.0% of the phenotypic variance, respectively. To detect epistasis QTLs, two-locus interactions were examined by whole genome scan. Interactions of five locus pairs were found to have significant effects on type I resistance with the LOD score ranging 3.8-6.5 and four of them conferred resistance in parental phase. The one with the most significant effect was Xcfd42--Xgwm469 (6D)/Xwmc390-2--Xbd04 (2A) pair. No QTL x E interaction was detected for PIS. It was found that flowering time did not have significant effects on PIS in this population. Our studies indicated that Wangshuibai is useful for breeding for both type I and type II scab resistance and the markers associated with the QTLs could be used in marker-assisted selection and isolation of scab-resistance QTLs.

Controlled release of levonorgestrel from biodegradable poly(D,L-lactide-co-glycolide) microspheres: in vitro and in vivo studies

Poly(D,L-lactide-co-glycolide) (PLG) biodegradable microspheres containing a contraceptive drug, levonorgestrel (LNG), were prepared using both the solvent evaporation method and a modified solvent extraction-evaporation method. The microspheres prepared with the solvent evaporation process had porous surfaces with low product yields and poor encapsulation efficiencies. On the other hand, the microspheres prepared using the modified solvent extraction-evaporation method were nonporous with encapsulation efficiencies close to 100%. In vitro drug release showed the nonporous microspheres had a lower initial burst and a slightly prolonged duration of release than those porous microspheres. In vivo release kinetics of the low burst microspheres were determined by measuring LNG plasma levels after a single intramuscular injection to female rats. At a LNG dose of 41.1 mg/kg, average plasma LNG levels were 6-10 ng/ml in the first 24 h and subsequently remained above 1 ng/ml until 126 days. The duration above the minimum effective LNG plasma level of 0.2 ng/ml was 168 days. By comparison, a similar dose of LNG microcrystals used as control produced a much higher plasma level of 15-21 ng/ml in the first day followed by a fast and continuous decline of LNG levels with a duration of only about 35 days.

Genetic and physical mapping of Pi36(t), a novel rice blast resistance gene located on rice chromosome 8

Blast resistance in the indica cultivar (cv.) Q61 was inherited as a single dominant gene in two F2 populations, F2-1 and F2-2, derived from crosses between the donor cv. and two susceptible japonica cvs. Aichi Asahi and Lijiangxintuanheigu (LTH), respectively. To rapidly determine the chromosomal location of the resistance (R) gene detected in Q61, random amplified polymorphic DNA (RAPD) analysis was performed in the F2-1 population using bulked-segregant analysis (BSA) in combination with recessive-class analysis (RCA). One of the three linked markers identified, BA1126(550), was cloned and sequenced. The R gene locus was roughly mapped on rice chromosome 8 by comparison of the BA1126(550) sequence with rice sequences in the databases (chromosome landing). To confirm this finding, seven known markers, including four sequence-tagged-site (STS) markers and three simple-sequence repeat (SSR) markers flanking BA1126(550) on chromosome 8, were subjected to linkage analysis in the two F2 populations. The locus was mapped to a 5.8 cM interval bounded by RM5647 and RM8018 on the short arm of chromosome 8. This novel R gene is therefore tentatively designated as Pi36(t). For fine mapping of the Pi36(t) locus, five additional markers including one STS marker and four candidate resistance gene (CRG) markers were developed in the target region, based on the genomic sequence of the corresponding region of the reference japonica cv. Nipponbare. The Pi36(t) locus was finally localized to an interval of about 0.6 cM flanked by the markers RM5647 and CRG2, and co-segregated with the markers CRG3 and CRG4. To physically map this locus, the Pi36(t)-linked markers were mapped by electronic hybridization to bacterial artificial chromosome (BAC) or P1 artificial chromosome (PAC) clones of Nipponbare, and a contig map was constructed in silico through Pairwise BLAST analysis. The Pi36(t) locus was physically delimited to an interval of about 17.0 kb, based on the genomic sequence of Nipponbare.

Reducing whole-body vibration and musculoskeletal injury with a new car seat design

A new car seat design, which allows the back part of the seat (BPS) to lower down while a protruded cushion supports the lumbar spine, was quantitatively tested to determine its effectiveness and potentials in reducing whole-body vibration (WBV) and musculoskeletal disorders in automobile drivers. Nine subjects were tested to drive with the seat in: 1) the conventional seating arrangement (Normal posture); and 2) the new seating design (without BPS (WO-BPS) posture). By reducing contact between the seat and the ischial tuberosities (ITs), the new seating design reduced both contact pressure and amplitude of vibrations transmitted through the body. Root-mean-squared values for acceleration along the z-axis at the lumbar spine and ITs significantly decreased 31.6% (p < 0.01) and 19.8% (p < 0.05), respectively, by using the WO-BPS posture. At the same time, vibration dose values significantly decreased along the z-axis of the lumbar spine and ITs by 43.0% (p < 0.05) and 34.5% (p < 0.01). This reduction in WBV allows more sustained driving than permitted by conventional seating devices, by several hours, before sustaining unacceptable WBV levels. Such seating devices, implemented in large trucks and other high-vibration vehicles, may reduce the risk of WBV-related musculoskeletal disorders among drivers.

Expression of secreted Wnt antagonists in gastrointestinal tissues: potential role in stem cell homeostasis

BACKGROUND

Wnt signalling dysregulation has been implicated in cancer, including colon and gastric cancer. Initiation of Wnt signalling is modulated by soluble Wnt antagonists (sWAs), including soluble frizzled related proteins, dickkopf (Dkk) proteins, and Wnt inhibitory factor-1 (Wif1).

AIMS

To evaluate the role of sWAs in upper (gastric) and lower (colon) gastrointestinal tract tumorigenesis.

METHODS

Dkk1-3, Wif1, and FrzB expression was evaluated by in situ RNA hybridisation on normal and malignant human gastric and colon tissues. Expression was graded semiquantitatively.

RESULTS

Wif1, Dkk1, and Dkk2 were not expressed in normal gastric tissue. Dkk3 was expressed in some samples, with stronger expression in deep gastric glands. FrzB was expressed in several normal gastric samples, but not in matched tumour specimens. In contrast, Dkk1 and FrzB were not expressed in normal colon. Wif1 was expressed in most colon samples, with stronger expression at crypt bases. Dkk3 and Dkk2 expression was also concentrated at crypt bases. There were no differences between sWA expression in malignant colon and matched normal tissue.

CONCLUSIONS

sWA expression differed between upper and lower gastrointestinal tract. The loss of FrzB in gastric cancer suggests that it acts as a tumour suppressor. The graded expression of Dkk3 in gastric tissue, and Dkk2, Dkk3, and Wif1 in colon tissue, with increased expression in the deep gastric glands/colonic crypt bases, where gastrointestinal stem cells reside, suggests that sWAs may be crucial Wnt signalling regulators in these tissues, and may contribute to stem cell pool maintenance. sWAs are important components of the gastrointestinal proliferative regulatory network.

Observation of period-doubling bifurcations in a femtosecond fiber soliton laser with dispersion management cavity

We report on the experimental observation of period-doubling bifurcation and period-doubling route to chaos in a femtosecond soliton fiber laser passively mode locked by using the nonlinear polarization rotation technique. Increasing energy of the solitons circulating in the laser cavity, it was revealed that the intensity pattern of the output solitons experiences a period doubling route to chaos. Period-doubling route to chaos is a universal property of the nonlinear dynamic systems transiting from a stable state to a chaotic state. This experimental result shows that the nonlinear propagation of soliton pulses in the laser cavity is an intrinsic dynamic process, which follows the universal laws of the nonlinear dynamic systems.

High viral loads despite absence of clinical and pathological findings in cats experimentally infected with feline coronavirus (FCoV) type I and in naturally FCoV-infected cats

Specified pathogen-free cats were naturally infected with FCoV or experimentally infected with FCoV type I. Seroconversion was determined and the course of infection was monitored by measuring the FCoV loads in faeces, whole blood, plasma and/or monocytes. Tissue samples collected at necropsy were examined for viral load and histopathological changes. Experimentally infected animals started shedding virus as soon as 2 days after infection. They generally displayed the highest viral loads in colon, ileum and mesenteric lymph nodes. Seroconversion occurred 3-4 weeks post infection. Naturally infected cats were positive for FCoV antibodies and monocyte-associated FCoV viraemia prior to death. At necropsy, most animals tested positive for viral shedding and FCoV RNA was found in spleen, mesenteric lymph nodes and bone marrow. Both experimentally and naturally infected cats remained clinically healthy. Pathological findings were restricted to generalized lymphatic hyperplasia. These findings demonstrate the presence of systemic FCoV infection with high viral loads in the absence of clinical and pathological signs.

Statin use and stroke outcomes in the Heart and Estrogen-Progestin Replacement Study (HERS)

The authors investigated the relationship between statin use and the risk of stroke in the Heart and Estrogen-Progestin Replacement Study (HERS). Despite large reductions in relative risk point estimates, statin use was not associated with differences in the risks of all fatal stroke (relative hazard [RH] 0.52, 95% CI 0.23 to 1.18, p = 0.12), fatal ischemic stroke (RH 0.51, 95% CI 0.18 to 1.45, p = 0.21), fatal hemorrhagic stroke (RH 0.18, 95% CI 0.02 to 1.46, p = 0.11), or TIA (RH 1.32, 95% CI 0.84 to 2.09, p = 0.23).

Compiling Causal Theories to Successor State Axioms and STRIPS-Like Systems

We describe a system for specifying the effects of actions. Unlike those commonly used in AI planning, our system uses an action description language that allows one to specify the effects of actions using domain rules, which are state constraints that can entail new action effects from old ones. Declaratively, an action domain in our language corresponds to a nonmonotonic causal theory in the situation calculus. Procedurally, such an action domain is compiled into a set of logical theories, one for each action in the domain, from which fully instantiated successor state-like axioms and STRIPS-like systems are then generated. We expect the system to be a useful tool for knowledge engineers writing action specifications for classical AI planning systems, GOLOG systems, and other systems where formal specifications of actions are needed.

Adjuvant effect of ginseng extracts on the immune responses to immunisation against Staphylococcus aureus in dairy cattle

A crude ginseng extract (GS) and the purified ginsenoside R(b1) (R(b1)) were evaluated for their adjuvant effects in dairy cattle at immunisation with ovalbumin (OVA) and/or a Staphylococcus aureus bacterin used for prevention of bovine mastitis. To evaluate a suitable dose of GS as an adjuvant, 36 lactating cows were randomly divided into six groups. The cows were inoculated twice intramuscularly with a 2-week interval, with saline solution, OVA in saline, or OVA in combination with 4, 16 or 64 mg GS, or Al(OH)(3). The level of specific antibodies to OVA in serum and milk whey was measured before immunisations and 1-5 weeks after the second immunisation. The antibody response in serum was significantly higher in animals immunised with OVA and GS than in animals immunised with OVA alone. A significant increase in milk antibody titres compared with OVA only was only found 2 weeks after the second immunisation in the group immunised with OVA and 4 mg GS. In the second part of the study, 18 heifers were randomly divided into three groups and were immunised twice intramuscularly with a two week interval, with the S. aureus bacterin (control), or with the bacterin in combination with 4 mg GS or 1mg R(b1). The specific antibody response to S. aureus and the lymphocyte proliferation after stimulation with PWM, concanavalin A (Con A) or a specific S. aureus antigen was evaluated in blood samples taken before and after immunisations as specified above. Addition of R(b1) resulted both in significantly higher antibody production and lymphocyte proliferation in response to PWM, Con A and S. aureus antigens than in the control group. Addition of GS induced a significantly higher lymphocyte proliferation in response to PWM and Con A than the control, but had no additional effect on the antibody production. In conclusion, both GS and R(b1) were safe adjuvants, and R(b1) had the strongest adjuvant effects, when used for immunisation against S. aureus in dairy cattle. Field trials are warranted to test the ability of GS and R(b1) to enhance the efficacy of mastitis vaccines in protection against intramammary infections.

Expression of Wnt ligands and Frizzled receptors in colonic mucosa and in colon carcinoma

AIMS

Signalling through the Wnt pathway is integrally associated with colon carcinogenesis. Although activating mutations in the genes for adenomatous polyposis coli (APC) and beta-catenin are clearly associated with colon cancer, less is understood about the role of the upstream secreted ligands (Wnts) and their receptors (frizzled, Fz) in this process. In other systems, increased Wnt signalling has been shown to alter the expression of components of this pathway. This study was designed to test the hypothesis that colon cancer is characterised by aberrant expression of specific Wnt genes and Fz receptors.

METHODS

The expression of Wnt genes was assessed by in situ, antisense RNA hybridisation in paraffin wax embedded samples of normal and malignant human colon tissues with probes specific for the individual Wnt genes. The expression of Fz1 and Fz2 was determined by immunoperoxidase based antibody staining on human tissues.

RESULTS

Changes in the expression of some ligands and receptors were seen in colon cancer. For example, Wnt2 mRNA was detected in colon cancer but was undetectable in normal colonic mucosa. Differential expression of Wnt5a in normal mucosa was also noted, with increased expression at the base of the crypts compared with the luminal villi and slightly increased expression in colon cancer. Wnt7a exhibited minimal expression in both normal and malignant colon tissues, whereas other Wnt ligands including Wnts 1, 4, 5b, 6, 7b, and 10b were expressed equally and strongly in both normal and malignant colon tissues. In defining cellular responses and phenotype, the type and distribution of Fz receptors may be as important as the pattern of Wnt ligand expression. No expression of Fz receptor 1 and 2 was seen in normal colonic mucosa and in well differentiated tumours. However, poorly differentiated tumours exhibited a high degree of Fz receptor expression, especially at the margin of cellular invasion.

CONCLUSIONS

These data indicate that the expression of members of the Wnt signal transduction pathway, distinct from APC and beta-catenin, is integrally associated with the process of colon carcinogenesis. Wnt2, and possibly Wnt5a, may be involved in the progression from normal mucosa to cancer and the expression of Fz1/2 receptors may be involved in processes associated with tumour invasion. Altered expression of these Wnts and Fz receptors may prove useful as prognostic or diagnostic markers for patients with colon cancer.

Effect of ultrasound on the removal of copper from the model solutions for copper electrolysis process

A novel combination of an ultrasonic field with electrolysis for the removal of copper is studied. In the ultrasonic field, cavitation acts as jets and agitates the solution and breaks the barrier layer between the cathode surface and the bulk of the solution, thus increases the metal deposition on the cathode surface. The results show that an ultrasonic field is successful for the removal of low copper concentrations in solution.