Abstract ES7-1: Next Generation Sequencing for the Clinician: A Breast Cancer Study

The ability to study genome-wide sequence alterations in cancer genomes has transformed our understanding of the intricacies of this disease. We have applied whole genome sequencing and analysis to tease apart the genomic predictors of aromatase inhibitor (AI) response, by selecting luminal breast cancer cases obtained within a clinical trial of aromatase inhibitor treatment (ACOSOG Z1031). Our study compared the constitutional genome to the cancer genome for patients that exhibit either a response or a resistance phenotype, based on their Ki67 IHC score following 4 month AI treatment and resection. My talk will highlight the process by which these genomes are sequenced and analyzed, and will provide our most recent insights into how the combination of the constitutional and somatic genomes determine whether a patient will respond to AI treatment.

Citation Information: Cancer Res 2010;70(24 Suppl):Abstract nr ES7-1.

Conformance Control of CSS and Steam Drive Process With a Carbamide Surfactant

Abstract

Based on physical modelling, this paper discusses the feasibility of injecting additives to control the conformance of the cyclic steam stimulation (CSS) and steam drive processes in the Biquan 10 Block of the Henan Oil Field. The lab test results show that waterflooding with the addition of a carbamide surfactant can decrease residual oil saturation by 4.7% and that steam drive with the addition of this same surfactant can improve the sweep volume and increase the oil recovery factor by 17.5%. Also, field application results confirmed that injecting this surfactant in the CSS and steam drive processes can increase oil production, lower steam-oil ratio (SOR) and improve the economic benefitssignificantly.

Introduction

The CSS process has been applied in developing the heavy oil reservoirs in the Henan Oil Field since the late 1980s. It has been clearly demonstrated that with increasing the cycles of steam stimulation, the oil production rate decreases and SOR can rapidly reach the economic limit. For improving the oil production rate and recovery factor, the steam drive process needs to be applied as a subsequent technology. However, the reservoir in the Henan Oil Field is thin and interbedded so it is a challenge to operate the conventional steam drive process. To reduce the steam channeling effect, a number of high temperature resistant plugging surfactants have been tested, but they could not achieve ideal and persistent results(1). This paper discusses the development of a new kind of conformance control agent ? carbamide surfactant. The lab testing results and field applications of the steam drive process with the addition of a carbamide surfactant in Well Group 577, Biqian 10 Block, Henan Oil Field, are described in detail below.

Mechanism and Physical Modelling

When the carbamide surfactant is injected into the reservoir with steam, carbamide decomposes into CO2 and NH3 under high temperatures. The decomposition can be expressed as follows:

Equation (available in full paper)

The physical modelling shows that, with increasing temperature and pressure, the carbamide decomposes even faster but its concentration does not affect the decomposition speed. The produced CO2 dissolves in heavy oil and NH3 can react with some acid in the oil. As a result, the heavy oil volume expands and viscosity decreases. At 50 °C, when the oil-carbamide solution (30 wt% carbamide) ratio is 4 to 1, the oil viscosity can be reduced by 73% to 80%. The single tube displacement efficiency test shows that adding carbamide solution (30 wt% carbamide) into hot water will increase the displacing efficiency by 6.5%.

Field Application and Discussion

Reservoir Geology and Production History

Well pattern 577 in the east of Biqian 10 block was selected for the field test. The well pattern is an inverted 9-spot with injector-producer spacing of 70 m and 100 m. The pay zone is the IV-9 layer of the H-3 interval in the Hetaoyuan Formation. The basic reservoir parameters are as follows:

Longitudinal pattern of regional brain volume change differentiates normal aging from MCI

BACKGROUND

Neuroimaging measures have potential as surrogate markers of disease through identification of consistent features that occur prior to clinical symptoms. Despite numerous investigations, especially in relation to the transition to clinical impairment, the regional pattern of brain changes in clinically normal older adults has not been established. We predict that the regions that show early pathologic changes in association with Alzheimer disease will show accelerated volume loss in mild cognitive impairment (MCI) compared to normal aging.

METHODS

Through the Baltimore Longitudinal Study of Aging, we prospectively evaluated 138 nondemented individuals (age 64-86 years) annually for up to 10 consecutive years. Eighteen participants were diagnosed with MCI over the course of the study. Mixed-effects regression was used to compare regional brain volume trajectories of clinically normal individuals to those with MCI based on a total of 1,017 observations.

RESULTS

All investigated volumes declined with normal aging (p < 0.05). Accelerated change with age was observed for ventricular CSF (vCSF), frontal gray matter, superior, middle, and medial frontal, and superior parietal regions (p < or = 0.04). The MCI group showed accelerated changes compared to normal controls in whole brain volume, vCSF, temporal gray matter, and orbitofrontal and temporal association cortices, including the hippocampus (p < or = 0.04).

CONCLUSION

Although age-related regional volume loss is apparent and widespread in nondemented individuals, mild cognitive impairment is associated with a unique pattern of structural vulnerability reflected in differential volume loss in specific regions. Early identification of patterns of abnormality is of fundamental importance for detecting disease onset and tracking progression.

Chlamydia pneumoniae infection, complement factor H variants and age-related macular degeneration

BACKGROUND/AIMS

Impaired inhibition of the alternative complement pathway by complement factor H (CFH) is linked to age-related macular degeneration (AMD) based on the strong association between CFH variant and AMD. Chlamydia pneumoniae (C pneumoniae) infection can trigger the alternative pathway, but the evidence for an association between C pneumoniae and AMD is contradictory. This study investigated whether C pneumoniae infection is associated with AMD and whether the presence of C pneumonia modulates AMD risk conferred by CFH variants.

METHODS

Genomic DNA extracted from peripheral blood of 148 advanced AMD patients and 162 controls was subjected to Taqman and PCR-RFLP for the CFH polymorphism and PCR for the C pneumoniae gene. Genomic DNA was also examined from microdissected macular cells from 59 AMD and 16 age-matched non-AMD archived slides. chi(2) testing was performed for case-control analysis.

RESULTS

C pneumoniae infection was associated with increased risk of AMD (OR = 2.17, p<0.017). A CFH variant was also linked to increased risk of AMD (OR = 1.98, p<0.0001). However, no relationship was found between risk-conferring CFH variant and C pneumoniae (OR = 1.81, p = 0.08).

CONCLUSION

There is a possible association between AMD and C pneumoniae infection, although CFH may not be directly involved in the pathogenesis of C pneumoniae infection-mediated AMD.

The role of hepatitis B virus x gene in development of primary hepatocellular carcinoma

Primary hepatocellular carcinoma (HCC) is one of the most common cancers occurring in human, and there is strong epidemiological evidence suggesting that persistent hepatitis B virus (HBV) infection is the most important risk factor for its development.HBx gene was found to be a transactivator recently. Its continuous expression in hepatocytes may transactivate cellular genes which can play a certain role in development of HCC. TheHBx gene fragment was used to construct a recombinant eukaryotic expression vector pCEP4 and introduced into HepG2 cells. The effect ofHBx gene on HCC cells growth and its molecular mechanism in HCC cells regulation were investigated.

Proteomic analysis of human bone marrow mesenchymal stem cells transduced with human telomerase reverse transcriptase gene during proliferation

OBJECTIVES

Previous studies have reported immortalization and tumorigenicity of human mesenchymal stem cells (hMSCs) transduced with exogenous human telomerase reverse transcriptase (hTERT). We also have established a line of hMSCs transduced with hTERT (hTERT-hMSCs) and we have cultured these cells for 290 population doublings (PDs) during which they demonstrated a large proliferation potential but with no tumorigenicity. The aim of this study was to investigate the protein expression profile of hTERT-hMSCs with two-dimensional gel electrophoresis and peptide mass fingerprinting by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry, to be able to analyse the effects of exogenous hTERT on protein expression in hMSCs.

MATERIALS AND METHODS

We generated proteome maps of primary hMSCs and hTERT-hMSCs at PD 95 and PD 275.

RESULTS

A total of 1543 +/- 145 protein spots in gels of primary MSCs at PD 12, 1611 +/- 186 protein spots in gels of hTERT-hMSCs at PD 95 and 1451 +/- 126 protein spots in gels of hTERT-hMSCs at 275 PD were detected. One hundred of these were successfully identified, including 20 which were differentially expressed.

CONCLUSIONS

The results suggest that sustaining levels of prohibitin and p53 expression along with differential expression of proteins in hTERT-hMSCs provide an insight into lack of transforming activity of hTERT-hMSCs during cell proliferation.

Segmenting lung fields in serial chest radiographs using both population-based and patient-specific shape statistics

This paper presents a new deformable model using both population-based and patient-specific shape statistics to segment lung fields from serial chest radiographs. There are two novelties in the proposed deformable model. First, a modified scale invariant feature transform (SIFT) local descriptor, which is more distinctive than the general intensity and gradient features, is used to characterize the image features in the vicinity of each pixel. Second, the deformable contour is constrained by both population-based and patient-specific shape statistics, and it yields more robust and accurate segmentation of lung fields for serial chest radiographs. In particular, for segmenting the initial time-point images, the population-based shape statistics is used to constrain the deformable contour; as more subsequent images of the same patient are acquired, the patient-specific shape statistics online collected from the previous segmentation results gradually takes more roles. Thus, this patient-specific shape statistics is updated each time when a new segmentation result is obtained, and it is further used to refine the segmentation results of all the available time-point images. Experimental results show that the proposed method is more robust and accurate than other active shape models in segmenting the lung fields from serial chest radiographs.

Anti-tumor activity of letrozole in patients with recurrent advanced low malignant potential or low-grade serous ovarian tumors

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Purpose: To evaluate the clinical activity of oral Letrozole in patients with recurrent and advanced low malignant potential or low grade serous ovarian tumors and to determine the impact of steroid receptor expression on this observed activity. Methods: In a phase II design, we recruited patients with confirmed recurrent advanced stage low malignant potential tumors and recurrent low-grade serous carcinomas. Measurable disease was required. Steroid hormone expression (ER and PR), EGFR, and Her2/neu expression were determined on available pathological material by IHC from the initial surgery or at documentation of recurrent disease and blood was obtained before enrollment and every other month while on therapy. Letrozole was administered orally at a dose of 2.5 mg once a day. The endpoints were objective response rate assessed by Response Evaluation Criteria in Solid Tumor. Adverse events were graded using the National Cancer Institute Common Toxicity Criteria. Results: Thirteen patients meeting eligibility have been enrolled are evaluable for response and toxicity. From objective clinical parameters (RECIST) no patients had a CR or PR; five patients (38%) had disease stabilizations, eight patients had progressive disease. However, using criteria for CA 125 response, we obtained a complete serologic response in 2 of 13 patients (15%), and a partial serologic response in 2 additional patients (15%); marker stabilization was seen in 5 other patients (38%). CA125 increased in four patients (31%). We also detected the presence of ER, PR, EGFR, Her-2/Neu by IHC, and estradiol in the plasma by ELISA. No significant correlation was observed between tumor marker response and ER expression alone. However, when we evaluated the co-expression of ER/PR we found 3 of 5 (60%) patients had a serologic response compared to just 1 of 8 patients with ER+/PR- tumors (P=0.07). We observed no severe adverse events. Conclusion: Our preliminary data suggests that oral Letrozole has some antitumor activity in recurrent advanced low grade or borderline ovarian tumors and is well tolerated. The analysis of correlation between objective response and combined prediction markers including phosphorylated ER, PR, AKT, and IGFR is ongoing (Supported by CTRF).

No significant financial relationships to disclose.

Amoxicillin pharmacokinetics in pregnant women: modeling and simulations of dosage strategies

Amoxicillin is recommended for anthrax prevention in pregnancy. The objective of this study was to evaluate the pharmacokinetics of amoxicillin during pregnancy and postpartum (PP). Sixteen women received amoxicillin during gestation (18-22 weeks (T2) and 30-34 weeks (T3)) as well as 3 months postpartum (PP) to evaluate single-dose pharmacokinetics. Amoxicillin compartmental pharmacokinetic parameters were used to simulate amoxicillin concentration-time profiles following different dosage strategies. Amoxicillin CL(renal) (T2: 24.8+/-6.7 l/h, P<0.001; T3: 24.0+/-3.9 l/h, P<0.001; and PP: 15.3+/-2.6 l/h) and renal CL(secretion) (T2: 280+/-105 ml/min, P<0.002; T3: 259+/-54 ml/min, P<0.001; and PP: 167+/-47 ml/min) were higher during pregnancy than postpartum. Simulations suggest that amoxicillin concentrations adequate to prevent anthrax may be difficult to achieve during pregnancy and postpartum. Increases in amoxicillin CL(renal) and renal CL(secretion) reflect increases in filtration and secretory transport or diminished reabsorption in the kidneys. Amoxicillin may not be an appropriate antibiotic for post-anthrax exposure prophylaxis.

Rice endophyte Pantoea agglomerans YS19 promotes host plant growth and affects allocations of host photosynthates

AIMS

The aims of the study were to identify the effects of rice endophyte Pantoea agglomerans YS19 on host plant growth and allocations of photosynthates.

METHODS AND RESULTS

Endophytic diazotrophic YS19 showed nitrogen-fixing activity in N-free medium, and produced four categories of phytohormones which were indole-3-acetic acid, abscisic acid, gibberellic acid and cytokinin in Luria-Bertani medium. Inoculation of YS19 improved the biomass of the 12-day-cultivated host rice seedlings by 63.4% on N-free medium or by 18.7% on N-supplemented medium. Spraying of YS19 cell culture onto the rice plants at the premilk stage enhanced the transportation of the photosynthetic assimilation product from the source (flag leaves) to the sink (stachys) significantly. The formation of the plant sink was obviously inhibited when YS19 cell culture was applied at the late milk stage.

CONCLUSIONS

This research suggests that endophyte YS19 promotes host rice plant growth and affects allocations of host photosynthates.

SIGNIFICANCE AND IMPACT OF THE STUDY

These findings suggested that YS19 possesses the potential for increasing rice production in field application. Meanwhile, a suitable plant growth stage must be selected for the foliar spraying of YS19 cell culture.

Past adult lead exposure is linked to neurodegeneration measured by brain MRI

OBJECTIVE

To determine whether cumulative lead dose in former organolead workers was associated with MRI measures of white matter lesions (WML) and global and structure-specific brain volumes.

METHODS

MRIs, tibia lead, and other measures were obtained from 532 former organolead workers with a mean age of 56 years and a mean of 18 years since last occupational exposure to lead. Cumulative lead dose was measured by tibia lead, obtained by X-ray fluorescence, and expressed as microg lead per gram of bone mineral (microg Pb/g). WML were evaluated using the Cardiovascular Health Study grading scale. A total of 21 global and specific brain regions were evaluated.

RESULTS

A total of 36% of individuals had WML grade of 1 to 7 (0 to 9 scale). Increasing peak tibia lead was associated with increasing WML grade (p = 0.004). The adjusted OR for a 1 microg Pb/g increase in tibia lead was 1.042 (95% CI = 1.021, 1.063) for a CHS grade of 5+ (> or = 5 vs < 5). In linear regression, the coefficient for tibia lead was negative for associations with all structures. Higher tibia lead was significantly related to smaller total brain volume, frontal and total gray matter volume, and parietal white matter volume. Of nine smaller specific regions of interest, higher tibia lead was associated with smaller volumes for the cingulate gyrus and insula.

CONCLUSIONS

These data suggest that cumulative lead dose is associated with persistent brain lesions, and may explain previous findings of a progressive decline in cognitive function.

Biomarkers detected by proteomic analysis predicts breast cancer response to neoadjuvant chemotherapy

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Background: Neoadjuvant chemotherapy provides an excellent opportunity for objective assessment of treatment-induced tumor response and for studying biomarkers characteristic of therapy-induced tumor responses. Methods: Proteomic analysis of T3/T4 breast cancer was performed in patients with locally advanced breast cancer in a phase II clinical trial. The breast cancer specimen was obtained before and after four cycles of Taxotere/Carboplatin/±Herceptin treatment. Two proteomic approaches, SELDI mass spectrometry and Clontech Ab Microarray 500, were used to screen for protein biomarkers that predict response of breast cancer to chemotherapy. Results: Five tumors with pathologically complete response (pCR) and 29 tumors with various amounts of residual tumors (Non-pCR) were analyzed by SELDI-TOF using the NP 20 chip. The normalized mass signals were compared between pCR vs Non-pCR at each aligned location by Wilcoxon rank sum test. Statistically significant differences were found at 22 m/z locations using a liberal p <0.20 criterion. The best univariate predictor occurred at m/z 14960 (p=0.004), which correctly classified 5/5 pCR spectra (100%) and 24/29 Non-pCR spectra (83%). A multivariate classification tree developed using m/z 14960 and m/z 12138 intensities correctly classified all 34 spectra. Ab microarray analysis was performed on five pCR tumors and in five tumors with the largest residual cancer. The Internal Normalization Ratio (INR) was calculated and used to compare the difference of protein expression between the two groups. Eight differentially expressed protein biomarkers were selected with the criteria of a statistically significant (Student t, p<0.05) expression change of <0.77 or >1.3 fold. Three proteins (Tat-SF1, PYK2 and PTP1B) were higher, and five (E2F2, IL1b, FEN1, CDC37 and ACM1) were lower in tumors with pCR. The unsupervised hierarchical clustering of the 10 samples by these eight proteins completely separated the pCR tumors from the poor responders. Conclusions: Our study suggests that bothSELDImass spectrometry and antibody microarray may be used to predict the tumor response to neoadjuvant chemotherapy. Proteomic analysis may be useful in developing tailored chemotherapy for breast cancer.

[Table: see text]

Virus-induced chalazion

PURPOSE

To investigate a viral etiology in certain chalazia.

METHODS

A prospective study over 7.5 years of all newly presenting chalazia associated with diffuse follicular conjunctivitis but without any other aetiological factors. Patients were investigated for ocular or systemic infections by history, physical exam, slit-lamp exam, and/or histology of conjunctival biopsy (including transmission electron microscopy).

RESULTS

A total of 27 patients developed follicular conjunctivitis without meibomian gland dysfunction, blepharitis, or sexually transmitted diseases. Evidence for a viral aetiology included: recent systemic viral illness (15/27), recent contact with subjects with chalazia or follicular conjunctivitis (5/27), preauricular lymphadenopathy (4/27), viral corneal disease (4/27), or viral particles by ultrastructure (4/4).

CONCLUSIONS

Chalazia may be associated with viral conjunctivitis. Intralesional corticosteroids should be considered with great caution for viral-induced chalazia.

Dissemination of CTX-M type β-lactamases in Enterobacteriaceae isolates in the People’s Republic of China

Previously there have been a number of reports of extended spectrum beta-lactamase (ESBL) producing isolates of the family Enterobacteriaceae in Asia. We first reported the occurrence of bla(CTX-M) in Guangzhou, China, subsequently there have been reports of bla(CTX-M) from a number of other south Asian countries. Initial surveillance study data suggested that bla(CTX-M) might be widely distributed in China. This study examines the type of bla(CTX-M) occurring in other major population centres in China. Initial disk diffusion method susceptibility testing (NCCLS) selected ESBL producing Escherichia coli and Klebsiella pneumoniae isolates from Beijing and near Wuhan, PRC. After screening in both China and the UK, 13 isolates producing CTX-M ESBLs were identified and studied, 11 also produced TEM-1, and 4 also produced SHV-1. Sequence analysis of the bla(CTX-M) containing isolates revealed these isolates contained two different bla(CTX-M), three with bla(CTX-M-3) and 10 with bla(CTX-M-14). After comparison with other previously published studies in the English language, we conclude that the most prevalent bla(CTX-M) so far reported in Asia are bla(CTX-M-14) and bla(CTX-M-3).

Superinfection of Laodelphax striatellus with Wolbachia from Drosophila simulans

Wolbachia are maternally inherited, intracellular alpha-proteobacteria that infect a wide range of arthropods. They manipulate the reproduction of hosts to facilitate their spread into host populations, through ways such as cytoplasmic incompatibility (CI), parthenogenesis, feminization and male killing. The influence of Wolbachia infection on host populations has attracted considerable interest in their possible role in speciation and as a potential agent of biological control. In this study, we used both microinjection and nested PCR to show that the Wolbachia naturally infecting Drosophila simulans can be transferred into a naturally Wolbachia-infected strain of the small brown planthopper Laodelphax striatellus, with up to 30% superinfection frequency in the F(12) generation. The superinfected males of L. striatellus showed unidirectional CI when mated with the original single-infected females, while superinfected females of L. striatellus were compatible with superinfected or single-infected males. These results are, to our knowledge, the first to establish a superinfected horizontal transfer route for Wolbachia between phylogenetically distant insects. The segregation of Wolbachia from superinfected L. striatellus was observed during the spreading process, which suggests that Wolbachia could adapt to a phylogenetically distant host with increased infection frequency in the new host population; however, it would take a long time to establish a high-frequency superinfection line. This study implies a novel way to generate insect lines capable of driving desired genes into Wolbachia-infected populations to start population replacement.

[Application of dot immunogold filtration assay for diagnosis of Schistosomiasis japonica]

AIM

To quest for a simple and convenient assay for the diagnosis of schistosomiasis.

METHODS

Three monoclonal antibodies against different epitopes of antigens of S. japonicum were used to develop a dot immunogold filtration assay for detection of schistosomal antigen-antibody reaction on the membrane during the filtration process. The results could be read with the naked eye within a few minutes.

RESULTS

The sensitivity of the SEA assay was 16 ng/ml. In 69 serum samples from patients with chronic schistosomiasis, the positive rate and specificity of this assay were 60.8% and 95.2%, respectively. Dot-ELISA was used in detecting 137 serum samples from patients with chronic schistosomiasis, the positive rate and specificity were 54.7% and 94.6%, respectively. When sandwich-ELISA was used in detecting 118 serum samples from patients with chronic schistosomiasis, the positive rate and specificity were 61.9% and 95.7%, respectively.

CONCLUSION

The sensitivity and specificity of DIFA were similar to those of ELISA, but DIFA required less time and no special equipment.