Genome-wide discovery of genetic variants affecting tamoxifen sensitivity and their clinical and functional validation

BACKGROUND

Beyond estrogen receptor (ER), there are no validated predictors for tamoxifen (TAM) efficacy and toxicity. We utilized a genome-wide cell-based model to comprehensively evaluate genetic variants for their contribution to cellular sensitivity to TAM.

DESIGN

Our discovery model incorporates multidimensional datasets, including genome-wide genotype, gene expression, and endoxifen-induced cellular growth inhibition in the International HapMap lymphoblastoid cell lines (LCLs). Genome-wide findings were further evaluated in NCI60 cancer cell lines. Gene knock-down experiments were performed in four breast cancer cell lines. Genetic variants identified in the cell-based model were examined in 245 Caucasian breast cancer patients who underwent TAM treatment.

RESULTS

We identified seven novel single-nucleotide polymorphisms (SNPs) associated with endoxifen sensitivity through the expression of 10 genes using the genome-wide integrative analysis. All 10 genes identified in LCLs were associated with TAM sensitivity in NCI60 cancer cell lines, including USP7. USP7 knock-down resulted in increasing resistance to TAM in four breast cancer cell lines tested, which is consistent with the finding in LCLs and in the NCI60 cells. Furthermore, we identified SNPs that were associated with TAM-induced toxicities in breast cancer patients, after adjusting for other clinical factors.

CONCLUSION

Our work demonstrates the utility of a cell-based model in genome-wide identification of pharmacogenomic markers.

Competition among memes in a world with limited attention

The wide adoption of social media has increased the competition among ideas for our finite attention. We employ a parsimonious agent-based model to study whether such a competition may affect the popularity of different memes, the diversity of information we are exposed to, and the fading of our collective interests for specific topics. Agents share messages on a social network but can only pay attention to a portion of the information they receive. In the emerging dynamics of information diffusion, a few memes go viral while most do not. The predictions of our model are consistent with empirical data from Twitter, a popular microblogging platform. Surprisingly, we can explain the massive heterogeneity in the popularity and persistence of memes as deriving from a combination of the competition for our limited attention and the structure of the social network, without the need to assume different intrinsic values among ideas.

Loss of bacterial diversity during antibiotic treatment of intubated patients colonized with Pseudomonas aeruginosa

Management of airway infections caused by Pseudomonas aeruginosa is a serious clinical challenge, but little is known about the microbial ecology of airway infections in intubated patients. We analyzed bacterial diversity in endotracheal aspirates obtained from intubated patients colonized by P. aeruginosa by using 16S rRNA clone libraries and microarrays (PhyloChip) to determine changes in bacterial community compositions during antibiotic treatment. Bacterial 16S rRNA genes were absent from aspirates obtained from patients briefly intubated for elective surgery but were detected by PCR in samples from all patients intubated for longer periods. Sequencing of 16S rRNA clone libraries demonstrated the presence of many orally, nasally, and gastrointestinally associated bacteria, including known pathogens, in the lungs of patients colonized with P. aeruginosa. PhyloChip analysis detected the same organisms and many additional bacterial groups present at low abundance that were not detected in clone libraries. For each patient, both culture-independent methods showed that bacterial diversity decreased following the administration of antibiotics, and communities became dominated by a pulmonary pathogen. P. aeruginosa became the dominant species in six of seven patients studied, despite treatment of five of these six with antibiotics to which it was sensitive in vitro. Our data demonstrate that the loss of bacterial diversity under antibiotic selection is highly associated with the development of pneumonia in ventilated patients colonized with P. aeruginosa. Interestingly, PhyloChip analysis demonstrated reciprocal changes in abundance between P. aeruginosa and the class Bacilli, suggesting that these groups may compete for a similar ecological niche and suggesting possible mechanisms through which the loss of microbial diversity may directly contribute to pathogen selection and persistence.

Intervertebral administration of 153Samarium with kyphoplasty for vertebral metastases

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Background: Kyphoplasty is an effective procedure to alleviate pain in metastatic vertebrae. 153Samarium-EDTMP (153Sm) is used for palliative treatment of multiple bone metastases. The hematological toxicity is the main limiting factor. Objectives: Study the feasibility of intervertebral administration of 153 SM with Kyphoplasty. Assess procedure related morbidities specifically haematological since a direct vertebral route is planned though to a much smaller dose. Methods: IRB approval for an off label use of 153Sm-EDTMP was obtained. Six patients with documented vertebral bone metastasis and pathological compression fractures were studied (Thoracic in 2 and lumbar in 4). Primary cancer was lung in 2, prostate (1), maxillary sinus (1), myeloma (1) and colon (1). Serial dilution of 153 SM was performed to obtain 2 mci/1ml. Kyphoplasty procedure was carried out using the known protocol. 2 mCi of 153Sm was admixed with the bone cement and administered under tight radiation safety measures. Serial nuclear body scans were obtained. Pain assessment was evaluated using analog pain score at 1, 7 and 30 days. Serial blood counts are followed. Results: All patients tolerated procedure well. No immediate procedure(s) related morbidities were noted. One case was not technically satisfactory and no significant uptake was detected in the injected vertebra. Nuclear scan done on 0 revealed excellent radiotracer uptake in the other 5 vertebrae injected. The absorbed radiotracer was seen to target other skeletal metastatic lesions in 2 patients. There was no significant change in WBC, HCT or Platelets seen in blood counts obtained over one month post-procedure. Except for the first patient, no appreciable radiation leakage was encountered. Pain score was reduced from a mean of 8.5 to 3.2 during the first week and was maintained below score of 4 at one month assessment. Conclusions: The combination of intervertebral administration of 153SM and Kyphoplasty seems to be well tolerated. No haematological side effects were encountered; probably due to the use of only 2 mci compared to over 70 mci in intravenous administration. Pain control seems to be satisfactory at areas treated. Analysis of procedure related radiological changes is underway.

No significant financial relationships to disclose.

Excretory nitrogen metabolism in the Chinese fire-belly newt Cynops orientalis in water, on land, or in high concentrations of environmental ammonia

The Chinese fire-belly newt Cynops orientalis reverts to an aquatic mode of living when sexually mature. Despite living in water, sexually mature C. orientalis maintained high capacity for hepatic urea synthesis. However, it had a lower rate of urea production than other terrestrial amphibians because endogenous ammonia could diffuse out to the external medium as NH3. This conserves cellular energy because urea synthesis is energetically expensive. Simultaneously, C. orientalis also reduced the rate of urea excretion, and excreted 33% of the total nitrogenous waste as ammonia. Upon exposure to land, C. orientalis increased the rate of urea synthesis from accumulating endogenous ammonia. The increased rate of urea synthesis was within the inherent capacity of the hepatic ornithine-urea cycle; there was no induction of hepatic carbamoyl phosphate synthetase or ornithine transcarbamoylase activities and there was no reduction in ammonia production. When exposed to water containing 75 mmol.l(-1) NH4Cl, the rates of both urea synthesis and urea excretion increased. Under such experimental conditions, the ornithine-urea cycle may be operating close to its limit; glutamine began to accumulate in the body, and endogenous ammonia production via amino acid catabolism was reduced.

[Effects of XW630 on mechanical properties and trabecular structure parameters of bone tissue in ovariectomized rats]

OBJECTIVE

The study aimed at investigating the effects of a new anti-osteoporotic drug, XW630 on promoting the osteogenic activity of bone tissue in ovariectomized rats.

METHODS

Thirty-six female SD rats, three months old, were randomly divided into four groups: sham-operated group (sham), the ovariectomized group (OVX), the esterone-therapy group (OVX + CFT) and the XW630-therapy group (OVX + XW630). Three rats in each group were killed on the 30th, 60th, and 90th day after the operation. The femur of one side was taken for the three-point bending resistance test, and the bilateral tibias were taken for the HE stain and scanning electronic microscopy (SEM) examination.

RESULTS

The HE and SEM results indicated that the bone loss appeared in the OVX group 30 days after the operation, which lasted for the whole observing period. While after application of ester-one and XW630, there were different degrees of bone repairing around the trabeculae, and the osteogenic activity was obviously active in the XW630 group than that in the esterone group. During the experimental period, the three-point bending resistance of the OVX group gradually decreased and there was a significant difference compared with that of the sham group (P < 0.01), while the three-point bending resistance of the two therapy group gradually increased and there was significant difference between the OVX group and the XW630 group (P < 0.05 and P < 0.01).

CONCLUSION

XW630 can effectively promote osteogenic action and prevent osteoporostic fracture in ovariectomized rats.

[Regulation of XW630 on TGF-beta 1 and collagen I gene expression in osteoblasts]

OBJECTIVE

The purpose of this part of study was to investigate the mechanism of a new anti-osteoporotic drug, XW630 on promoting osteogenic activity.

METHODS

Total RNA were isolated from osteoblasts of the mice after the reaction with XW630 in 24 and 72 hours, that were hybridized with the extracted and digoxigenin-labeled TGF-beta 1 and the collagen I cDNA probes.

RESULTS

XW630 significantly promoted TGF-beta 1 and collagen I gene expression in osteoblasts, and this drug was superior than other two kinds of estrogen in promoting osteogenic activity (P < 0.05).

CONCLUSION

XW630 promote osteogenic activity of osteoblasts, probably by enhancing the mRNA expression of TGF-beta 1 and collagen I.

Contribution of individual sorbents to the control of heavy metal activity in sandy soil

A multisurface model is used to evaluate the contribution of various sorption surfaces to the control of heavy metal activity in sandy soil samples at pH 3.7-6.1 with different sorbent contents. This multisurface model considers soil as a set of independent sorption surfaces, i.e. organic matter (NICA-Donnan), clay silicate (Donnan), and iron hydroxides (DDL, CD-MUSIC). The activities of Cu2+, Cd2+, Zn2+, Ni2+, and Pb2+ in equilibrium with the soil have been measured using a Donnan membrane technique. The metal activities predicted by the model agree with those measured reasonably well over a wide concentration range for all the metals of interest except for Pb. The modeling results suggest that soil organic matter is the most important sorbent that controls the activity of Cu2+, Cd2+, Zn2+, and Ni2+ in these sandy soils. When metal loading is high in comparison with soil organic matter content, the contribution of clay silicates to metal binding becomes more important. Adsorption to iron hydroxides is found not significant in these samples for Cu, Cd, Zn, and Ni. However, for Pb the model estimates strong adsorption on iron hydroxides. The model predicts that acidification will not only lead to increased solution concentrations but also to a shift toward more nonspecific cation-exchange type binding especially for the metals Cd, Zn, and Ni. Lowering the pH has led to a loss of 56% of Cd, 69% of Zn, and 66% of Ni during 16 years due to increased leaching.