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.

Identification of a 4-microRNA signature for clear cell renal cell carcinoma metastasis and prognosis

Renal cell carcinoma (RCC) metastasis portends a poor prognosis and cannot be reliably predicted. Early determination of the metastatic potential of RCC may help guide proper treatment. We analyzed microRNA (miRNA) expression in clear cell RCC (ccRCC) for the purpose of developing a miRNA expression signature to determine the risk of metastasis and prognosis. We used the microarray technology to profile miRNA expression of 78 benign kidney and ccRCC samples. Using 28 localized and metastatic ccRCC specimens as the training cohort and the univariate logistic regression and risk score methods, we developed a miRNA signature model in which the expression levels of miR-10b, miR-139-5p, miR-130b and miR-199b-5p were used to determine the status of ccRCC metastasis. We validated the signature in an independent 40-sample testing cohort of different stages of primary ccRCCs using the microarray data. Within the testing cohort patients who had at least 5 years follow-up if no metastasis developed, the signature showed a high sensitivity and specificity. The risk status was proven to be associated with the cancer-specific survival. Using the most stably expressed miRNA among benign and tumorous kidney tissue as the internal reference for normalization, we successfully converted his signature to be a quantitative PCR (qPCR)-based assay, which showed the same high sensitivity and specificity. The 4-miRNA is associated with ccRCC metastasis and prognosis. The signature is ready for and will benefit from further large clinical cohort validation and has the potential for clinical application.

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.

MicroRNA profiling of clear cell renal cell carcinoma by whole-genome small RNA deep sequencing of paired frozen and formalin-fixed, paraffin-embedded tissue specimens

Renal cell carcinoma (RCC) is one of the leading causes of cancer mortality. Characterization of microRNA (miRNA) expression of RCC will help disclose new pathogenic pathways in tumourigenesis and progression and may lead to the development of molecular biomarkers and target-specific therapies for diagnosis, prognostication and treatment. With limitations in test specificity and the ability to detect novel miRNA and other small non-coding RNAs (smRNAs), microarray and RT-PCR techniques are being replaced by the evolving deep-sequencing technologies, at least in the discovery phase. Until now, cancer miRNA profiling of human benign and tumour specimen sets, using smRNA deep-sequencing (smRNA-seq), has not been reported. Specifically, due to concern over possible poor RNA quality/integrity, formalin-fixed paraffin-embedded (FFPE) samples have not been used for such studies. Here, we performed whole-genome smRNA-seq analysis using a benign and RCC specimen set and have successfully profiled the miRNA expression. Studies performed on paired frozen and FFPE specimens showed very similar results. Moreover, a comparison study of microarray, deep-sequencing and RT-PCR methodologies also showed a high correlation among the three technologies. To our knowledge, this is the first study to demonstrate that FFPE specimens can be used reliably for miRNA deep-sequencing analysis, making future large-scale clinical cohort/trial-based studies possible.

Abstract LB-275: 5-miRNA signature to predict clear cell renal cell carcinoma metastasis and prognosis

Introduction: Clear cell renal cell carcinoma (ccRCC) represents the most common renal cancer histology. In the setting of metastatic disease, few patients achieve a durable remission with currently available therapies. Early determination of metastatic potential may help guide therapy and improve clinical outcome. MicroRNA (miRNA) is a group of small non-coding RNAs that regulate gene expression during development and differentiation. miRNA expression is altered in malignant tissue, and signatures based on miRNA expression can aid in diagnosis and prognostication. In this study, we have characterized ccRCC miRNA expression in a 28-sample training cohort using microarray technology. From this, we have developed a 5-miRNA expression signature to predict the risk of metastasis and overall prognosis. This signature has been further validated by an independent 34-sample testing cohort.

Study Design: Training and testing cohorts were established, comprised of 28 and 34 ccRCC frozen tissue specimens, respectively. The training cohort included specimens from patients characterized as stage I (T1; n=14) and stage IV (M1; n=14). The testing cohort included specimens from patients with (n=20) and without (n=14) metastatic disease. All cases used for the testing cohort had been followed for at least 5 years if there was no tumor metastasis reported. Total RNAs of these samples were analyzed using Agilent miRNA microarray (probes for 723 human miRNAs, Sanger miRBase 10.1).

Results: (1) Differentially expressed miRNAs between metastatic ccRCCs and their non-metastatic counterparts in the training cohort were identified, using the criteria of fold change >1.5 (p value <0.05 by ANOVA). The 28 samples in the cohort were found to form distinct groups with different miRNA expression profiles using hierarchical clustering method. (2) A 5-miRNA ccRCC metastasis-specific signature has been identified using a customized computational method, which was based on logistic regression and Linear Discriminant Analysis classification, by comparing miRNA expression between metastatic and non-metastatic samples. (3) The signature has been successfully validated in the 34-sample testing cohort. With the clinical follow-up information (> 5 years if no metastasis reported), the signature had very high sensitivity (77%) and specificity (100%) when it was used to predict the tumor status of metastasis and metastatic potential. (4) This 5-miRNA signature may supplement widely used prognostic tools in RCC, such as the UCLA Integrated Staging System (UISS). The 5-miRNA signature stratified outcome within groups classified as high, intermediate or low risk by this schema.

Conclusions: We have developed a 5-miRNA expression signature to determine ccRCC metastasis and prognosis. With further validation in larger cohorts, the signature may be applied towards early prediction of metastatic potential, and may augment currently available risk stratification tools for RCC.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr LB-275.

Abstract LB-356: Characterization of microRNA expression of clear cell renal cell carcinoma by whole genome small RNA deep sequencing using human tissue cohort

Introduction: MicroRNA (miRNA) is a group of small non-coding regulating RNA and has shown altered expression in cancer. With great advantages in test specificity and capability to detect novel (unknown) miRNA and other small RNA targets, the next-generation deep sequencing technology is replacing microarray platforms, at least in the discovery phase. Clear cell renal cell carcinoma (ccRCC) is the most common type of kidney malignancies and one of the leading causes of death. Characterizing miRNA expression of ccRCC will enhance the understanding of its tumorigenesis and progression and will, therefore, lead to the development of cancer-specific molecular therapy. In this study, we analyzed miRNA expression using a human ccRCC cohort by whole genome small RNA deep sequencing. We characterized the miRNA expression in association with CCRCC and further validated the altered miRNA expression in a larger clinical cohort by RT-PCR. A group of tumor associated novel miRNAs have been discovered.

Design: (1) Deep sequencing of whole genome small RNA (17-52 nucleotides in size) in a 6-sample frozen CCRCC cohort (3 benign and 3 ccRCC samples) using Illumina system (Solexa) was performed. (2) The miRNA expression of benign kidney and ccRCC samples was quantitatively compared. (3) 8 miRNAs, which were randomly selected from the list of top 20 aberrantly expressed miRNAs detected by deep sequencing, were tested using ABI RT-PCR technology in a 38-sample ccRCC cohort (9 benign kidney and 29 different stage ccRCC samples) for validation. (4) Analysis of unknown small RNAs was performed to find tumor associated novel miRNAs.

Results: (1) Using a deep sequencing technology, we detected miRNAs and other small RNAs in frozen human samples of ccRCC cohort and successfully profiled miRNA expression in association with tumor. (2) We validated the altered expression of 8 selected miRNA targets in the 38-sample clinical ccRCC cohort using an RT-PCR method. (3) We discovered a group of novel miRNAs associated with ccRCC.

Conclusions: We performed whole genome small RNA deep sequencing of human ccRCC tissue with further RT-PCR validation in a clinical sample cohort. We have characterized miRNA expression and discovered a group of novel miRNAs in association with ccRCC.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr LB-356.

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.