P1-06-09: Patient-Specific Integrative Pathway Analysis Using PARADIGM Identifies Key Activities in I-SPY 1 Breast Cancer Patients (CALGB 150007/150012; ACRIN 6657)

Background: A major challenge in interpreting high-throughput multianalyte genomic data sets such as those produced by the ISPY clinical trials is data integration and interpretation within the context of biologically relevant pathways. To address this need, the data analysis tool PARADIGM (PAthway Recognition Algorithm using Data Integration on Genomic Models) was developed to infer the activities of genetic pathways by integrating any number of functional genomic data sets for a given patient sample into a pathway activity profile.

Methods: We used PARADIGM to integrate gene expression (Agilent 44K) and DNA copy number data (AFFY 22K and 330K MIP) from 133 ISPY-1 patients into pathway component activity levels for approximately 1400 curated signal transduction, transcriptional and metabolic pathways superimposed onto a single non-redundant ‘SuperPathway'. These pathway activities then become the substrate for statistical analyses to identify pathways characterizing different breast cancer subtypes, as well as those associated with recurrence and response to neoadjuvant chemotherapy within breast cancer subgroups. To identify subtype-specific pathway activities, we used ANOVA for initial feature filtering followed by Tukey analysis with Benjamini Hochberg multiple testing correction. For other binary outcome comparisons we used Mann-Whitney (2-sample Wilcoxon) analysis. PARADIGM results were corroborated with pathway enrichment analysis and filtered for significance.

Results: In agreement with breast cancer cell line and other prior studies, basal-like and triple negative cancers are dominated by upregulation of the FOXM1 and MYC/Max subnetworks and downregulation of the FOXA1/ER signal transduction pathway, the converse of the activity pattern seen in luminal breast cancers. These and other subtype associations pass stringent multiple testing corrected significance tests. Though an association study of recurrence over the entire patient cohort mostly yields pathways characteristic of basal-like tumors, alternative pathway associations emerge when subtypes are analyzed individually for outcome and significance tests are relaxed to include features that pass un-corrected Wilcoxon significance tests and also generate highly significant pathway enrichment scores. Subtype-specific drivers of recurrence and chemo-resistance supported by this level of evidence include ALK1/2 (TGFB-BMP) and p53 effector signaling for basals and Syndecan-1 and c-MYC for luminals. Chemo-sensitivity pathways, assessed by association with pCR and RCB1, appear to be subtype-specific as well, with HDAC class 1 signaling, LRP6-Wnt, and IRE1alpha chaperones dominating basal-like cancers and c-MYB activity dominating Her2+ cancers, whereas chemo-sensitivity of HR+Her2- cancers though rare appears to be driven by the DNA damage axis (BRCA/BARD1). Conclusion: These and other similar analyses suggest that patients with TN or basal-like disease might benefit from the addition of ALK1 pathway inhibitors to treatment, whereas high risk HR+ patients might benefit from Syndecan-1 inhibitors. C-MYC/MAX inhibitors might benefit all high risk patients.

Citation Information: Cancer Res 2011;71(24 Suppl):Abstract nr P1-06-09.

Gemcitabine versus gemcitabine plus dalteparin thromboprophylaxis in pancreatic cancer

BACKGROUND

Annualised figures show an up to 7-fold higher incidence of vascular thromboembolism (VTE) in patients with advanced pancreatic cancer (APC) compared to other common malignancies. Concurrent VTE has been shown to confer a worse overall prognosis in APC.

METHODS

One hundred and twenty three APC patients were randomised to receive either gemcitabine 1000 mg/m(2) or the same with weight-adjusted dalteparin (WAD) for 12 weeks. Primary end-point was the reduction of all-type VTE during the study period. NCT00462852, ISRCTN: 76464767.

FINDINGS

The incidence of all-type VTE during the WAD treatment period (<100 days from randomisation) was reduced from 23% to 3.4% (p = 0.002), with a risk ratio (RR)of 0.145, 95% confidence interval (CI) (0.035-0.612) and an 85% risk reduction. All-type VTE throughout the whole follow-up period was reduced from 28% to 12% (p = 0.039), RR = 0.419, 95% CI (0.187-0.935) and a 58% risk reduction. Lethal VTE <100 days was seen only in the control arm, 8.3% compared to 0% (p = 0.057), RR = 0.092, 95% CI (0.005-1.635).

INTERPRETATION

Weight adjusted dalteparin used as primary prophylaxis for 12 weeks is safe and produces a highly significant reduction of all-type VTE during the prophylaxis period. The benefit is maintained after dalteparin withdrawal although decreases with time.

Genome-wide copy number analysis of circulating tumor cells from patients (pts) with metastatic breast cancer (MBC)

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Background: We developed a novel approach to isolate circulating tumor cells (CTCs) via immunomagnetic enrichment followed by fluorescence activated cell sorting (IE/FACS) and examined copy number alterations in these cells.

Methods: Magnetic beads coated with EpCAM mAb were added to blood to enrich for tumor cells. Enriched samples were then subjected to FACS analysis using differentially labeled mAbs to distinguish tumor cells (EpCAM+) from leukocytes (CD45+) during sorting. DNA from isolated tumor cells was subjected to whole genome amplification (WGA) and copy number analysis via array comparative genomic hybridization (aCGH). The assay was evaluated in CTCs from 5 MBC pts with matched archival primary tumors and later extended to an additional 176 MBC pts, 97 of which were successfully profiled.

Results: Comparison of CTCs with matched archival primary tumors confirmed shared lineage with notable divergence. In addition, serial testing of CTCs confirmed reproducibility, and indicated genomic change over time. Genomic profiling of CTCs from 102 MBC pts revealed a wide range of copy number alterations including those previously reported in breast cancer. Comparison with a published aCGH dataset of primary breast tumors revealed similar frequencies of recurrent genomic copy number aberrations.

Conclusions: It is feasible to isolate CTCs away from hematopoietic cells with high purity via IE/FACS and profile them via aCGH analysis following WGA. Our approach may be utilized to explore genomic events involved in cancer progression and to monitor therapeutic efficacy of targeted therapies in clinical trials in a relatively non-invasive manner. This work was supported by grants from the CALGB, BCRF, TBCRC (Avon, Komen), EDRN and U54.

Neoadjuvant chemoradiotherapy for resectable oesophageal and gastro-oesophageal junction cancer--do we need another randomised trial?

AIMS

The optimal neoadjuvant therapy option for locally advanced oesophageal cancer remains elusive. Neoadjuvant chemoradiotherapy (CRT) is the preferred modality of choice in the USA. In contrast, neoadjuvant chemotherapy is commonly used in the UK. We provide a comprehensive overview of the available evidence for defining the ideal neoadjuvant treatment algorithm.

MATERIALS AND METHODS

The PubMed database combined with American Society of Clinical Oncology and American Society for Therapeutic Radiology and Oncology websites were searched online to identify randomised studies and published meta-analyses that have compared these modalities compared with surgery alone. In particular, we searched for randomised trials that may have directly compared outcomes after neoadjuvant CRT or chemotherapy.

RESULTS

We identified 17 published randomised studies of neoadjuvant CRT (n = 9) and chemotherapy (n = 8) compared with surgery alone and one prospective series that compared the above modalities against each other. Studies evaluating CRT have reported pathological complete response rates of 15-40% and no increase in postoperative mortality was observed, except in one study that used a hypofractionated radiation schedule. Two randomised studies showed significant survival benefit and the remaining (n = 7) were negative, but showed a trend towards improved survival. Furthermore, at least four meta-analyses have shown improved survival in favour of CRT extending up to an absolute benefit of 13% at 2 years. In comparison, five studies of neoadjuvant chemotherapy showed no survival difference and two of the remaining studies that showed significant benefit included gastric adenocarcinomas and used peri-operative chemotherapy. All the above studies have shown uniformly poor pathological complete response rates of less than 10 percent. Moreover, three meta-analyses were negative, but two showed up to 7% absolute survival benefit at 2 years in favour of chemotherapy. The trial comparing the above modalities showed a trend towards improved survival in favour of CRT, but closed early due to poor recruitment.

CONCLUSION

Data from the above studies are potentially conflicting and inconclusive for defining the optimal neoadjuvant treatment schedule. In our opinion, the above question can only be answered within the context of a randomised control trial. We have included a proposal for a trial design for direct comparison of these modalities.

Identification of gene copy number and whole-genome methylation changes associated with lethal metastatic castration-resistant prostate cancer (CRPC)

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Background: Metastatic CRPC undergoes significant genomic evolution compared to primary, localized disease. Multiple genetic mechanisms contribute to this evolution including changes in gene copy number as well as and changes in CpG island methylation. In this study, copy number and methylation status of metastatic CRPC tissue obtained at autopsy were assessed by high-resolution array comparative genomic hybridization (aCGH) and whole genome methylation microarray profiling.

Methods: Array CGH was performed on DNA isolated from metastatic CRPC samples obtained from the University of Michigan Rapid Autopsy Program, using the Agilent Human Genome 244K CGH Microarray. A total of 15 samples comprising 7 metastatic liver implants and 8 soft tissue metastases were analyzed with DNA Analytics 4.0 software. Expression of genes identified as commonly amplified or deleted was assessed in a confirmatory fashion using existing Agilent 4×44 Expression Array data. The Illumina Infinium HumanMethylation27 BeadChip was used to determine whole genome methylation status.

Results: A total of 79 amplified and 419 deleted genes common to >66% of samples were identified. There was significant correlation (p<0.05) of gene copy number to the mRNA level for 9 of the amplified and 76 of the deleted genes, including amplification/overexpression of AR and deletion/underexpression of the tumor suppressors PTEN and RB. While copy number was normal for the androgen synthesis genes CYP17A1, HSD17B3, HSD17B4, and HSD3B2, methylation analysis indicates their upregulation in the majority of samples, suggesting an alternative mechanism of intratumoral hormone production. There was promoter hypermethylation and gene deletion of RB1 in >85% of samples, suggesting that inactivation of this tumor suppressor through multiple pathways is critical to tumor cell survival.

Conclusions: This is the first known study examining both gene copy number and whole genome CpG island methylation status in metastatic CRPC. Integration of this data allows for identification of specific genes or pathways that confer a selective growth advantage to prostate cancer cells harboring those changes.

No significant financial relationships to disclose.

Batch Process for Microwave Sintering of Si3N4

A method for sintering silicon nitride using microwave energy at 2.45 GHz is described. Sintering takes place in air, in times of between 30 and 120 minutes and has been scaled up to give isothermal conditions over a batch size of 150 mm diameter by 200 mm in height and weighs approximately 1.0 kg. Additions of 5% alumina and 5% yttria result in a sintered product density of approximately 97% of theoretical, with a density variation better than:±0.5% throughout the batch.

It has been estimated that a load of 7.0 kg can be conventionally sintered using a 12 hour cycle and an energy consumption of 19.7 kWh/kg. In contrast with microwave energy, a batch of 540 g can be sintered in 120 minutes with an energy consumption of approximately 3.1 kWh/kg. This results in a possible energy savings of up to 78% for microwave heating.

Fabrication of Hydroxyapatite Ceramics by Microwave Processing

Various hydroxyapatite (HAp) ceramics were fabricated by microwave processing. By carefully selecting the starting material and controlling the processing conditions, regular HAp ceramics with density up to 97% of the theoretical density, porous HAp ceramics with porosity up to 76%, and fully densified transparent HAp ceramics were obtained by using a 2.45 GHz, 500W microwave oven. These ceramics were characterized for density, microstructure, strength, and phase composition, and the results were compared with the conventionally processed ceramics.

Low-Temperature (<300°C) Phosphate Ceramics from Reactive Aluminas

Reactive aluminas, including rapidly calcined gibbsites, offer exciting potential for forming ceramic materials at low temperatures. New x-ray amorphous aluminas will react with water at room temperatures to form compacts with 10–50 MPa tensile strengths, via viscous slurries. The cementious behavior of these materials has been examined. The results of TGA, x-ray diffraction, SEM, mechanical properties, and other characterization techniques, as applied to these systems, will be discussed.

Bacteria in bovine semen can increase sperm DNA fragmentation rates: a kinetic experimental approach

Cryopreserved straws of semen (n=228) from Holstein bulls (n=47) were examined for bacterial presence and sperm DNA fragmentation (SDF) dynamics. Commercial semen doses (representing six ejaculates per individual) were randomly selected from a bull stud in Spain. The dynamics of SDF were assessed after thawing (T0) and at 4, 24, 48, 72 and 96h of incubation at 37°C, using the commercial variant of the sperm chromatin dispersion test for Bovine (Halomax®). One group of bulls showed a bacterial presence in semen samples between 0 and 96h of incubation (n=23, group A) while the other did not (n=24, group B). Immediate post-thaw differences in SDF were not observed when both groups were compared. However, the rate of increase in SDF (rSDF) over time, considered as an estimate of the kinetic behaviour of sperm DNA survival, was significantly higher (P<0.05) in semen samples from group A (0.7% per hour) versus group B (0.05% per hour). Polymerase Chain Reaction (PCR) assay was used for DNA amplification using primers designed for specific regions of the bacterial gene that codifies for 16S rRNA. Different species within the phyla Bacteroidetes, Firmicutes, Proteobacteria, Cyanobacteria, Fusobacteria and Actinobacteria were identified. The results show that (1) SDF at baseline (T0) may not be affected by the presence of bacteria but the rSDF can increase due to bacterial growth during incubation, (2) the increase in the rSDF is characteristic of some bulls but not for others, and (3) certain bacterial strains are repeatedly found in separate ejaculates from the same bull.

New scalings in nuclear fragmentation

Fragment partitions of fragmenting hot nuclei produced in central and semiperipheral collisions have been compared in the excitation energy region 4-10 MeV per nucleon where radial collective expansion takes place. It is shown that, for a given total excitation energy per nucleon, the amount of radial collective energy fixes the mean fragment multiplicity. It is also shown that, at a given total excitation energy per nucleon, the different properties of fragment partitions are completely determined by the reduced fragment multiplicity (i.e., normalized to the source size). Freeze-out volumes seem to play a role in the scalings observed.

Outcomes of respiratory diphtheria in a tertiary referral infectious disease hospital

BACKGROUND

Diphtheria is a fatal disease and may cause serious complications if not recognized early and treated properly.

OBJECTIVES

To study the epidemiology, clinical features, complications, and outcomes in respiratory diphtheria.

MATERIALS AND METHODS

Diphtheria cases admitted in the infectious disease hospital, Beliaghata, Kolkata, India between January 2009 to January 2011 were evaluated in respect to demographic profile, immunization status, clinical features, complications, and outcomes.

RESULTS

200 diphtheria cases were studied. 150 (75%) patients had history of an adequate immunization, and 100 (50%) patients were from lower socio-economic groups. Common clinical features observed were throat pain in 148 (74%) cases and fever in 112 (56%) cases. Complications observed were myocarditis in 136 (68%) cases, neuropathy in 30 (15%) cases, and respiratory compromise in 14 (7%) cases. Death occurred in 5 (2.5%) patients.

CONCLUSIONS

diphtheria is still a public health problem in many developing countries. Strict public health measures like an increased immunization coverage, improvement of socio-economic status, easy availability of anti-diphtheritic serum (ADS), early recognition and effective treatment-all may reduce the incidence and mortality.

Ceramics by the solution-sol-gel route

The use of solution mixing followed by gelation to make ultrahomogeneous glasses and ceramics of various oxide compositions for laboratory experimentation, with first organic and later principally colloidal inorganic, precursors was developed over 30 years ago. Major technologies that use the solution-sol-gel route have been developed to make nuclear fuel pellets, ceramic fibers, thin coatings, and abrasive grain. This article reviews the early history and summarizes present research in this field, particularly new processes aimed at achieving xerogel precursors of maximum heterogeneity with respect either to composition or to structure. Such nanocomposites provide major advantages in lowering sintering temperatures, refining microstructure, and controlling morphology and final phase composition.

Characterization of casein gene complex and genetic diversity analysis in Indian goats

Milk protein polymorphism plays an important role in genetic diversity analysis, phylogenetic studies, establishing geographical diversity, conservation decision, and improving breeding goals. Milk protein polymorphism in Indian goat breeds has not been well studied; therefore, an investigation was carried out to analyze the genetic structure of the casein gene and milk protein diversity at six milk protein loci in nine Indian goat breeds/genetic groups from varied agro-climatic zones. Milk protein genotyping was carried out in 1098 individual milk samples by SDS-PAGE at alphaS1-CN (CSN1S1), beta-CN (CSN2), alphaS2-CN (CSN1S2), kappa-CN (CSN3), beta-LG, and alpha-LA loci. Indian goats exhibited alphaS1-casein A allele in higher frequency in the majority of breeds except Ganjam and local goats. The alphaS1-casein A allele frequencies varied from 0.45 to 0.77. A total of 16 casein haplotypes were observed in seven breeds and breed specific haplotypes were observed with respect to geographic region. The average number of alleles was lowest in Ganjam (1.66 +/- 0.81) and highest in Sirohi goats (2.50 +/- 1.05). Expected heterozygosity at six different loci demonstrated genetic diversity and breed fragmentation. Neighbor-Joining tree was built basing on Nei's distance. There was about 16.95% variability due to differences between breeds, indicating a strong subdivision. Principal component analysis was carried out to highlight the relationship among breeds. The variability among goat breeds was contributed by alphaS2-CN, beta-LG and alphaS1-CN. The Indian goats exhibited alphaS1-CN (CSN1S1) A allele in higher frequency in all the breeds indicating the higher casein yield in their milk.