Rule-based multi-scale simulation for drug effect pathway analysis

Background

Biological systems are robust and complex to maintain stable phenotypes under various conditions. In these systems, drugs reported the limited efficacy and unexpected side-effects. To remedy this situation, many pharmaceutical laboratories have begun to research combination drugs and some of them have shown successful clinical results. Complementary action of multiple compounds could increase efficacy as well as reduce side-effects through pharmacological interactions. However, experimental approach requires vast cost of preclinical experiments and tests as the number of possible combinations of compound dosages increases exponentially. Computer model-based experiments have been emerging as one of the most promising solutions to cope with such complexity. Though there have been many efforts to model specific molecular pathways using qualitative and quantitative formalisms, they suffer from unexpected results caused by distant interactions beyond their localized models.

Results

In this work, we propose a rule-based multi-scale modelling platform. We have tested this platform with Type 2 diabetes (T2D) model, which involves the malfunction of numerous organs such as pancreas, circulation system, liver, and adipocyte. We have extracted T2D-related 190 rules by manual curation from literature, pathway databases and converting from different types of existing models. We have simulated twenty-two T2D drugs. The results of our simulation show drug effect pathways of T2D drugs and whether combination drugs have efficacy or not and how combination drugs work on the multi-scale model.

Conclusions

We believe that our simulation would help to understand drug mechanism for the drug development and provide a new way to effectively apply existing drugs for new target. It also would give insight for identifying effective combination drugs.

Global analysis of phosphorylation networks in humans

Phosphorylation-mediated signaling plays a crucial role in nearly every aspect of cellular physiology. A recent study based on protein microarray experiments identified a large number of kinase-substrate relationships (KSRs), and built a comprehensive and reliable phosphorylation network in humans. Analysis of this network, in conjunction with additional resources, revealed several key features. First, comparison of the human and yeast phosphorylation networks uncovered an evolutionarily conserved signaling backbone dominated by kinase-to-kinase relationships. Second, although most of the KSRs themselves are not conserved, the functions enriched in the substrates for a given kinase are often conserved. Third, the prevalence of kinase-transcription factor regulatory modules suggests that phosphorylation and transcriptional regulatory networks are inherently wired together to form integrated regulatory circuits. Overall, the phosphorylation networks described in this work promise to offer new insights into the properties of kinase signaling pathways, at both the global and the protein levels. This article is part of a Special Issue entitled: Computational Proteomics, Systems Biology & Clinical Implications. Guest Editor: Yudong Cai.

Construction of human activity-based phosphorylation networks

The landscape of human phosphorylation networks has not been systematically explored, representing vast, unchartered territories within cellular signaling networks. Although a large number of in vivo phosphorylated residues have been identified by mass spectrometry (MS)-based approaches, assigning the upstream kinases to these residues requires biochemical analysis of kinase-substrate relationships (KSRs). Here, we developed a new strategy, called CEASAR, based on functional protein microarrays and bioinformatics to experimentally identify substrates for 289 unique kinases, resulting in 3656 high-quality KSRs. We then generated consensus phosphorylation motifs for each of the kinases and integrated this information, along with information about in vivo phosphorylation sites determined by MS, to construct a high-resolution map of phosphorylation networks that connects 230 kinases to 2591 in vivo phosphorylation sites in 652 substrates. The value of this data set is demonstrated through the discovery of a new role for PKA downstream of Btk (Bruton's tyrosine kinase) during B-cell receptor signaling. Overall, these studies provide global insights into kinase-mediated signaling pathways and promise to advance our understanding of cellular signaling processes in humans.

Insight into the sharing of medical images: physician, other health care providers, and staff experience in a variety of medical settings

BACKGROUND

Scant knowledge exists describing health care providers' and staffs' experiences sharing imaging studies. Additional research is needed to determine the extent to which imaging studies are shared in diverse health care settings, and the extent to which provider or practice characteristics are associated with barriers to viewing external imaging studies on portable media.

OBJECTIVE

This analysis uses qualitative data to 1) examine how providers and their staff accessed outside medical imaging studies, 2) examine whether use or the desire to use imaging studies conducted at outside facilities varied by provider specialty or location (urban, suburban, and small town) and 3) delineate difficulties experienced by providers or staff as they attempted to view and use imaging studies available on portable media.

METHODS

Semi-structured interviews were conducted with 85 health care providers and medical facility staff from urban, suburban, and small town medical practices in North Carolina and Virginia. The interviews were audio recorded, transcribed, then systematically analyzed using ATLAS.ti.

RESULTS

Physicians at family and pediatric medicine practices rely primarily on written reports for medical studies other than X-rays; and thus do not report difficulties accessing outside imaging studies. Subspecialists in urban, suburban, and small towns view imaging studies through internal communication systems, internet portals, or portable media. Many subspecialists and their staff report experiencing difficulty and time delays in accessing and using imaging studies on portable media.

CONCLUSION

Subspecialists have distinct needs for viewing imaging studies that are not shared by typical primary care providers. As development and implementation of technical strategies to share medical records continue, this variation in need and use should be noted. The sharing and viewing of medical imaging studies on portable media is often inefficient and fails to meet the needs of many subspeciality physicians, and can lead to repeated imaging studies.

Construction and analysis of an integrated regulatory network derived from high-throughput sequencing data

We present a network framework for analyzing multi-level regulation in higher eukaryotes based on systematic integration of various high-throughput datasets. The network, namely the integrated regulatory network, consists of three major types of regulation: TF→gene, TF→miRNA and miRNA→gene. We identified the target genes and target miRNAs for a set of TFs based on the ChIP-Seq binding profiles, the predicted targets of miRNAs using annotated 3′UTR sequences and conservation information. Making use of the system-wide RNA-Seq profiles, we classified transcription factors into positive and negative regulators and assigned a sign for each regulatory interaction. Other types of edges such as protein-protein interactions and potential intra-regulations between miRNAs based on the embedding of miRNAs in their host genes were further incorporated. We examined the topological structures of the network, including its hierarchical organization and motif enrichment. We found that transcription factors downstream of the hierarchy distinguish themselves by expressing more uniformly at various tissues, have more interacting partners, and are more likely to be essential. We found an over-representation of notable network motifs, including a FFL in which a miRNA cost-effectively shuts down a transcription factor and its target. We used data of C. elegans from the modENCODE project as a primary model to illustrate our framework, but further verified the results using other two data sets. As more and more genome-wide ChIP-Seq and RNA-Seq data becomes available in the near future, our methods of data integration have various potential applications.

The precise control of gene expression lies at the heart of many biological processes. In eukaryotes, the regulation is performed at multiple levels, mediated by different regulators such as transcription factors and miRNAs, each distinguished by different spatial and temporal characteristics. These regulators are further integrated to form a complex regulatory network responsible for the orchestration. The construction and analysis of such networks is essential for understanding the general design principles. Recent advances in high-throughput techniques like ChIP-Seq and RNA-Seq provide an opportunity by offering a huge amount of binding and expression data. We present a general framework to combine these types of data into an integrated network and perform various topological analyses, including its hierarchical organization and motif enrichment. We find that the integrated network possesses an intrinsic hierarchical organization and is enriched in several network motifs that include both transcription factors and miRNAs. We further demonstrate that the framework can be easily applied to other species like human and mouse. As more and more genome-wide ChIP-Seq and RNA-Seq data are going to be generated in the near future, our methods of data integration have various potential applications.

The anti-tumour activity of allogeneic cytokine-induced killer cells in patients who relapse after allogeneic transplant for haematological malignancies

We performed a Phase I/II clinical trial to study the feasibility, toxicity and efficacy of allogeneic cytokine-induced killer (CIK) cell expansion, and treatment for patients with haematological malignancies who relapsed after allogeneic haemopoietic SCT (allo-HSCT). Allogeneic CIK cells were successfully generated for a total of 24 patients, including those from patients' own leukapheresis products in 5 patients who had no access to further donor cells. The median CD3(+) T-cell expansion was 9.33 (1.3-38.97) fold, and CD3(+)CD56(+) natural killer (NK)-like T-cell expansion was 27.77 (2.59-438.93) fold. A total of 55 infusions were done for 16 patients who had either failed or progressed after initial response to various individualized chemotherapy regimens and donor lymphocyte infusion (DLI), at doses ranging from 10 to 200 million CD3(+) cells/kg. Response attributable to CIK cell infusion was observed in five patients. These included two with ALL, two with Hodgkin's disease (HD) and one with AML, and two of whom had a response sustained for more than 2 years. Acute GVHD occurred in three and was easily treatable. This study provides some evidence suggestive of the efficacy of allogeneic CIK cells even after failure of DLI in some cases.

Multi-agent modeling of the South Korean avian influenza epidemic

Background

Several highly pathogenic avian influenza (AI) outbreaks have been reported over the past decade. South Korea recently faced AI outbreaks whose economic impact was estimated to be 6.3 billion dollars, equivalent to nearly 50% of the profit generated by the poultry-related industries in 2008. In addition, AI is threatening to cause a human pandemic of potentially devastating proportions. Several studies show that a stochastic simulation model can be used to plan an efficient containment strategy on an emerging influenza. Efficient control of AI outbreaks based on such simulation studies could be an important strategy in minimizing its adverse economic and public health impacts.

Methods

We constructed a spatio-temporal multi-agent model of chickens and ducks in poultry farms in South Korea. The spatial domain, comprised of 76 (37.5 km × 37.5 km) unit squares, approximated the size and scale of South Korea. In this spatial domain, we introduced 3,039 poultry flocks (corresponding to 2,231 flocks of chickens and 808 flocks of ducks) whose spatial distribution was proportional to the number of birds in each province. The model parameterizes the properties and dynamic behaviors of birds in poultry farms and quarantine plans and included infection probability, incubation period, interactions among birds, and quarantine region.

Results

We conducted sensitivity analysis for the different parameters in the model. Our study shows that the quarantine plan with well-chosen values of parameters is critical for minimize loss of poultry flocks in an AI outbreak. Specifically, the aggressive culling plan of infected poultry farms over 18.75 km radius range is unlikely to be effective, resulting in higher fractions of unnecessarily culled poultry flocks and the weak culling plan is also unlikely to be effective, resulting in higher fractions of infected poultry flocks.

Conclusions

Our results show that a prepared response with targeted quarantine protocols would have a high probability of containing the disease. The containment plan with an aggressive culling plan is not necessarily efficient, causing a higher fraction of unnecessarily culled poultry farms. Instead, it is necessary to balance culling with other important factors involved in AI spreading. Better estimations for the containment of AI spreading with this model offer the potential to reduce the loss of poultry and minimize economic impact on the poultry industry.

The biology and prognostic value of lymphatic vessel density (LD) and lymphatic invasion (LI) in regression in melanoma

9017

Background: Regression in melanoma is characterized by increased vascularity, lymphocytic infiltrate and fibroplasia in the papillary dermis, accompanied by the absence (complete regression, CoR) or presence (partial regression, PaR) of melanoma cells in the epidermis. The prognostic value of regression is controversial. We noticed that LD and LI were increased in the areas of regression (AR) or areas with brisk lymphocytic infiltration (AB). Our goal was to clarify the prognostic value of regression in melanoma. Methods: Dual immunohistochemical staining was done using antibodies to podoplanin (lymphatic vessels) and S100 (melanoma cells) on paraffin tissues from 321 patients with vertical growth phase (VGP) primary melanomas who had 10 years or more of follow-up. LD in AR (both CoR and PaR) was compared with that of normal dermis adjacent and distant, as well as LD in the AB. LI in these areas was also scored. Unadjusted and adjusted hazard rates were obtained from univariate and multivariate Cox models for time to melanoma-specific death using established melanoma prognostic factors. Results: 116 patients (36%) had regression: 75 CoR (23%) and 41 PaR (13%). LD significantly decreased stepwise from CoR (mean ± se, 23.7 ± 2.7) to PaR (15.5 ± 1.1), adjacent normal dermis (7.3 ± 0.28) and distant normal dermis (5.4±0.31) and it was significantly elevated in the AB (18.5±0.78). Melanomas with CoR had the highest percentage of LI in both AR and AB. In addition, the percentage of LI in AB was highest for men and for those with VGP tumor infiltrating lymphocytes (TILs). Both high LD in AR and more LI in AB were associated with poor prognosis (p=0.004 and p=0.002, respectively). Six factors were significant in the final multivariate model: LI in AB (HR=2.3), LD in AR (HR=1.04), thickness (HR=1.44), axial (HR=7.7), ulceration (HR=2.5) and no VGP TILs (HR=2.8). Conclusions: AR and AB were associated with increased LD and higher incidence of LI in primary melanomas. LD and LI in AR or AB are independent prognostic factors. Our data suggest that the effects of regression on prognosis are mediated at least in part through lymphangiogenesis and LI.

No significant financial relationships to disclose.

The relationship between adherence to adjuvant hormonal therapy and survival among low-income, insured women with primary breast cancer

e11522

Background: Clinical trials and meta-analyses show that adjuvant hormonal therapy for hormone receptor positive breast cancer significantly decreases risk of death. We explored the relationship between adherence to adjuvant hormonal therapy and death in a low-income, Medicaid-insured population. Methods: Using a Medicaid claims-tumor registry linked database and National Death Index data (NDI), we evaluated adherence to adjuvant hormonal therapy [defined as >80% Medication Possession Ratio (MPR)] and mean six-year overall and cancer-specific survival by local versus regional stage for all female breast cancer diagnosed in years 2000–2002, in North Carolina. The Kaplan-Meier and Cox Proportional Hazards models were used to determine the role of adherence on cancer-specific survival. Models were adjusted for age, race, Charlson comorbidity score, number of prescription medications, type of surgery, use of radiation therapy, prior chemotherapy, hormone receptor status (positive or unknown). Results: The final sample consisted of 1,042 cases [ages range 29–97 years (mean 65.9 years; 56% Caucasian; mean Charlson comorbidity score 4.1 (SD 2.9); 680 local and 362 regional stage], of which 732 filled a prescription for adjuvant hormonal therapy within the year after breast cancer diagnosis. Filling a prescription for adjuvant hormonal therapy, versus not, was not significantly associated with cancer-related death: HR 1.04 (95% CI 0.66 - 1.64) overall; HR 0.75 (95% CI 0.39 - 1.43) for local stage and HR 1.01 (95% CI 0.51 - 2.00) for regional stage. However, adherence in the highest quartile (MPR>95) is associated with an increase in mortality risk. Conclusions: In this low income insured group of breast cancer patients, no statistically significant association was found between death rates and use of adjuvant hormonal therapy. However, an unexpected association between very high adherence and increase in mortality was found. This may reflect methodological limitations of claims data involving bias and unidentified patient risk. More research is needed to explore reasons for higher mortality among low-income women with high medication adherence.

[Table: see text]

Prognostic risk group classification for patients (pts.) with platinum-refractory metastatic urothelial cancer (UC) treated with second-line chemotherapy

5078

Background: Second-line chemotherapy in pts. with platinum-refractory metastatic UC is associated with low objective response rates and short progression-free and overall survival. Prognostic risk groups in this setting have not been reported. Methods: We studied 151 pts. with platinum-refractory metastatic UC treated with second-line vinflunine (VFL) (Vaughn, GU Cancer Symposium. 2008). Using progression at 6 months as the primary endpoint, baseline patient characteristics were examined in univariate and multivariate analyses. Multivariate logistic regression was used to identify independent predictors of progression at 6 months, and the variable selection result was validated by nonparametric bootstrap. Risk scores were generated from summing the relative importance of the factors identified on multivariate analysis. Patients were classified into risk groups and compared. Results: Of the 151 pts., 80% were male, 54% were aged > 65 years, and 68% had Karnofsky performance status (KPS) > 90%. 115 pts. (76%) progressed or died by 6 months after initiating VFL. The factors associated with an increased odds ratio (OR) for disease progression at 6 months were presence of visceral metastases (OR 8.08; p < 0.001; 2 points), KPS < 90% (OR 6.63; p = 0.002; 2 points), and age < 65 years (OR 3.53; p = 0.008; 1 point). Only 41% of the low-risk group (score 0–1) progressed by 6 months compared to 74% of the intermediate-risk group (score 2) and 91% of the high-risk group (score 3–5). Compared to the low-risk group, the intermediate-risk group had OR for disease progression at 6 months of 4.01 (p = 0.006) and the high-risk group had OR of 15.5 (p < 0.001). Conclusions: We identified risk factors and developed a scoring system that classifies pts. with platinum-refractory UC treated with second-line chemotherapy into risk groups based upon probability of disease progression at 6 months. Similar to the first-line setting, the presence of visceral metastases and decreased KPS predict a worse prognosis. This system should be validated in other independent populations.

[Table: see text]

Ki67 as a prognostic biomarker for patients with vertical growth phase (VGP) melanomas

9043

Background: In VGP melanomas proliferation is reflected in dermal mitotic figures (“mitogenic” VGP) and/or tumor cell nests larger than any epidermal nest. An alternative to mitotic rate (MR) to characterize cell proliferation is the expression of Ki67 protein. Since Ki67 is expressed in all phases of the cell cycle except G0, it is potentially a more robust biomarker for proliferation and prognosis than mitoses. Methods: To test the hypothesis that Ki67 would replace MR as a prognostic factor, we did a retrospective cohort study of 432 patients with Stage I/II primary VGP melanomas who had at least 10 years of follow up. Tissue sections were stained using the monoclonal antibody MIB-1 to Ki67 and the % of positive melanoma cells were evaluated by two readers. ROC curves for Ki67 and MR were computed. Predicted probabilities (PP) of 10-year melanoma-specific death were computed from 3 multivariate logistic regression models, one for each biomarker (Models 1 and 2) and one with both (Model 3), controlling for established melanoma prognostic factors (thickness, gender, anatomic site, ulceration, regression and tumor infiltrating lymphocytes), and compared. Cross-validation was used to assess differences between using Ki67 and using MR including the differences in PP, Brier scores and the misclassification rates. A decision curve analysis was done to assess the clinical net benefit of the two. Results: The areas under the ROC curve (AUCs) for Ki67 and MR, both continuous factors, were 0.69 and 0.79, respectively. In the multivariate analysis, Ki67 expression was significant in Model 1 (OR=1.03, 95% CI: 1.01–1.05), mitotic rate was not significant in Model 2 (1.05, 0.99–1.1), and only Ki67 was significant in Model 3 (1.03, 1.01–1.05). The AUCs for the three models were 0.84, 0.84, and 0.85, respectively. Based on cross-validation, there was no difference between the two biomarkers in PP, Brier scores, or misclassification rates. The decision cost analysis demonstrated the same net benefit for the two. Conclusions: A prospective study needs to be conducted to confirm that Ki67 and MR are equivalent.

No significant financial relationships to disclose.

The prognostic significance of lymphatic invasion in primary melanoma

9050

Background: Lymphatic invasion (LI) is an under-observed phenomenon in primary malignancies that can be better detected by immunostaining and that may associate with prognosis. In this study we sought to test the hypothesis that LI was associated with melanoma-specific survival (MSS) and was an independent prognostic factor. Methods: This study included 277 patients with stage I/II melanomas in vertical growth phase (VGP) who had at least 10 years of follow up. The log-rank test was used to test the study hypothesis - 72 melanoma-specific deaths were needed for 80% power to detect an odds ratio of 2.1. Paraffin sections were stained with antibodies to podoplanin (lymphatic vessels) and S-100 (melanoma cells) to identify LI. Univariate and multivariate Cox models were used to evaluate the prognostic significance of LI. An independent cohort of 106 similar patients was used for validation of the 10-year MSS rates. Results: LI was observed in 44.5% (95% CI: 38.6% - 50.4%) of the melanomas and its presence was significantly associated with thickness, mitotic rate, gender, age, and ulceration (U). The Kaplan-Meier survival curves for those with and without LI were significantly different (log-rank test p=0.022). The final multivariate model for time to MSD identified 4 independent prognostic factors: thickness (HR=1.5, p<0.001), U (HR=2.2 p=0.013), site (HR=3.9, p<0.001) and LI (HR=1.9, p=0.015). These factors were used to define a prognostic tree with 5 risk groups defined by melanomas that were thin (≤1.0mm) with no LI or U; thin with LI but no U; 1–3mm with no U; 1–3mm with U; and >3mm. Respectively, MSS rates were 100%, 88.6%, 77%, 48% and 42%. In the validation set, observed 10-year MSS rates in each risk group were not significantly different from those predicted from the survival curves for the tree-based risk groups. Conclusions: LI is an independent prognostic factor for MSS. Among patients with thin melanomas without U the 10-year MSS was lower for those patients with LI (89%, 95% CI=78% - 99%; n=41) compared to those without (100%, n=78). LI is an important prognostic factor that needs further validation in a population of patients from the sentinel node biopsy era.

No significant financial relationships to disclose.

Comparison of iridium implant boost versus electron boost as a component of breast conservation treatment for early-stage breast carcinoma

Abstract #5144

Background: Breast conservation treatment includes lumpectomy followed by definitive radiation therapy, with radiation delivered to the whole breast followed by tumor bed boost. Currently, the boost is typically delivered by electron beams, but was previously delivered by iridium-192 implants. With re-emergence of implant radiotherapy techniques in current practice, long-term outcomes of both boost techniques are important.&#x2028; Methods: From 1977 to 1983, 141 patients with early-stage breast cancer were treated with iridium-192 boost after whole breast radiation. These patients were matched 1:1 to 141 patients who received electron boost from 1980 to 1990. Most implant patients were treated before widespread electron availability. Matching criteria included age at diagnosis, final pathologic margin status, pathologic tumor stage, and pathologic nodal stage. All patients had AJCC Stage I or II invasive breast carcinoma, had surgical excision of the primary tumor, and underwent definitive radiation to at least 60 grays. Chemotherapy was administered to 30 implant patients and 41 electron patients (p=0.014), and hormonal treatment to 3 implant patients and 12 electron patients (p=0.032). These systemic treatment variations were expected due to treatment era differences. Median follow-up was 16.7 years for implant patients (range 0.7-28.5) and 12.6 years for electron patients (range 1.4-25.4) (p&lt;0.001).&#x2028; Results: Electron boost patients were more likely to have excellent/good cosmesis versus fair/poor cosmesis than implant boost patients. At 1-year follow-up, this was significant (p=0.014). This trend continued, with odds ratio of having excellent/good cosmesis versus fair/poor cosmesis in implant patients compared to electron patients being 0.29 after 5 years (95% CI 0.027-1.38, p=0.114) and 0.24 after 10 years (95% CI 0.005-1.93, p=0.266).&#x2028; Incidence of all complications evaluated did not differ between the two groups (all p≥0.07). Incidence of breast fibrosis was 3% per year in implant patients and 4% per year in electron patients (p=0.17). In total, breast fibrosis developed in 41% of implant patients and 16% of electron patients. Incidence of infection was 14% per year in the implant group and 6% per year in the electron group (p=0.09). In total, infection developed in 7% of implant patients and 9% of electron patients. Incidence of rib fracture was 2% per year in both groups (p=0.8). Incidence of cardiopulmonary complications was 4% per year in implant patients and 3% per year in electron patients (p=0.7). Incidence of non-cardiac vascular complications was 4% per year in both groups (p=0.1). Incidence of neuropathy was 4% per year in implant patients and 1% per year in electron patients (p=0.07).&#x2028; Conclusions: Patients treated with electron boost were more likely than those treated with implant boost to have excellent/good cosmesis, though this observation did not reach statistical significance at 5- and 10-year follow-up. Complication rates did not differ significantly between the groups with long-term follow-up.

Citation Information: Cancer Res 2009;69(2 Suppl):Abstract nr 5144.

CASCADE: a novel quasi all paths-based network analysis algorithm for clustering biological interactions

BACKGROUND

Quantitative characterization of the topological characteristics of protein-protein interaction (PPI) networks can enable the elucidation of biological functional modules. Here, we present a novel clustering methodology for PPI networks wherein the biological and topological influence of each protein on other proteins is modeled using the probability distribution that the series of interactions necessary to link a pair of distant proteins in the network occur within a time constant (the occurrence probability).

RESULTS

CASCADE selects representative nodes for each cluster and iteratively refines clusters based on a combination of the occurrence probability and graph topology between every protein pair. The CASCADE approach is compared to nine competing approaches. The clusters obtained by each technique are compared for enrichment of biological function. CASCADE generates larger clusters and the clusters identified have p-values for biological function that are approximately 1000-fold better than the other methods on the yeast PPI network dataset. An important strength of CASCADE is that the percentage of proteins that are discarded to create clusters is much lower than the other approaches which have an average discard rate of 45% on the yeast protein-protein interaction network.

CONCLUSION

CASCADE is effective at detecting biologically relevant clusters of interactions.

Semantic integration to identify overlapping functional modules in protein interaction networks

Background

The systematic analysis of protein-protein interactions can enable a better understanding of cellular organization, processes and functions. Functional modules can be identified from the protein interaction networks derived from experimental data sets. However, these analyses are challenging because of the presence of unreliable interactions and the complex connectivity of the network. The integration of protein-protein interactions with the data from other sources can be leveraged for improving the effectiveness of functional module detection algorithms.

Results

We have developed novel metrics, called semantic similarity and semantic interactivity, which use Gene Ontology (GO) annotations to measure the reliability of protein-protein interactions. The protein interaction networks can be converted into a weighted graph representation by assigning the reliability values to each interaction as a weight. We presented a flow-based modularization algorithm to efficiently identify overlapping modules in the weighted interaction networks. The experimental results show that the semantic similarity and semantic interactivity of interacting pairs were positively correlated with functional co-occurrence. The effectiveness of the algorithm for identifying modules was evaluated using functional categories from the MIPS database. We demonstrated that our algorithm had higher accuracy compared to other competing approaches.

Conclusion

The integration of protein interaction networks with GO annotation data and the capability of detecting overlapping modules substantially improve the accuracy of module identification.

Low-dose dexamethasone and thalidomide with higher frequency zoledronic acid (dtZ) for newly diagnosed multiple myeloma

18506

Background: Although dexamethasone (Dex), thalidomide (Thal) and zoledronic acid (Zol) have frequently been combined for the treatment of multiple myeloma (MM), the ideal dosing schedule is unknown. We previously reported that lower doses of Dex and Thal can be effectively combined with high-frequency dosing of Zol (Haematologica 2005). Methods: This “dtZ” regimen - which comprises weekly Dex 20 mg OM for 4 days, Thal 50 mg ON, and 3-weekly Zol 4 mg - resulted in an impressive response rate (RR) of 61.6% and near complete remission (nCR)/complete remission (CR) rate of 7.7% in 26 patients with relapsed/refractory MM. Results: In this present study, we treated 22 newly diagnosed MM patients with “dtZ” and report an even more impressive RR of 100.0% and nCR/CR rate of 20–35%. The median time to response was 1.8 months and median time to maximum response was 2.2 months. The median time to progression (TTP) has not been achieved yet. As expected, low-dose Dex/Thal resulted in lower (18.1%) grade 3 or 4 toxicities. These were all infections; which lead to further dose-reduction of Dex. There were no thromboembolic events, despite the fact that aspirin was not routinely given. Of particular interest, 3- weekly Zol was not associated with any significant decrease in renal function, and none of our patients developed osteonecrosis of the jaw (ONJ). In fact, at the time of writing of this abstract, more than 1,000 doses of Zol had been administered in a 3-weekly fashion to these as well as other patients, and only 1 patient developed ONJ. This patient who had already received greater than 20 doses of Zol healed uneventfully after receiving appropriate outpatient dental treatment, and subsequently received another 8 doses of Zol with no recurrence of ONJ. Conclusion: In conclusion, the Zol-based “dtZ” regimen is potentially a highly-effective and safe frontline regimen for MM. Using Zol every 3 weeks with lower doses of Dex and Thal does not appear to increase the rate or severity of nephrotoxicity or ONJ. Although we do not know exactly why every patient responded to “dtZ”, we speculate that this could be due to a critical balance that has been achieved between the anti-MM, anti-osteoclastic and immunostimulatory effects of the individual drugs of the combination.

No significant financial relationships to disclose.

A novel functional module detection algorithm for protein-protein interaction networks

Background

The sparse connectivity of protein-protein interaction data sets makes identification of functional modules challenging. The purpose of this study is to critically evaluate a novel clustering technique for clustering and detecting functional modules in protein-protein interaction networks, termed STM.

Results

STM selects representative proteins for each cluster and iteratively refines clusters based on a combination of the signal transduced and graph topology. STM is found to be effective at detecting clusters with a diverse range of interaction structures that are significant on measures of biological relevance. The STM approach is compared to six competing approaches including the maximum clique, quasi-clique, minimum cut, betweeness cut and Markov Clustering (MCL) algorithms. The clusters obtained by each technique are compared for enrichment of biological function. STM generates larger clusters and the clusters identified have p-values that are approximately 125-fold better than the other methods on biological function. An important strength of STM is that the percentage of proteins that are discarded to create clusters is much lower than the other approaches.

Conclusion

STM outperforms competing approaches and is capable of effectively detecting both densely and sparsely connected, biologically relevant functional modules with fewer discards.

Comorbidity and outcomes in elderly women treated with breast-conserving therapy

599

Background: Breast cancer incidence increases with age and is a major cause of morbidity and mortality among elderly women. Co-morbidities are often considered in treatment management of elderly women. Methods: Between 1979 and 2002, 238 women age 70 or older with unilateral stage I or II invasive breast cancer underwent conventional breast conservation treatment with radiation. The age distribution was 122 women (51%) age 70–74 years, 71 women (30%) age 75–79 years, and 45 women (19%) age ≥80 years. Surgical axillary staging was performed in 73% (n= 173) of patients, of which 73% (n=126) were N0, and 27% (n=47) were N1. Co-morbidities were scored using the Charlson Comorbidity Index and Cumulative Illness Rating Scale (CIRS). Median follow-up was 6.2 years. Results: On analysis by age groups, the 10-year cancer specific outcomes were not significantly different (see Table ). However, distant metastases were the most common site of first failure in all age groups: 9% for age 70–74; 12% for age 75–79 and 11% for age >/= 80. Second malignancies were the second most common cause of first failure in all age groups. Death from intercurrent disease was significantly more likely in the older age groups. In this cohort, moderate and severe co-morbidities were not significantly more common in the older age groups, and CIRS score did not correlate with overall survival. Conclusions: Breast conserving surgery and definitive breast irradiation provide excellent outcomes in appropriately selected elderly women. Older age itself is not a contraindication to breast conserving therapy. Women of any age with lower co-morbidity indices should be offered standard treatment.

[Table: see text]

No significant financial relationships to disclose.

Addition of bortezomib to thalidomide, dexamethasone and zoledronic acid (VTD-Z regimen) significantly improves complete remission rates in patients with relapsed/refractory multiple myeloma

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Background: We previously treated 26 patients with relapsed/refractory multiple myeloma (MM) with thalidomide (Thal), dexamethasone (Dex) and zoledronic acid (Zol); dtZ regimen; and demonstrated an overall response rate of 75.0%. However, the rate immunofixation (IF)-negative complete remissions (CR) was only 7.7%. Recently, the bortezomib (Velcade) has been shown to be effective against MM. In this study, we added bortezomib (Vel) to dtZ (VTD-Z regimen) in a subgroup of patients to determine whether the CR rate can be improved. Methods: A non-randomized, single-arm study was conducted. Consecutive patients (n = 14) who either failed to achieve a partial response (PR) after 3 cycles; or CR after 9 cycles of dtZ were treated with 2 to 11 three-weekly cycles of VTD-Z; comprising: Vel 1.3 mg/m2 on days 1, 4, 8 and 11; Thal 50 mg ON; Dex 20 mg OM on days 1 to 4, 8 to 11, 15 to 18; and Zol 4 mg on day 1. The primary study objective was to determine the maximal response rates (RR). The end-point of the study was maximum response, graded by Bladè’s criteria. Results: Fourteen patients (3 males, 11 females; median age 63.3 years) were studied. Complex karyotypes, including 5 patients with deletion of chromosome 13 (del(13)), were present in 11 patients at diagnosis. The overall RR was 92.9% (13 out of 14), of which 42.9% (6) achieved CR (p < 0.001, chi-squared test). In addition, 21.4% (3) achieved near-CR (nCR), and 28.6% (4) achieved PR. There were no minimal responders (MR) and 1 (7.1%) non-responder (NR). Two patients who achieved CR had del(13). Painful grade 3 peripheral neuropathy was observed in 2 (14.3%) patients. Grade 1 and 2 peripheral neuropathy was observed in another 4 (25.0%) of patients; transient grade 3 thrombocytopenia was observed in 5 (35.7%) patients; and papular rashes were observed in 3 (21.4%) patients. The single NR was the only death that occurred during the period of study. Conclusions: Our study demonstrates that the VTD-Z regimen is exceptionally effective and safe in patients with relapsed/refractory MM. Addition of Vel to dtZ significantly increases the CR rate from 7.7% to 42.9%. These data suggest that combination of these 4 drugs may be at least additive, if not, even synergistic.

No significant financial relationships to disclose.

Successful treatment of primary granulocytic sarcoma by non-myeloablative stem cell transplant

Pre-leukemic granulocytic sarcoma (GS) may pose an initial diagnostic problem and its therapeutic approach has never been formally established. To our knowledge, non-myeloablative stem cell transplantation has been reported in cases of leukemic GS, but not in primary GS. We report a case of primary GS with extensive and aggressive presenting features and successfully treated with intensive chemotherapy followed by non-myeloablative allogeneic stem cell transplant. This resulted in complete remission with minimal complications. Our case demonstrates the potential of graft-vs.-tumour effect in the treatment of GS and suggests that non-myeloablative allogeneic stem cell transplant may be a feasible therapeutic approach for primary GS.

Therapeutic leukapheresis in hyperleukocytic leukaemias--the experience of a tertiary institution in Singapore

INTRODUCTION

Hyperleukocytic leukaemias are associated with early mortality due to respiratory or neurological complications. They result from endothelial damage secondary to leukostasis. Leukapheresis, which aims to lower the white blood cell (WBC) count, has been used in certain patients to reduce the threat from leukostasis. However, there are very few published clinical investigations on the most appropriate use of leukapheresis in hyperleukocytosis.

MATERIALS AND METHODS

We performed a retrospective analysis of 14 patients with hyperleukocytic leukaemia who presented to our institution and underwent therapeutic leukapheresis. We compare their clinical and biological characteristics and investigate the impact of leukapheresis on early mortality and long-term prognosis.

RESULTS

The median presenting WBC count was 439 x 10(3)/mm(3). Although patients with acute myeloid leukaemia (AML) had the lowest median presenting WBC counts, they constituted the largest group of patients with symptomatic hyperleukocytosis. Leukapheresis was highly effective, with the mean absolute and percentage reduction in WBC after each cycle being 126 x 10(3)/mm(3) and 31.9% respectively. Four patients with AML died within 2 weeks of presentation despite prompt and effective leukapheresis.

CONCLUSION

The interaction between the leukaemic cells and the vascular environment, a mechanism that none of the current therapies directly address, is probably more important in causing leukostasis than the absolute cell count itself.

Force transmission, compliance, and viscoelasticity are altered in the alpha7-integrin-null mouse diaphragm

Alpha7beta1 integrin is a transmembrane structural and receptor protein of skeletal muscles, and the absence of alpha7-integrin causes muscular dystrophy. We hypothesized that the absence of alpha7-integrin alters compliance and viscoelasticity and disrupts the mechanical coupling between passive transverse and axial contractile elements in the diaphragm. In vivo the diaphragm is loaded with pressure, and therefore axial and transverse length-tension relationships are important in assessing its function. We determined diaphragm passive length-tension relationships and the viscoelastic properties of its muscle in 1-month-old alpha7-integrin-null mice and age-matched controls. Furthermore, we measured the isometric contractile properties of the diaphragm from mutant and normal mice in the absence and presence of passive force applied in the transverse direction to fibers in 1-month-old and 5-month-old mutant mice. We found that compared with controls, the diaphragm direction of alpha7-integrin-null mutants showed 1) a significant decrease in muscle extensibility in 1-year-old mice, whereas muscle extensibility increased in the 1-month-old mice; 2) altered muscle viscoelasticity in the transverse direction of the muscle fibers of 1-month-old mice; 3) a significant increase in force-generating capacity in the diaphragms of 1-month-old mice, whereas in 5-month-old mice muscle contractility was depressed; and 4) significant reductions in mechanical coupling between longitudinal and transverse properties of the muscle fibers of 1-month-old mice. These findings suggest that alpha7-integrin serves an important mechanical function in the diaphragm by contributing to passive compliance, viscoelasticity, and modulation of its muscle contractile properties.

In vitro biological characteristics of human cord blood-derived megakaryocytes

INTRODUCTION

Umbilical cord blood (CB) has been used as an alternative source for haematopoietic stem cell transplantation (HSCT) in recent years. However, delayed platelet recovery is frequently associated with CB HSCT. Megakaryocytes (Mk) are the specialised precursors of platelets and they are among the rarest haemopoietic cell types. Despite the rapid expansion of our knowledge of megakaryopoiesis in recent years, many questions, such as the molecular regulatory mechanisms in Mk differentiation and maturation, platelet formation and release, remain unanswered in CB-derived megakaryopoiesis. Variations can be seen from the literature by individual investigators using different approaches for Mk-specific differentiation and maturation induction. The development of in vitro culture methods to obtain sufficient numbers of Mks from readily available haematopoietic stem cells is of value for both basic research and clinical applications.

MATERIALS AND METHODS

The CD34+ cells from cord blood samples were cultured in serum-free medium with haematopoietic growth factors (GFs), such as IL-3, stem cell factor (SCF), and thrombopoietin (Tpo). The differentiation of Mk was monitored using Mk- and platelet-specific monoclonal antibodies and flow cytometric analysis. The morphology of the cultured cells was studied by both light and electronic microscopy (LM and EM). The involvement of the human Notch gene family members was studied by real time-polymerase chain reaction (RT-PCR). Maturation of the cultured Mks was studied using flow cytometric analysis for both platelet-specific surface markers and enodomitosis. Platelet activation was assessed in the cytoplasmic fragments harvested from the cultures.

RESULTS

Specific Mk differentiation of >70% resulted from a 2-step culture approach using IL-3, SCF and Tpo for 7 days followed by Tpo only for another 14 days. RT-PCR showed high-level expression of both Notch-1 and its ligand, Jagged-1, in the cultured Mks. Limited levels of polyploidy (>4N, endomitosis, EnM) were observed in the cultured Mks. The results also showed that the cytoplasmic fragments from the cultures responded to platelet activation reagents, including ADP and collagen, marked by upregulation of platelet-specific activation markers, such as CD62P (P-selectin) and PAC-1 (gpalphaIIbbeta3).

CONCLUSION

The methods used in this study are specific for differentiation of Mk from CB CD34+ cell, which can partially mature and produce functional platelets in vitro. This approach for human Mk differentiation could be further optimised and may be adapted on larger scales for clinical purposes.

Successful treatment of idiopathic hypereosinophilic syndrome with imatinib mesylate: a case report

Patients with idiopathic hypereosinophilic syndrome (HES) show persistent hypereosinophilia of unknown etiology that is associated with end-organ damage. Different treatments, including the use of corticosteroids and cytotoxics, have been investigated for HES with modest success. We describe a patient with HES who had significant end-organ damage from hypereosinophilia and remained refractory to conventional therapy. Therapy with imatinib mesylate, a selective tyrosine kinase inhibitor that is highly effective in treating patients with BCR-ABL-positive chronic myeloid leukemia, was tried with the patient. The result was impressive, with hematologic remission achieved after 12 days of administration. Our finding concurs with recent reports that imatinib mesylate may be a promising agent in the treatment of some cases of HES.

Fitness versus longevity in age-structured population dynamics

We examine the dynamics of an age-structured population model in which the life expectancy of an offspring may be mutated with respect to that of the parent. While the total population of the system always reaches a steady state, the fitness and age characteristics exhibit counter-intuitive behavior as a function of the mutational bias. By analytical and numerical study of the underlying rate equations, we show that if deleterious mutations are favored, the average fitness of the population reaches a steady state, while the average population age is a decreasing function of the average fitness. When advantageous mutations are favored, the average population fitness grows linearly with time t, while the average age is independent of the average fitness. For no mutational bias, the average fitness grows as t2/3.

Out-of-pocket medical spending for care of chronic conditions

We examined out-of-pocket medical spending by persons with and without chronic conditions using data from the 1996 Medical Expenditure Panel Survey (MEPS). Our results show that mean out-of-pocket spending increased with the number of chronic conditions. The level of this spending also varied by age and insurance coverage, among other characteristics. Out-of-pocket spending for prescription drugs was substantial for both elderly and nonelderly persons with chronic conditions. As policymakers continue to use cost sharing and design of benefit packages to contain health spending, it is important to consider the impact of these policies on persons with chronic conditions and their families.

Dissolution in a field

We study the dissolution of a solid by continuous injection of reactive "acid" particles at a single point, with the reactive particles undergoing biased diffusion in the dissolved region. When acid encounters the substrate material, both an acid particle and a unit of the material disappear. We find that the lengths of the dissolved cavity parallel and perpendicular to the bias grow as t(2/(d+1)) and t(1/(d+1)), respectively, in d dimensions, while the number of reactive particles within the cavity grows as t(2/(d+1)). We also obtain the exact density profile of the reactive particles and the relation between this profile and the motion of the dissolution boundary. The extension to variable acid strength is also discussed.

Does growth retardation indicate suboptimal clinical care in children with chronic renal disease and those undergoing dialysis?

Growth failure is an important problem for children with end-stage renal disease (ESRD). Patients receiving replacement therapy for longstanding renal failure since childhood are likely to report dissatisfaction with certain aspects of their lives, especially with final adult height. Additionally, recent data suggest that growth failure in children with ESRD is associated with adverse clinical outcomes, including more frequent hospitalizations, and increased mortality. Although poor growth is unlikely to be the cause of this increased morbidity, growth failure may be a marker for a group of patients at high risk of adverse events. In this review, the authors describe the prevalence of growth retardation in children in the US with chronic renal disease, and present recent data on morbidity associated with growth failure. After reviewing published reports documenting available strategies to optimize growth, the authors conclude that despite vigilance and aggressive clinical management, a subset of children with long-term renal insufficiency and ESRD may still have poor linear growth. A discussion of "optimal care" leads one to consider evidence of current variability in the management of growth retardation in ESRD, and the strengths and limitations of developing practice guidelines to optimize growth in this population.

Comparison of risk adjusters for medicaid-enrolled children with and without chronic health conditions

OBJECTIVE

Several capitation payment systems have been developed and implemented recently by public and private insurers as well as by individual managed care organizations. Many pediatricians have expressed concern that methods for establishing capitation rates may not adequately account for the higher expected expenditures for children with chronic health conditions. In this study, we evaluate a demographic- and 4 diagnosis-based models, paying particular attention to their performance for children with chronic health conditions.

METHODS

We selected children 18 years of age and under who were enrolled in the Maryland Medicaid Program in 1995 and 1996. We defined the population of children with chronic health conditions using ICD-9 codes. Individual and group-level analyses were utilized to measure the ability of the different risk adjustment models to predict expenditures in 1996 based upon information available in 1995.

RESULTS

All 4 diagnosis-based models significantly outperformed the demographic model for children overall and for children with chronic health conditions. Differences between diagnosis-based models were small, especially as the size of test populations increased.

CONCLUSIONS

Risk adjustment methods that account directly for health status promise to reduce incentives to exclude children with chronic illnesses from managed care plans and to provide a foundation for more appropriate payments to pediatricians who care for these children.

Relation between pediatric experience and treatment recommendations for children and adolescents with kidney failure

CONTEXT

Children and adolescent patients with renal failure are frequently cared for by adult subspecialists. While peritoneal dialysis is used in less than 17% of adults with kidney failure, it is the preferred dialysis treatment for children. National data show that 45% of children receiving dialysis are treated with peritoneal dialysis and pediatric nephrologists report its use in 65% of patients receiving dialysis. Whether differences in peritoneal dialysis use among children are due to the pediatric experience of the clinician has not been examined.

OBJECTIVE

To assess whether the pediatric experience of nephrologists directly affects treatment recommendations for children with kidney failure.

DESIGN

Cross-sectional survey using 10 case vignettes per survey based on random combinations of 8 patient characteristics (age, sex, race, distance from facility, cause of renal failure, family structure, education, and compliance).

SETTING AND PARTICIPANTS

National random sample of office-, hospital-, and academic medical center-based adult and pediatric nephrologists, stratified by geographic region and conducted June to November 1999. Of 519 eligible physicians, 316 (61%) responded, including 191 adult and 125 pediatric nephrologists.

MAIN OUTCOME MEASURE

Treatment recommendations for peritoneal dialysis vs hemodialysis, compared based on nephrologists' pediatric experience.

RESULTS

After controlling for patient characteristics, pediatric nephrologists were 60% more likely than adult nephrologists to recommend peritoneal dialysis for identical patients (odds ratio, 1.61; 95% confidence interval, 1.35-1.92). This was true regardless of dialysis training, years in practice, practice setting, geography, or patient characteristics.

CONCLUSIONS

Our data indicate that pediatric specialization of clinicians influences treatment recommendations for children and adolescents with end-stage renal disease. Referring children to adult subspecialists may lead to differences in treatment choices and processes of care.

Infiltration through porous media

We study the kinetics of infiltration in which contaminant particles, which are suspended in a flowing carrier fluid, penetrate a porous medium. The progress of the "invader" particles is impeded by their trapping on active "defender" sites which are on the surfaces of the medium. As the defenders are used up, the invader penetrates further and ultimately breaks through. We study this process in the regime where the particles are much smaller than the pores so that the permeability change due to trapping is negligible. We develop a family of microscopic models of increasing realism to determine the propagation velocity of the invasion front, as well as the shapes of the invader and defender profiles. The predictions of our model agree qualitatively with experimental results on breakthrough times and the time dependence of the invader concentration at the output. Our results also provide practical guidelines for improving the design of deep bed filters in which infiltration is the primary separation mechanism.