Optimal control for probabilistic Boolean networks

Aberrant gene functions usually contribute to the pathology or diseases. Avoiding undesirable cellular phenotypes as many as possible is a major purpose of external control for gene regulatory networks. An interesting question is how to control a gene network subjected to the condition that the genes reach some undesirable states with minimal probability during a cell cycle. In this paper, we make use of the theory of the first passage model for discrete-time Markov decision processes to determine the optimal control for a gene intervention model. Specifically, we first use a control model for a probabilistic Boolean network to model interactions among genes and then solve an optimal control problem for maximising the probability of the first arrival time to desirable gene states. In order to illustrate the validity of our approach, examples are also displayed.

Homeobox gene IRX1 is a tumor suppressor gene in gastric carcinoma

The IRX1 tumor suppressor gene is located on 5p15.33, a cancer susceptibility locus. Loss of heterozygosity of 5p15.33 in gastric cancer was identified in our previous work. In this study, we analyzed the molecular features and function of IRX1. We found that IRX1 expression was lost or reduced in gastric cancer. However, no mutations were identified in IRX1-encoding regions. IRX1 transcription was suppressed by hypermethylation, and the expression of IRX1 mRNA was partially restored in gastric cancer cells after 5-Aza-dC treatment. Restoring IRX1 expression in SGC-7901 and NCI-N87 gastric cancer cells inhibited growth, invasion and tumorigenesis in vitro and in vivo. We identified a number of target genes by global microarray analysis after IRX1 transfection combined with real-time PCR and chromatin immunoprecipitation assay. BDKRB2, an angiogenesis-related gene, HIST2H2BE and FGF7, cell proliferation and invasion-related genes, were identified as direct IRX1 target genes. The hypermethylation of IRX1 was not only detected in primary gastric cancer tissues but also in the peripheral blood of gastric cancer patients, suggesting IRX1 could potentially serve as a biomarker for gastric cancer.

Replication study of candidate genes/loci associated with osteoporosis based on genome-wide screening

Osteoporosis is a major public health problem characterized by low bone mineral density (BMD). This replication study confirmed 38 single-nucleotide polymorphisms (SNPs) out of 139 SNPs previously reported in three recent genome-wide association studies (GWASs) in an independent US white sample. Ten SNPs achieved combined p < 3.6 x 10(-4).

INTRODUCTION

BMD is under strong genetic control. This study aims to verify the potential associations between BMD and candidate genes/loci reported by GWAS of FHS100K, Icelandic deCODE, and UK-NL.

METHODS

Eight promising (at the genome-wide significant level after Bonferroni correction) and 131 available sub-promising (at the most stringent p value, p < 5.5 x 10(-5) in the three GWASs reports) SNPs were selected. By using genotypic information from Affymetrix 500 K SNP arrays, we tested their associations with BMD in 1,000 unrelated US whites. Fisher's combined probability method was used to quantify the overall evidence of association. BMD was measured by dual energy X-ray absorptiometry.

RESULTS

Two promising SNPs, rs3762397 and rs3736228, were replicated in the current study with p < 0.05. Besides, 36 sub-promising SNPs were replicated at the same significant level. Ten SNPs achieved significant combined p < 3.6 x 10(-4) (0.05/139 SNPs, corrected for multiple testing).

CONCLUSIONS

Osteoporosis susceptibility of 38 SNPs was replicated in 1,000 unrelated US whites. This study showed promise for replication of some initial genome-wide association signals.

Smoking duration, intensity, and risk of Parkinson disease

OBJECTIVE

To evaluate the relative importance of smoking duration vs intensity in reducing the risk of Parkinson disease (PD).

METHODS

The study included 305,468 participants of the NIH-AARP Diet and Health cohort, of whom 1,662 had a PD diagnosis after 1995. We estimated odds ratios (OR) and 95% confidence intervals from multivariate logistic regression models.

RESULTS

Compared with never smokers, the multivariate ORs were 0.78 for past smokers and 0.56 for current smokers. Among past smokers, a monotonic trend toward lower PD risk was observed for all indicators of more smoking. Stratified analyses indicated that smoking duration was associated with lower PD risk within fixed intensities of smoking. For example, compared with never smokers, the ORs among past smokers who smoked >20 cigarettes/day were 0.96 for 1-9 years of smoking, 0.78 for 10-19 years, 0.64 for 20-29 years, and 0.59 for 30 years or more (p for trend = 0.001). In contrast, at fixed duration, the typical number of cigarettes smoked per day in general was not related to PD risk. Close examination of smoking behaviors in early life showed that patients with PD were less likely to be smokers at each age period, but if they smoked, they smoked similar numbers of cigarettes per day as individuals without PD.

CONCLUSIONS

This large study suggests that long-term smoking is more important than smoking intensity in the smoking-Parkinson disease relationship.

Alkali-activated complex binders from class C fly ash and Ca-containing admixtures

Processes that maximize utilization of industrial solid wastes are greatly needed. Sodium hydroxide and sodium silicate solution were used to create alkali-activated complex binders (AACBs) from class C fly ash (CFA) and other Ca-containing admixtures including Portland cement (PC), flue gas desulfurization gypsum (FGDG), and water treatment residual (WTR). Specimens made only from CFA (CFA100), or the same fly ash mixed with 40 wt% PC (CFA60-PC40), with 10 wt% FGDG (CFA90-FGDG10), or with 10 wt% WTR (CFA90-WTR10) had better mechanical performance compared to binders using other mix ratios. The maximum compressive strength of specimens reached 80.0 MPa. Geopolymeric gel, sodium polysilicate zeolite, and hydrated products coexist when AACB reactions occur. Ca from CFA, PC, and WTR precipitated as Ca(OH)(2), bonded in geopolymers to obtain charge balance, or reacted with dissolved silicate and aluminate species to form calcium silicate hydrate (C-S-H) gel. However, Ca from FGDG probably reacted with dissolved silicate and aluminate species to form ettringite. Utilization of CFA and Ca-containing admixtures in AACB is feasible. These binders may be widely utilized in various applications such as in building materials and for solidification/stabilization of other wastes, thus making the wastes more environmentally benign.

Quantitation of thyroid-stimulating hormone receptor mRNA with real-time PCR for early diagnosis of papillary thyroid microcarcinoma

Recently, the value of thyroid-stimulating hormone receptor(TSHR) mRNA as a molecular marker in diagnosis of thyroid cancer has been greatly explored. However, its role in detecting thyroid microcarcinoma has never been reported. In this study, we aim to investigate the value of TSHR mRNA in diagnosis of papillary thyroid microcarcinoma(PTMC). To do that, TSHR mRNA levels were measured by real time PCR in 30 healthy subjects and 72 patients (benign thyroid nodules, n=38; PTMC, n=34). TSHR mRNA levels were then compared with cancer volume in surgical specimen. We found that TSHR mRNA levels in PTMC were significantly higher than benign thyroid nodules(P<0.01). At a cutoff value of 0.71 ng/microg total RNA, the TSHR mRNA correctly classified 77.8% of patients preoperatively (sensitivity= 76.5%; specificity= 79.4%). Comparatively, it performed better in larger PTMC of 0.5-1.0 cm than <0.5 cm(sensitivity, 83.4% vs 72.4%; specificity, 88.5% vs 74.1%). Combining TSHR mRNA and ultra sound examination correctly detect 97.1% of PTMC and could spared surgery in 86.8% of patients with benign thyroid nodules. Thus, TSHR mRNA measured with real time PCR enhances the preoperative detection of PTMC in patients with thyroid nodules, which dramatically reduces unnecessary surgeries.

KEYWORDS

thyroid-stimulating hormone receptor, papillary thyroid microcarcinoma, diagnosis.

A Phase I/II Clinical Trial of Accelerated Partial Breast Irradiation Using External Beam and Image-Guidance in Early-Stage Breast Cancer Patients Treated with Breast Conservative Surgery

Purpose: To evaluate the early therapeutic outcome of accelerated partial breast irradiation(APBI) in low-risk breast cancer patients treated with breast conservative surgery(BCS) in a Chinese population, to analyze the intra-fractional and residual error with image-guidance.Material and methods: Eligible patients were age ≥18 years, unicentric Stage I invasive carcinoma or ductal carcinoma in situ(DCIS), treated with BCS with margin&gt;2mm. Sixteen patients were enrolled between June 2008 and April 2009, with median age 53 ys (46-71). Clinical target volume(CTV) is defined by surgical cavities plus 1.5cm margin, another 1cm is expanded to form the planning target volume(PTV), with edition to no closer than 5 mm to the skin surface and no deeper than the anterior chest wall. Three-dimensional treatment plannings with field in field technique were generated with dose of 38.5Gy/10F, bid with interval≥6 hours. Two online cone beam CTs (CBCT) was acquired for each fraction, using Elekta Synergy, X- Ray Imaging system. One is after setup with skin-markers and the other at the end of fraction. Three different registrations: bony structure, grey and grey with manual adjustment(gmanual) were compared. The clip box included: whole breast, ipsilateral lung and part of the vertebras. The registration results of each fraction were recorded. The mean shifts and standard deviation (SD) were calculated on the CBCT pre and post-treatment.Results: The ratio of APBI PTV/whole breast PTV was 25%-40% (median 29.3%). 6MV photon with median fields of 4(3-6) was used. Grade I skin toxicity was found in all the 16 patients after 15-20(median 17) days of treatment, grade II skin reaction occured in 2 patients.The setup errors detected by the initial CBCT are 7mm in lateral(X), 10mm in longitudinal(Y) and 7mm in vertical directions(Z).Table 1 Setup errors detected by the differences between pre-treatment CBCT with skin marker and planning CT  grey  gmanual  x (cm)y(cm)z(cm)x (cm)y(cm)z(cm)Mean-0.010.14-0.1 0.15-0.13SD0.260.370.290.280.370.28system error0.210.320.230.210.310.23random error0.180.190.180.180.230.2margin0.650.930.700.650.940.72 The bony algorithm showed statistical difference with grey or gmanual algorithms (p&lt;0.05). Shift was applied when the registration result by gmanual was &gt;3mm in any directions. The residual error and intra-fraction error was then analyzed after on-line shift and the post-fraction CBCT, which resulted in 6.9mm(X)l, 6.4mm(Y)and 7.3mm (Y) directions, see Table 2.Table 2 The summary of residual errors and intra-fraction errors after shift alignment x (cm)y (cm)z (cm)mean0.010.00-0.07SD0.260.290.29system error0.210.200.23random error0.230.200.22margin0.690.640.73 Conclusion: APBI with 3-D conformal external beam and image guidance is a feasible technique. Grey registration with manual adjustment is recommended for clinical application. The initial set-up error data confirmed the safety of 1cm margin from CTV to PTV. With online shift of any error above 3mm, the combination of residual error and intra-fraction error is 6.9mm, 6.4mm and 7.3mm in X, Y and Z directions, which might provide potential for margin reduction with image guidance.

Citation Information: Cancer Res 2009;69(24 Suppl):Abstract nr 4111.

Impact of IL17B on Endothelial Cells and Angiogenesis

Introduction:Tumour angiogenesis plays a vital role in cancer development and spread. In the current study, IL17B was found to be unregulated in endothelial cells in response to Hepatocyte Growth Factor (HGF). IL17B shares structural similarities to IL17A, which has been previously proposed to promote angiogenesis and tumourgenicity, though currently the role of this cytokine in cancer or angiogenesis is largely unknown.Methods:HECV gene expression in response to HGF treatment was examined over a wide range of genes using micro array analysis to detect differential gene expression over the U133+2 chip. Recombinant human IL17B (rhIL17B) was subsequently used to treat human HECV endothelial cells over a range of concentrations. The impact of rhIL17B on HECV cell motility and angiogenic potential was assessed using Matrigel migration/wounding and tubule formation.Results:Micro array analysis detected a significant increase in IL17B expression in response to 4 hour treatment of HECV human endothelial cells with 40ng/ml HGF (p &lt; 0.05 vs HGF untreated HECV cells). rhIL17B negatively influenced HECV tubule formation at the higher concentrations with substantial reduction in tubule formation being seen following treatment with 250ng/ml rhIL17B. Higher concentrations of rhIL17B were also seen to reduce the capacity of HECV cells to migrate in a scratch wounding assay and significant differences in migrated distance were observed following 75 minute incubation (P &lt; 0.05 vs control untreatment group).Conclusions:Micro array analysis suggests that IL17B gene expression in the HECV human endothelial cell line can be upregulated in response to treatment with HGF. Subsequently high levels of rhIL17B were seen to negatively impact on the tubule formation and migratory capacity of this cell line. Together this data suggests that IL17B is unlikely to play a key role in the pro-angiogenic response initiated through HGF signalling but at higher concentrations may itself be able to negatively impact the angiogenic potential of the HECV endothelial cell line.

Citation Information: Cancer Res 2009;69(24 Suppl):Abstract nr 2157.

Adiposity indicators and dementia over 32 years in Sweden

BACKGROUND

High midlife and late-life adiposity may increase risk for dementia. Late-life decrease in body mass index (BMI) or body weight within several years of a dementia diagnosis has also been reported. Differences in study designs and analyses may provide different pictures of this relationship.

METHODS

Thirty-two years of longitudinal body weight, BMI, waist circumference, and waist-to-hip ratio (WHR) data, from the Prospective Population Study of Women in Sweden, were related to dementia. A representative sample of 1,462 nondemented women was followed from 1968 at ages 38-60 years, and subsequently in 1974, 1980, 1992, and 2000, using neuropsychiatric, anthropometric, clinical, and other measurements. Cox proportional hazards regression models estimated incident dementia risk by baseline factors. Logistic regression models including measures at each examination were related to dementia among surviving participants 32 years later.

RESULTS

While Cox models showed no association between baseline anthropometric factors and dementia risk, logistic models showed that a midlife WHR greater than 0.80 increased risk for dementia approximately twofold (odds ratio 2.22, 95% confidence interval 1.00-4.94, p = 0.049) among surviving participants. Evidence for reverse causality was observed for body weight, BMI, and waist circumference in years preceding dementia diagnosis.

CONCLUSIONS

Among survivors to age 70, high midlife waist-to-hip ratio may increase odds of dementia. Traditional Cox models do not evidence this relationship. Changing anthropometric parameters in years preceding dementia onset indicate the dynamic nature of this seemingly simple relationship. There are midlife and late-life implications for dementia prevention, and analytical considerations related to identifying risk factors for dementia.

Role of shear stress on nitrite and NOS protein content in different size conduit arteries of swine

AIM

Inherent fundamental difference exists among arteries of different sizes. The purpose of this study was to evaluate the relation between regional difference of wall shear stress (WSS) in various sizes arteries and contents of nitrite and NO synthase (NOS) isoforms.

METHODS

Five different conduit arteries in a wide range of diameter (1-8 mm) were examined in the hind limbs of 13 pigs. Blood flow rate and outer diameter were measured in vivo to determine WSS. Arterial tissues were harvested for the measurement of nitrite and NOS protein contents. The concentration of nitrite, a product of NO synthesis, was determined by high-performance liquid chromatography method. Western blot analysis was used to assess the protein contents of endothelial NOS (eNOS), inducible NOS (iNOS) and neuronal NOS (nNOS).

RESULTS

Our data show that WSS increases with a decrease in artery diameter. Nitrite level increases with increasing WSS and hence decreases with artery diameter. The eNOS protein contents decrease with an increase in diameter. No significant difference for iNOS and nNOS protein contents was found with different artery diameter. A significant positive correlation between tissue nitrite and eNOS protein contents was also observed. Finally, the WSS-normalized eNOS is not significantly different in various size vessels.

CONCLUSION

Regional difference in blood flow has no effect on iNOS and nNOS protein contents in these conduit arteries. Regional difference in eNOS expression and nitrite contents may be related to the WSS-induced NO by the endothelium under normal physiological conditions.

Resistive Switching in Ge0.3Se0.7 Films by Means of Copper Ion Migration

Cu/Ge0.3Se0.7/Pt cells were prepared and bipolar resistive switching in Ge0.3Se0.7 films by means of copper ion migration was examined. The cell was switched from the high to the low resistance state at about -50mV, and it was switched back to the high resistance state at about 100mV. The resistance ratio between the high and the low state was up to 200. Up to approximately 104 switching cycles were achieved. Pulse measurements showed that the two resistance states were tuneable by varying the applied voltage and the pulse length. Therefore, it is possible to store more than one bit per cell. The current density is independent of the electrode diameter, indicating that the cell can be scaled down to the range of nanometers. Due to the low switching voltages, non-destructive read out operation, high storage density, and scalability, such cells are promising for future memory applications.

Relationship between a family history of malignancy and the incidence of laryngeal carcinoma in the Liaoning province of China

OBJECTIVE

The purpose of this study was to determine the contribution of family history of malignancy to the incidence of laryngeal squamous cell carcinoma.

DESIGN

We performed a retrospective review of classified statistics from the detailed information of cases and matched controls.

SETTING

First Hospital of China Medical University in the Liaoning province of China, between October 2005 and November 2007.

PARTICIPANTS

A total of 288 previously untreated patients with laryngeal cancer and 296 control subjects with non-malignant diseases were analysed by use of a hospital-based case-control study.

MAIN OUTCOME MEASURES

Incidence rates and family history of malignancy.

RESULTS

Single-factor logistic regression analysis indicated that the odds ratio value of a family history of malignancy was 2.0 (95% confidence interval: 1.3-3.2). Multiple logistic regression analysis confirmed this result, with an odds ratio value of 2.3 (95% confidence interval: 1.2-4.5). There was significant association between a family history of malignancy and the development of laryngeal squamous cell carcinoma.

CONCLUSIONS

A family history of malignancy plays an important role in and is an independent risk factor for the incidence of laryngeal carcinoma.

Identification of a novel mutation in a Chinese family with X-linked ocular albinism

PURPOSE

The purpose of the study was to evaluate the GPR143 gene (G-protein coupled receptor 143) in a Chinese three-generation family with OA1, including four carriers and a proband with clinical features of X-linked ocular albinism.

METHODS

The proband underwent a detailed ophthalmologic evaluation. Blood samples of family members were obtained and genomic DNA isolated. Mutational analysis by SSCP and direct sequencing of the GPR143 gene was used to screen all nine exons including the intron/exon junctions. The novel mutation c.943G>T (p.G315X) found in the study was confirmed by DHPLC to exclude the possibility of polymorphism.

RESULTS

Ophthalmic features of the proband were characteristic of X-linked ocular albinism. The authors identified a novel nonsense mutation p.G315X on exon 8 that was not found in 100 non-albinism subjects by DHPLC. This novel mutation in the GPR143 gene is predicted to subject to nonsense mediated decay.

CONCLUSIONS

The novel mutation p.G315X in the OA1 gene was identified in a Chinese family with ocular albinism, which is predicted to generate a premature stop codon. These findings extend the mutational spectrum of GPR143 gene and will be useful for gene diagnosis and genetic counseling in Chinese OA1 patients.

Effect of metronomic use of zoledronic acid (ZOL) on antitumor and antiosteoclastic effects in breast cancer patients with bone metastasis

e14603

Background: Zoledronic acid (ZOL) can reduce the risk of skeletal-related events (SREs) and may have direct and indirect antitumor effects, which have been shown in animal models, pilot clinical studies as well as in recent phase III randomized trials. However, the pharmacokinetics of the drug in breast cancer patients remains to be elucidated and optimized. The purpose of this randomized study was to compare the effects of ZOL on osteoclasts and angiogenesis between a weekly low-dose versus a conventional dosage. Methods: Sixty breast cancer patients with bone metastases were recruited in this randomized phase II clinical study. The participants either received ZOL 1mg IV weekly for 4 doses or a single dose of ZOL 4mg IV. No other antitumor treatments were administered. During the first month after initial infusion of ZOL, serial blood samples were collected on day 1, 15 and 29 measuring markers for bone resorption (NTx), angiogenesis (VEGF), and tumor burden (CEA and CA15–3). Results: Compared to a single-dose administration, weekly low dose of ZOL resulted in a greater reduction in serum levels of VEGF and NTx, with a significant trend over time during one month observation. There were no statistically significant differences in circulating levels of CEA and CA15–3 between the two dosing regimens. Patients who received metronomic ZOL had a longer median time to disease progression (TTP) (7.0 months, 95%CI, 6.1–7.9 months) than those who had a single dose of ZOL (2.8 months, 95%CI, 0–5.7 months; p=0.076). Conclusions: The metronomic use of low-dose ZOL 1 mg appeared to be more effective than the conventional regimen in the long-lasting reduction of VEGF and NTx, and in prolonging TTP. This dosing schedule should be further assessed in phase III trials as we demonstrated that ZOL 1mg has greater antitumor properties in our study.

No significant financial relationships to disclose.