Mapping quantitative trait loci using the MCMC procedure in SAS

The MCMC procedure in SAS (called PROC MCMC) is particularly designed for Bayesian analysis using the Markov chain Monte Carlo (MCMC) algorithm. The program is sufficiently general to handle very complicated statistical models and arbitrary prior distributions. This study introduces the SAS/MCMC procedure and demonstrates the application of the program to quantitative trait locus (QTL) mapping. A real life QTL mapping experiment in wheat female fertility trait was used as an example for the demonstration. The fertility trait phenotypes were described under three different models: (1) the Poisson model, (2) the Bernoulli model and (3) the zero-truncated Poisson model. One QTL was identified on the second chromosome. This QTL appears to control the switch of seed-producing ability of female plants but does not affect the number of seeds produced once the switch is turned on.

hSSB1 binds and protects p21 from ubiquitin-mediated degradation and positively correlates with p21 in human hepatocellular carcinomas

Downregulation of hSSB1, a single-stranded DNA-binding protein, causes increased radiosensitivity, defective checkpoint activation and genomic instability. However, the mechanisms of hSSB1 function in these responses remain to be uncovered. Here, we present evidence that hSSB1 directly binds p21 and this interaction may prevent p21 from ubiquitin-mediated degradation. Furthermore, both promotion of the G1/S transition and abrogation of the G2/M checkpoints induced by hSSB1 knockdown are partially dependent on p21. Most importantly, hSSB1 and p21 levels are positively correlated in human hepatocellular carcinomas (HCC), as determined by immunostaining. Therefore, hSSB1 may positively modulate p21 to regulate cell cycle progression and DNA damage response, implicating hSSB1 as a novel, promising therapeutic target for cancers such as HCC.

Edaravone alleviates delayed neuronal death and long-dated cognitive dysfunction of hippocampus after transient focal ischemia in Wistar rat brains

Edaravone is currently being used in acute ischemic stroke both in clinical and experimental research as a potent antioxidant. Here we explore the effects of edaravone on delayed neuronal death (DND) and long-dated cognitive dysfunction of hippocampus after cerebral ischemia-reperfusion (IR) injury and explain the underlying mechanisms and pathways. Our findings suggested that edaravone not only significantly alleviated delayed neuronal death and cognitive dysfunction of hippocampus after cerebral focal ischemia, but also markedly decreased malondialdehyde (MDA) levels. In addition, edaravone increased superoxide dismutase (SOD) levels and reduced the levels of inflammatory cytokines such as IL-1β and TNF-α expression; edaravone, also suppressed glial fibrillary acidic protein (GFAP) proliferation at days 3, 7 and 30 after reperfusion. Overall, the consensus emerging from this body of data indicated that edaravone exerts a later neuroprotective effect to hippocampus through its ability to inhibit inflammation, suppression of astrocyte activation and scavenging free radicals in stroke events.

Abstract P5-01-12: Specific Tumor Component Spectrum as a Predictor of Response to Neoadjuvant Chemotherapy in Breast Cancer

BACKGROUND: Monitoring individual tumor response to neoadjuvant chemotherapy could provide surrogate markers for oncologists to adjust therapeutics in order to minimize collateral damage from ineffective therapies. Diffuse optical spectroscopy imaging (DOSI), by increasing the wavelength range and resolution, has been employed to characterize malignant tumor and its response to neoadjuvant chemotherapy since it measures the abundance in the four major chromophores (lipid, oxy-hemoglobin, deoxy-hemoglobin and water). Through the application of a spectral analysis method, Self-Referencing Differential Spectroscopy (SRDS) analysis, which accounts for only intersubject variability, a novel optical intrinsic biomarker which is unique to cancer was revealed. By fitting the difference spectrum between tumor and normal tissues to the four component basis spectra, the residuals disclose a spectral fingerprint called specific tumor component (STC) spectrum which contains specific absorption bands which separate normal from abnormal tissue and benign from malignant tumors.

PATIENTS AND METHODS: 14 patients were enrolled in this study and all the subjects provided informed written consent according to an institution-approved protocol. Measurements were taken pre-, post-neoajuvant chemotherapy and the midpoint in the treatment. The chemotherapy regimen is 2-4 cycles of doxorubicin-cyclophosphamide (A/C), followed by 2-4 cycles of carboplatin-taxol/abraxane-avastin (nabTC). Tumor classification was confirmed by pathology reports and 8 out of 14 patients were classified as complete responders (CR); the rest as noneresponders (NR). Pre and post-treatment STC spectra were compared in different pathological responding categories. Data were analyzed by using custom software designed for Matlab. The concentrations of NIR absorbers will be calculated from a spectral model of tissue absorption by using the basis spectra. For the SRDS method, the absorption spectra will be further analyzed by using custom software (Elantest; Laboratory for Fluorescence Dynamics, Irvine, Calif, www.lfd.edu). Details of SRDS method has been described previously.

RESULTS: The shape of STC spectra for non-responders was well preserved since insusceptible tumor structure will remain basically unaffected during the chemotherapy. Whereas in the completed responders, the therapy-induced changes in tumor microvasculature, edema, and necrosis lead to a significant dissimilarity in STC spectra.

CONCLUSION: STC spectrum, as an endogenous in vivo biomarker, can predict pathological response in breast tumors treated with neoadjuvant chemotherapy.

Integrated biomarker response index for the assessment of environmental stress of the Yangtze River (Nanjing section)

In the present study, multibiomarker effects of the river water of three representative sections in Nanjing section of the Yangtze River were investigated in goldfish (Carassius auratus). The organic toxicants were extracted from the water samples using solid phase extraction. Acetylcholinesterase (AChE), glutathione-S-transferase (GST), 7-ethoxyresorufin-O-deethylase (EROD), glutathione peroxidase (GPx) and Na+/K+-ATPase activities were determined after exposure of the extracted components. The fractions of water samples from three sections (Daqiao, Sanchahe and Jiangxinzhou) altered these enzymatic activities. With the change of the extracts polarity, the levels of AChE, GST, EROD, Na+/K+-ATPase activities were different. The responses of enzymatic activities were mostly significant for those exposures of intermediate polar components (50-80% methanol extracts) and weakly polar components (ether and ether/hexane extracts). It has been shown that toxicants were mainly concentrated in these fractions in the Yangtze River (Nanjing section). With regard to response for different sections, EROD and GST activities seem to be more sensitive biomarkers. Integrated biomarker response index (IBR) were calculated and used to evaluate an integrated impact of pollutants from different sampling sections. The order of negative biological effects of the three sections was Jiangxinzhou>Sanchahe>Daqiao. The wild fish living in Nanjing section of the Yangtze River were at potential ecological risk.

Part 5. Public health and air pollution in Asia (PAPA): a combined analysis of four studies of air pollution and mortality

BACKGROUND

In recent years, Asia has experienced rapid economic growth and a deteriorating environment caused by the increasing use of fossil fuels. Although the deleterious effects of air pollution from fossil-fuel combustion have been demonstrated in many Western nations, few comparable studies have been conducted in Asia. Time-series studies of daily mortality in Asian cities can contribute important new information to the existing body of knowledge about air pollution and health. Not only can these studies verify important health effects of air pollution in local regions in Asia, they can also help determine the relevance of existing air pollution studies to mortality and morbidity for policymaking and environmental controls. In addition, the studies can help identify factors that might modify associations between air pollution and health effects in various populations and environmental conditions. Collaborative multicity studies in Asia-especially when designed, conducted, and analyzed using a common protocol-will provide more robust air pollution effect estimates for the region as well as relevant, supportable estimates of local adverse health effects needed by environmental and public-health policymakers.

SPECIFIC OBJECTIVES

The Public Health and Air Pollution in Asia (PAPA*) project, sponsored by the Health Effects Institute, consisted of four studies designed to assess the effects of air pollution on mortality in four large Asian cities, namely Bangkok, in Thailand, and Hong Kong, Shanghai, and Wuhan, in China. In the PAPA project, a Common Protocol was developed based on methods developed and tested in NMMAPS, APHEA, and time-series studies in the literature to help ensure that the four studies could be compared with each other and with previous studies by following an established protocol. The Common Protocol (found at the end of this volume) is a set of prescriptive instructions developed for the studies and used by the investigators in each city. It is flexible enough to allow for adjustments in methods to optimize the fit of health-effects models to each city's data set. It provides the basis for generating reproducible results in each city and for meta-estimates from combined data. By establishing a common methodology, factors that might influence the differences in results from previous studies can more easily be explored. Administrative support was provided to ensure that the highest quality data were used in the analysis. It is anticipated that the PAPA results will contribute to the international scientific discussion of how to conduct and interpret time-series studies of air pollution and will stimulate the development of high-quality routine systems for recording daily deaths and hospital admissions for time-series analysis.

METHODS

Mortality data were retrieved from routine databases with underlying causes of death coded using the World Health Organization (WHO) International Classification of Diseases, 9th revision or 10th revision (ICD-9, ICD-10). Air quality measurements included nitrogen dioxide (NO2), sulfur dioxide (SO2), particulate matter with aerodynamic diameter < or = 10 microm (PM10), and ozone (O3) and were obtained from several fixed-site air monitoring stations that were located throughout the metropolitan areas of the four cities and that met the standards of procedures for quality assurance and quality control carried out by local government units in each city. Using the Common Protocol, an optimized core model was established for each city to assess the effects of each of the four air pollutants on daily mortality using generalized linear modeling with adjustments for time trend, seasonality, and other time-varying covariates by means of a natural-spline smoothing function. The models were adjusted to suit local situations by correcting for influenza activity, autocorrelation, and special weather conditions. Researchers in Hong Kong, for example, used influenza activity based on frequency of respiratory mortality; researchers in Hong Kong and Shanghai used autoregressive terms for daily outcomes at lag days; and researchers in Wuhan used additional smoothing for periods with extreme weather conditions.

RESULTS AND DISCUSSION

For mortality due to all natural (nonaccidental) causes at all ages, the effects of air pollutants per 10-microg/m3 increase in concentration was found to be higher in Bangkok than in the three Chinese cities, with the exception of the effect of NO2 in Wuhan. The magnitude of the effects for cardiovascular and respiratory mortality were generally higher than for all natural mortality at all ages. In addition, the effects associated with PM10 and O3 in all natural, cardiovascular; and respiratory mortality were found to be higher in Bangkok than in the three Chinese cities. The explanation for these three findings might be related to consistently higher daily mean temperatures in Bangkok, variations in average time spent outdoors by the susceptible populations, and the fact that less air conditioning is available and used in Bangkok than in the other cities. However, when pollutant concentrations were incorporated into the excess risk estimates through the use of interquartile range (IQR), the excess risk was more comparable across the four cities. We found that the increases in effects among older age groups were greater in Bangkok than in the other three cities. After excluding data on extremely high concentrations of PM10 in Bangkok, the effect estimate associated with PM10 concentrations decreased in Bangkok (suggesting a convex relationship between risk and PM10, where risk levels off at high concentrations) instead of increasing, as it did in the other cities. This leveling off of effect estimates at high concentrations might be related to differences in vulnerability and exposure of the population to air pollution as well as to the sources of the air pollutant. IMPLICATIONS OF THE STUDY: The PAPA project is the first coordinated Asian multicity air pollution study ever published; this signifies the beginning of an era of cooperation and collaboration in Asia, with the development of a common protocol for coordination, data management, and analysis. The results of the study demonstrated that air pollution in Asia is a significant public health burden, especially given the high concentrations of pollutants and high-density populations in major cities. When compared with the effect estimates reported in the research literature of North America and Western Europe, the study's effect estimates for PM10 were generally similar and the effect estimates for gaseous pollutants were relatively higher. In Bangkok, however, a tropical city where total exposures to outdoor pollution might be higher than in most other cities, the observed effects were greater than those reported in the previous (i.e., Western) studies. In general, the results suggested that, even though social and environmental conditions across Asia might vary, it is still generally appropriate to apply to Asia the effect estimates for other health outcomes from previous studies in the West. The results also strongly support the adoption of the global air quality guidelines recently announced by WHO.

Associations between the genetic polymorphisms of MTHFR and outcomes of methotrexate treatment in rheumatoid arthritis

OBJECTIVES

To determine whether 5, 10-methylenetetrahydrofolate reductase (MTHFR) rs1801133C/T, rs1801131A/C, rs2274976A/G, rs2066462C/T genetic polymorphisms are associated with clinical response and adverse effects (AEs) of methotrexate (MTX) treatment in Chinese Han patients with rheumatoid arthritis (RA).

METHODS

One hundred and ten RA patients defined by the American College of Rheumatology (ACR) 1987 revised criteria were involved in this study. All patients were treated with low-dose MTX (10-15 mg/week) without concomitant uses of other DMARDs. Clinical response (using ACR20 criteria) and AEs were evaluated at 0, 4, 12, 16 and 24 weeks. The genotypes of MTHFR rs1801133C/T, rs1801131A/C, rs2274976A/G and rs2066462C/T were detected by real-time fluorescent quantitative PCR.

RESULTS

The allele frequency of rs1801131C in the clinical response group was higher than in the non-response group (21.0% vs. 8.1%, p<0.05), and the patients with CC or AC genotype had greater clinical response than those with AA genotype. The allele frequencies of rs1801133T and rs2274976A were higher in the group with AEs than that without AEs (56.4% vs. 37.5% and 14.9% vs. 4.2%, respectively, both p<0.05). The patients with CT or TT genotype in rs1801133 had higher risks of AEs than those with CC genotype.

CONCLUSIONS

While rs1801131A/C genetic polymorphism is associated with the clinical response, rs1801133C/T and rs2274976A/G genetic polymorphisms are associated with MTX-related AEs in the treatment of RA. This suggests individualisation is necessary to achieve optimal outcomes in MTX therapy of RA.

Dexamethasone synergizes with lenalidomide to inhibit multiple myeloma tumor growth, but reduces lenalidomide-induced immunomodulation of T and NK cell function

To determine the effect of dexamethasone on the antimyeloma effects of lenalidomide, we tested in vitro proliferation, tumor suppressor gene expression, caspase activity, cell cycling, and apoptosis levels in a series of multiple myeloma (MM) and plasma cell leukemia cell lines treated with lenalidomide and dexamethasone, alone or in combination. The effect of dexamethasone on the immunomodulatory activities of lenalidomide such as T cell and natural killer (NK) cell activation was measured via interleukin [IL]-2 production, and interferon-gamma and granzyme B production respectively. Lenalidomide inhibited proliferation in most cell lines tested, and this effect was enhanced by dexamethasone. This effect was observed in MM cells containing the high-risk cytogenetic abnormalities t(4;14), t(14;16), del17p, del13, and hypodiploidy. Mechanistically, lenalidomide plus dexamethasone synergistically induced expression of the tumor suppressor genes Egr1, Egr2, Egr3, p15, p21, and p27 in MM cell lines and MM patient cells. The combination activated caspases 3, 8, and 9; and induced cell cycle arrest and apoptosis. Lenalidomide alone increased T cell production of IL-2, and NK cell production of interferon-gamma and granzyme B. Notably, dexamethasone antagonized these immunostimulatory effects of lenalidomide in a dose-dependent manner. These data further elucidate the mechanism of action of lenalidomide and dexamethasone in MM, and suggest that use of low-dose dexamethasone with lenalidomide may retain the antiproliferative effect of lenalidomide while permitting greater immunomodulatory effects of this combination regimen.

RNAi-mediated germline knockdown of FABP4 increases body weight but does not improve the deranged nutrient metabolism of diet-induced obese mice

Objective:

To investigate the impact of reduced adipocyte fatty acid-binding protein 4 (FABP4) in control of body weight, glucose and lipid homeostasis in diet-induced obese (DIO) mice.

Methods:

We applied RNA interference (RNAi) technology to generate FABP4 germline knockdown mice to investigate their metabolic phenotype.

Results:

RNAi-mediated knockdown reduced FABP4 mRNA expression and protein levels by almost 90% in adipocytes of standard chow-fed mice. In adipocytes of DIO mice, RNAi reduced FABP4 expression and protein levels by 70 and 80%, respectively. There was no increase in adipocyte FABP5 expression in FABP4 knockdown mice. The knockdown of FABP4 significantly increased body weight and fat mass in DIO mice. However, FABP4 knockdown did not affect plasma glucose and lipid homeostasis in DIO mice; nor did it improve their insulin sensitivity.

Conclusion:

Our data indicate that robust knockdown of FABP4 increases body weight and fat mass without improving glucose and lipid homeostasis in DIO mice.

Chips off of Asteroid 4 Vesta: Evidence for the Parent Body of Basaltic Achondrite Meteorites

For more than two decades, asteroid 4 Vesta has been debated as the source for the eucrite, diogenite, and howardite classes of basaltic achondrite meteorites. Its basaltic achondrite spectral properties are unlike those of other large main-belt asteroids. Telescopic measurements have revealed 20 small (diameters </= 10 kilometers) main-belt asteroids that have distinctive optical reflectance spectral features similar to those of Vesta and eucrite and diogenite meteorites. Twelve have orbits that are similar to Vesta's and were previously predicted to be dynamically associated with Vesta. Eight bridge the orbital space between Vesta and the 3:1 resonance, a proposed source region for meteorites. These asteroids are most probably multikilometer-sized fragments excavated from Vesta through one or more impacts. The sizes, ejection velocities of 500 meters per second, and proximity of these fragments to the 3:1 resonance establish Vesta as a dynamically viable source for eucrite, diogenite, and howardite meteorites.

State-dependent radial elasticity of attached cross-bridges in single skinned fibres of rabbit psoas muscle

1. In a single skinned fibre of rabbit psoas muscle, upon attachment of cross-bridges to actin in the presence of ADP or pyrophosphate (PP(i)), the separation between the contractile filaments, as determined by equatorial X-ray diffraction, is found to decrease, suggesting that force is generated in the radial direction.2. The single muscle fibres were subjected to compression by 0-8% of dextran T(500). The changes in lattice spacings by dextran compression were compared with changes induced by cross-bridge attachment to actin. Based on this comparison, the magnitude and the direction of the radial force generated by the attached cross-bridges were estimated. The radial cross-bridge force varied with filament separation, and the magnitude of the radial cross-bridge force reached as high as the maximal axial force produced during isometric contraction.3. One key parameter of the radial elasticity, i.e. the equilibrium spacing where the radial force is zero, was found to depend on the ligand bound to the myosin head. In the presence of ADP, the equilibrium spacing was 36 nm. In the presence of MgPP(i) the equilibrium spacing shifted to 35 nm and Ca(2+) had little effect on the equilibrium spacing.4. The equilibrium spacing was independent of the fraction of cross-bridges attached to actin. The fraction of cross-bridges attached in rigor was modulated from 100% to close to 0% by adding up to 10 mM of ATPgammaS in the rigor solution. The lattice spacing remained at 38 nm, the equilibrium spacing for nucleotide-free cross-bridges at mu = 170 mM.5. Radial force generated by cross-bridges in rigor at large lattice spacings (38 nm </= d(10) </= 46 nm) appeared to vary linearly with lattice spacing.6. The titration of ATPgammaS to fibres in rigor provided a correlation between the radial stiffness of the nucleotide-free cross-bridges and the equatorial intensities. The relation between the equatorial intensity ratio I(11)/I(10) and radial stiffness appeared to be approximately linear.7. The fibres under different conditions showed a wide range of radial stiffness, which was not proportional to the apparent axial stiffness of the fibre. If the apparent axial stiffness is a measure of the fraction of cross-bridges bound to actin, it follows that the radial elastic constant is state dependent; or vice versa.8. Differences in equilibrium lattice spacing and in radial elastic constant, most probably reflect differences in the molecular structure of the acto-myosin complex and there is more than one single conformation of the various strongly bound cross-bridge states.9. Determining equilibrium spacings of the radial elasticity appears to be an effective new approach in detecting structural differences among the attached cross-bridges, since this approach is independent of the fraction of cross-bridges attached, a factor that frequently encumbers the interpretation of structural studies of attached cross-bridge states.

Efficient inhibition of B-cell lymphoma xenografts with a novel recombinant fusion protein: anti-CD20Fab-LDM

Lidamycin (LDM) is a new member of enediyne antitumor antibiotics family that can be separated and reconstituted. It consists of a labile active enediyne chromophore (AE) and a noncovalently bound apoprotein (LDP). LDM is now in phase II clinical trials. In this study, we described the antitumor features of a fusion protein of LDM, anti-CD20Fab-LDM, targeted to CD20 expressed by B-lymphoid malignancies. Especially, LDM was prepared by a novel two-step method including DNA recombination and molecular reconstitution. Anti-CD20Fab-LDM exerted potent cytotoxicity against CD20+ B-cell lymphoma cell lines in vitro (IC50: 10-30 pM) and in the Raji xenograft model. Two Raji xenografts were allowed to grow to an initial mass of 80 and 500 mm³, respectively, and then anti-CD20Fab-LDM was administered intravenously with the highest dose of 4 nmol kg⁻¹ . The inhibition rates of tumor growth were 90.1 and 85%, which were saliently superior to those of nontargeted LDM. It is noteworthy that anti-CD20Fab-LDM can inhibit the growth of patient-derived cells, including rituximab-resistant patient-derived cells. Thus, CD20-targeted delivery of LDM is a specific and potent therapeutic strategy for B-lymphoid malignancies. In addition, the two-step approach could serve as a new technology platform for making a series of highly potent engineered antibody-based drugs.

Corticotrophin-releasing hormone (CRH) facilitates axon outgrowth

OBJECTIVE

To evaluate the role of corticotrophin-releasing hormone (CRH) in facilitating axon outgrowth.

BACKGROUND

Injured neural tissue is difficult to regenerate; the mechanism has not been fully understood.

METHODS

A rat model of spinal cord transection injury was developed. Levels of BDNF, CRH and oligodendrocyte glycoprotein (OMgp) in injured spinal cord were monitored dynamically after surgery. Cellular interaction among rat dorsal root ganglia (DRG) cells, oligocondrocytes and microglial cells was observed with a coculture model. The axon outgrowth from DRG cells was examined by confocal microscopy.

RESULTS

After spinal cord transection, levels of BDNF and CRH increased the next day and decreased afterward, whereas OMgp levels increased from day 3. Administration with BDNF suppressed the levels of OMgp in vitro. The results from a coculture model showed that CRH increased microglial cells to release BDNF; BDNF inhibited OMgp levels in oligodendrocytes and enhanced the axon outgrowth from DRG cells.

CONCLUSIONS

This study shows that CRH has the ability to facilitate the outgrowth of axon in spinal neurons, which has therapeutic potential in the treatment of spinal cord injury.

Mutations of the KISS1 gene in disorders of puberty

CONTEXT

Kisspeptin, encoded by the KISS1 gene, is a key stimulatory factor of GnRH secretion and puberty onset. Inactivating mutations of its receptor (KISS1R) cause isolated hypogonadotropic hypogonadism (IHH). A unique KISS1R-activating mutation was described in central precocious puberty (CPP).

OBJECTIVE

Our objective was to investigate KISS1 mutations in patients with idiopathic CPP and normosmic IHH.

PATIENTS

Eighty-three children with CPP (77 girls) and 61 patients with IHH (40 men) were studied. The control group consisted of 200 individuals with normal pubertal development.

METHODS

The promoter region and the three exons of KISS1 were amplified and sequenced. Cells expressing KISS1R were stimulated with synthetic human wild-type or mutant kisspeptin-54 (kp54), and inositol phosphate accumulation was measured. In a second set of experiments, kp54 was preincubated in human serum before stimulation of the cells.

RESULTS

Two novel KISS1 missense mutations, p.P74S and p.H90D, were identified in three unrelated children with idiopathic CPP. Both mutations were absent in 400 control alleles. The p.P74S mutation was identified in the heterozygous state in a boy who developed CPP at 1 yr of age. The p.H90D mutation was identified in the homozygous state in two unrelated girls with CPP. In vitro studies revealed that the capacity of the P74S and H90D mutants to stimulate IP production was similar to the wild type. After preincubation of wild-type and mutant kp54 in human serum, the capacity to stimulate signal transduction was significantly greater for P74S compared with the wild type, suggesting that the p.P74S variant is more stable. Only polymorphisms were found in the IHH group.

CONCLUSION

Two KISS1 mutations were identified in unrelated patients with idiopathic CPP. The p.P74S variant was associated with higher kisspeptin resistance to degradation in comparison with the wild type, suggesting a role for this mutation in the precocious puberty phenotype.