Phase II study of concomitant thalidomide during radiotherapy for hepatocellular carcinoma

PURPOSE

Thalidomide has been demonstrated to possess antitumor activity in patients with advanced hepatocellular carcinoma (HCC). The objective of the present study was to determine whether the combined treatment of thalidomide with radiotherapy (RT) is associated with acceptable toxicity and an improved clinical outcome in HCC patients.

METHODS AND MATERIALS

A total of 24 patients were enrolled to receive RT combined with thalidomide. A total dose of 50 Gy was delivered in 2-Gy fractions within 5 weeks. Thalidomide was administered 100 mg twice daily starting 3 days before RT until the development of unacceptable toxicity or disease progression. Blood samples were collected before, during, and after treatment to measure the levels of angiogenic factors and cytokines. The results of patients receiving the combined therapy were compared with those from 18 HCC patients receiving RT only.

RESULTS

No significant difference in the clinical parameters was noted between the two groups, except for the baseline interleukin-6 level, which was greater in the concomitant group (p = .05). The most common toxicities related to thalidomide use were skin rash (54.2%), somnolence (37.5%), and constipation (33.3%). No significant differences were seen in the response rate (55.6% vs. 58.3%, p = .48), median progression-free survival (182 ± 48.9 vs. 148 ± 6.2 days, p = .15), or median overall survival (258 ± 45.6 vs. 241 ± 38.6, p = .16) between those who received concomitant therapy and those who received RT alone. Thalidomide suppressed the serum basic fibroblast growth factor level significantly during RT (p = .03) and, to a lesser extent, the interleukin-6 and tumor necrosis factor-α levels. After adjusting for other potential prognostic factors in the multivariate analysis, only the baseline interleukin-6 level and stem cell-derived factor-1 during RT independently predicted the progression-free survival. A decreased serum stem cell-derived factor-1 level 1 month after RT completion was a significant predictor of the overall survival of HCC patients receiving RT.

CONCLUSIONS

Despite the acceptable toxicity, thalidomide provided no additional benefit for HCC patients undergoing RT.

A flow cytometry-based assay to assess RSV-specific neutralizing antibody is reproducible, efficient and accurate

Respiratory syncytial virus (RSV) is an important cause of respiratory infection in people of all ages, and is the leading cause of hospitalization in infants. Although commercially available monoclonal antibody is available for passive prophylaxis of neonates at risk of severe disease, there is no available vaccine to prevent RSV. Measurement of neutralizing activity will be a key endpoint for vaccine evaluation. Assessment of neutralizing antibody against RSV has been limited to traditional plaque reduction, which is time-consuming and inherently operator dependent and highly variable. Here, we describe a flow cytometry-based RSV-specific neutralization assay which is more rapid than traditional methods, highly sensitive and highly reproducible.

Genetic polymorphisms in adaptive immunity genes and childhood acute lymphoblastic leukemia

BACKGROUND

Childhood acute lymphoblastic leukemia (ALL) has been hypothesized to have an infection- and immune-related etiology. The lack of immune priming in early childhood may result in abnormal immune responses to infections later in life and increase ALL risk.

METHODS

The current analyses examined the association between childhood ALL and 208 single-nucleotide polymorphisms (SNP) of 29 adaptive immune function genes among 377 ALL cases and 448 healthy controls. Single SNPs were analyzed with a log-additive approach using logistic regression models adjusted for sex, age, Hispanic ethnicity, and race. Sliding window haplotype analyses were done with haplotypes consisting of 2 to 6 SNPs.

RESULTS

Of the 208 SNPs, only rs583911 of IL12A, which encodes a critical modulator of T-cell development, remained significant after accounting for multiple testing (odds ratio for each copy of the variant G allele, 1.52; 95% confidence interval, 1.25-1.85; P = 2.9 x 10(-5)). This increased risk was stronger among firstborn children of all ethnicities and among non-Hispanic children with less day care attendance, consistent with the hypothesis about the role of early immune modulation in the development of childhood ALL. Haplotype analyses identified additional regions of CD28, FCGR2, GATA3, IL2RA, STAT4, and STAT6 associated with childhood ALL.

CONCLUSION

Polymorphisms of genes on the adaptive immunity pathway are associated with childhood ALL risk.

IMPACT

Results of this study support an immune-related etiology of childhood ALL. Further confirmation is required to detect functional variants in the significant genomic regions identified in this study, in particular for IL12A.

Backtracking RAS mutations in high hyperdiploid childhood acute lymphoblastic leukemia

High hyperdiploidy is the single largest subtype of childhood acute lymphoblastic leukemia (ALL) and is defined by the presence of 51-68 chromosomes in a karyotype. The 5 or more extra chromosomes characterizing this subtype are known to occur in a single mitotic event, prenatally. We screened for RAS mutations among 517 acute childhood leukemias (including 437 lymphocytic, of which 393 were B-cell subtypes) and found mutations in 30% of high hyperdiploids compared to only 10% of leukemias of other subtypes (P<0.0001). We assessed whether KRAS mutations occurred before birth using a PCR-restriction enzyme-mediated Taqman quantitative PCR reaction, and found no evidence for prenatal KRAS mutations in 14 patients tested. While RAS mutations were previously associated with prior chemical exposures in childhood and adult leukemias, in this study RAS-mutated cases were not significantly associated with parental smoking when compared to study controls. IGH rearrangements were backtracked in three RAS-positive patients (which were negative for KRAS mutation at birth) and found to be evident before birth, confirming a prenatal origin for the leukemia clone. We posit a natural history for hyperdiploid leukemia in which prenatal mitotic catastrophe is followed by a postnatal RAS mutation to produce the leukemic cell phenotype.

Inherited variation in immune genes and pathways and glioblastoma risk

To determine whether inherited variations in immune function single-nucleotide polymorphisms (SNPs), genes or pathways affect glioblastoma risk, we analyzed data from recent genome-wide association studies in conjunction with predefined immune function genes and pathways. Gene and pathway analyses were conducted on two independent data sets using 6629 SNPs in 911 genes on 17 immune pathways from 525 glioblastoma cases and 602 controls from the University of California, San Francisco (UCSF) and a subset of 6029 SNPs in 893 genes from 531 cases and 1782 controls from MD Anderson (MDA). To further assess consistency of SNP-level associations, we also compared data from the UK (266 cases and 2482 controls) and the Mayo Clinic (114 cases and 111 controls). Although three correlated epidermal growth factor receptor (EGFR) SNPs were consistently associated with glioblastoma in all four data sets (Mantel-Haenzel P values = 1 × 10⁻⁵ to 4 × 10⁻³), independent replication is required as genome-wide significance was not attained. In gene-level analyses, eight immune function genes were significantly (minP < 0.05) associated with glioblastoma; the IL-2RA (CD25) cytokine gene had the smallest minP values in both UCSF (minP = 0.01) and MDA (minP = 0.001) data sets. The IL-2RA receptor is found on the surface of regulatory T cells potentially contributing to immunosuppression characteristic of the glioblastoma microenvironment. In pathway correlation analyses, cytokine signaling and adhesion-extravasation-migration pathways showed similar associations with glioblastoma risk in both MDA and UCSF data sets. Our findings represent the first systematic description of immune genes and pathways that characterize glioblastoma risk.

Decolorization and biodegradation of reactive dyes and dye wastewater by a developed bacterial consortium

A bacterial consortium (consortium GR) consisting of Proteus vulgaris NCIM-2027 and Micrococcus glutamicus NCIM-2168 could rapidly decolorize and degrade commonly-used sulfonated reactive dye Green HE4BD and many other reactive dyes. Consortium GR shows markedly higher decolorization activity than that of the individual strains. The preferable physicochemical parameters were identified to achieve higher dye degradation and decolorization efficiency. The supplementation of cheap co-substrates (e.g., extracts of agricultural wastes) could enhance the decolorization performance of consortium GR. Extent of mineralization was determined with TOC and COD measurements, showing nearly complete mineralization of Green HE4BD by consortium GR (up to 90% TOC and COD reduction) within 24 h. Oxidoreductive enzymes seemed to be involved in fast decolorization/degradation process with the evidence of enzymes induction in the bacterial consortium. Phytotoxicity and microbial toxicity studies confirm that the biodegraded products of Green HE4BD by consortium GR are non-toxic. Consortium GR also shows significant biodegradation and decolorization activities for mixture of reactive dyes as well as the effluent from actual dye manufacturing industry. This confers the possibility of applying consortium GR for the treatment of industrial wastewaters containing dye pollutants.

Diffusion-weighted MR imaging derived apparent diffusion coefficient is predictive of clinical outcome in primary central nervous system lymphoma

BACKGROUND AND PURPOSE

There is evidence that increased tumor cellular density within diagnostic specimens of primary central nervous system lymphoma (PCNSL) may have significant prognostic implications. Because cellular density may influence measurements of apparent diffusion coefficient (ADC) by using diffusion-weighted MR imaging (DWI), we hypothesized that ADC measured from contrast-enhancing regions might correlate with clinical outcome in patients with PCNSL.

MATERIALS AND METHODS

PCNSL tumors from 18 immunocompetent patients, treated uniformly with methotrexate-based chemotherapy, were studied with pretherapeutic DWI. Enhancing lesions were diagnosed by pathologic analysis as high-grade B-cell lymphomas. Regions of interest were placed around all enhancing lesions allowing calculation of mean, 25th percentile (ADC(25%)), and minimum ADC values. Histopathologic tumor cellularity was quantitatively measured in all patients. High and low ADC groups were stratified by the median ADC value of the cohort. The Welch t test assessed differences between groups. The Pearson correlation examined relationships between ADC measurements and tumor cellular density. Single and multivariable survival analysis was performed.

RESULTS

We detected significant intra- and intertumor heterogeneity in ADC measurements. An inverse correlation between cellular density and ADC measurements was observed (P < .05). ADC(25%) measurements less than the median value of 692 (low ADC group) were associated with significantly shorter progression-free and overall survival. Patients with improved clinical outcome were noted to exhibit a significant decrease in ADC measurements following high-dose methotrexate chemotherapy.

CONCLUSIONS

Our study provides evidence that ADC measurements within contrast-enhancing regions of PCNSL tumors may provide noninvasive insight into clinical outcome.

Ecofriendly degradation of sulfonated diazo dye C.I. Reactive Green 19A using Micrococcus glutamicus NCIM-2168

Micrococcus glutamicus NCIM-2168 exhibited complete decolorization and degradation of C.I. Reactive Green 19A (an initial concentration of 50 mg l(-1)) within 42 h at temperature 37 degrees C and pH 8, under static condition. Extent of mineralization was determined with total organic carbon (TOC) and chemical oxygen demand (COD) measurement, showing a satisfactory reduction of TOC (72%) and COD (66%) within 42 h. Enzyme studies shows involvement of oxidoreductive enzymes in decolorization/degradation process. Analytical studies of the extracted metabolites confirmed the significant degradation of Reactive Green 19A into various metabolites. The microbial toxicity and phytotoxicity assay revealed that the degradation of Reactive Green 19A produced nontoxic metabolites. In addition, the M. glutamicus strain was applied to decolorize a mixture of ten reactive dyes showing a 63% decolorization (in terms of decrease in ADMI value) within 72 h, along with 48% and 42% reduction in TOC and COD under static condition.

Variants in the CDKN2B and RTEL1 regions are associated with high-grade glioma susceptibility

The causes of glioblastoma and other gliomas remain obscure. To discover new candidate genes influencing glioma susceptibility, we conducted a principal component-adjusted genome-wide association study (GWAS) of 275,895 autosomal variants among 692 adult high-grade glioma cases (622 from the San Francisco Adult Glioma Study (AGS) and 70 from the Cancer Genome Atlas (TCGA)) and 3,992 controls (602 from AGS and 3,390 from Illumina iControlDB (iControls)). For replication, we analyzed the 13 SNPs with P < 10(-6) using independent data from 176 high-grade glioma cases and 174 controls from the Mayo Clinic. On 9p21, rs1412829 near CDKN2B had discovery P = 3.4 x 10(-8), replication P = 0.0038 and combined P = 1.85 x 10(-10). On 20q13.3, rs6010620 intronic to RTEL1 had discovery P = 1.5 x 10(-7), replication P = 0.00035 and combined P = 3.40 x 10(-9). For both SNPs, the direction of association was the same in discovery and replication phases.

Decolorization and biodegradation of textile dye Navy blue HER by Trichosporon beigelii NCIM-3326

Navy blue HER was decolorized and degraded within 24h by Trichosporon beigelii NCIM-3326 under static condition. In the present study, we investigated various physicochemical parameters such as agitation, temperature, pH, cell concentration, initial dye concentration and different carbon and nitrogen sources to achieve maximum dye degradation by T. beigelii. Sequentially, decolorization and decrease in the total organic carbon (TOC) of Navy blue HER by T. beigelii were measured. Among five strains T. beigelii gave the better performance on the decolorization of Navy blue HER along with a 95% TOC reduction within 24h. A significant increase in the activities of NADH-DCIP (dichlorophenolindophenol) reductase and azoreductase in the cells obtained after complete decolorization presumably indicates involvement of these enzymes in decolorization process. UV-vis, TLC, HPLC and FTIR analysis of extracted products confirmed the biodegradation of Navy blue HER. Phytotoxicity study demonstrated no toxicity of the biodegraded products with respect to plants viz. Phaseolus mungo and Sorghum vulgare. In addition to Navy blue HER, this strain also shows ability to decolorize various industrial dyes, including Red HE7B, Golden yellow 4BD, Green HE4BD, Orange HE2R, Malachite green, Crystal violet and Methyl violet.

Maternal immunoglobulin E and childhood leukemia

Childhood leukemia, particularly acute lymphoblastic leukemia (ALL), has long been hypothesized to be affected by abnormal immune responses to microbial challenges stemming from a lack of immune modulation in early childhood. Studies of allergies suggest that a child's immune development may be modulated by maternal immune status. We conducted a study to explore the relationship between maternal immunoglobulin E (IgE) and childhood leukemia and to investigate whether maternal immune status can influence childhood leukemia risk. Serum total and specific IgE (respiratory and food) were measured in biological mothers of 352 children (193 healthy controls and 159 leukemia cases, including 139 ALL cases) ages <8 years who were enrolled in the Northern California Childhood Leukemia Study. Odds ratios associated with maternal IgE were calculated using unconditional logistic regression adjusted for child's age, sex, race/ethnicity, and annual household income. A positive association between childhood leukemia or ALL and elevated levels of maternal serum total IgE was observed, especially among Hispanics. In addition, a positive association was observed between childhood leukemia or ALL and maternal respiratory or food IgE status. These results suggest that maternal immune function may play a crucial role in the etiology of childhood leukemia, although additional studies need to be conducted to confirm the results of this study and provide a perspective on mechanisms.

Enhanced decolorization and biodegradation of textile azo dye Scarlet R by using developed microbial consortium-GR

A developed consortium-GR, consisting of Proteus vulgaris NCIM-2027 (PV) and Micrococcus glutamicus NCIM-2168 (MG), completely decolorized an azo dye Scarlet R under static anoxic condition with an average decolorization rate of 16,666 microg h(-1); which is much faster than that of the pure cultures (PV, 3571 microg h(-1); MG, 2500 microg h(-1)). Consortium-GR gave best decolorization performance with nearly complete mineralization of Scarlet R (over 90% TOC and COD reduction) within 3h, much shorter relative to the individual strains. Induction in the riboflavin reductase and NADH-DCIP reductase was observed in the consortium, suggesting the involvement of these enzymes during the fast decolorization process. The FTIR and GC-MS analysis showed that 1,4-benzenediamine was formed during decolorization/degradation of Scarlet R by consortium-GR. Phytotoxicity studies revealed no toxicity of the biodegraded products of Scarlet R by consortium-GR. In addition, consortium-GR applied for mixture of industrial dyes showed 88% decolorization under static condition with significant reduction in TOC (62%) and COD (68%) within 72 h, suggesting potential application of this microbial consortium in bioremediation of dye-containing wastewater.

Parental smoking and childhood leukemia

Childhood leukemia is the most common cancer among children, representing 31% of all cancer cases occurring in children younger than the age of 15 years in the USA. There are only few known risk factors of childhood leukemia (sex, age, race, exposure to ionizing radiation, and certain congenital diseases, such as Down syndrome and neurofibromatosis), which account for only 10% of the childhood leukemia cases. Several lines of evidence suggest that childhood leukemia may be more due to environmental rather than genetic factors, although genes may play modifying roles. Human and animal studies showed that the development of childhood leukemia is a two-step process that requires a prenatal initiating event(s) plus a postnatal promoting event(s). Despite a substantial public health effort to reduce cigarette smoking, a large proportion of the US and world population still smoke. Tobacco smoke contains at least 60 known human or animal carcinogens, with the major chemical classes being volatile hydrocarbons, aldehydes, aromatic amines, polycyclic aromatic hydrocarbons, and nitrosamines; among these chemicals, only benzene is an established leukemogen, although other chemicals in the tobacco could interact with one another in a complex way to jointly attain a significant carcinogenic effect on the development of leukemia. Although tobacco smoke is an established risk factor for adult myeloid leukemia, the studies of association between parental smoking and childhood leukemia have produced inconsistent results. The majority of the studies on maternal smoking and childhood leukemia did not find a significant positive association and some even reported an inverse association. In contrast to studies of maternal smoking, studies of paternal smoking and childhood leukemia reported more positive associations but only by less than half of the studies. Future directions to be considered for improving the study of parental smoking and childhood leukemia are: 1) consider all sources of benzene exposure in addition to smoking, including occupational exposure and traffic exhausts; 2) childhood leukemia is a heterogeneous disease and epidemiologic studies of childhood leukemia can be greatly improved by grouping childhood leukemia into more homogeneous groups by molecular techniques (e.g., structural and numerical chromosomal changes); and 3) assess gene-environment interaction. It is hoped that through the continual effort, more will be uncovered regarding the causes of childhood leukemia. In the meantime, more effort should be spent on educating the parents to quit smoking, because parental smoking is known to affect many childhood diseases (e.g., asthma, respiratory tract infection, and otitis media) that are much more prevalent than childhood leukemia.

Base excision repair genes and risk of lung cancer among San Francisco Bay Area Latinos and African-Americans

Base excision repair (BER) is the primary DNA damage repair mechanism for repairing small base lesions resulting from oxidation and alkylation damage. This study examines the association between 24 single-nucleotide polymorphisms (SNPs) belonging to five BER genes (XRCC1, APEX1, PARP1, MUTYH and OGG1) and lung cancer among Latinos (113 cases and 299 controls) and African-Americans (255 cases and 280 controls). The goal was to evaluate the differences in genetic contribution to lung cancer risk by ethnic groups. Analyses of individual SNPs and haplotypes were performed using unconditional logistic regressions adjusted for age, sex and genetic ancestry. Four SNPs among Latinos and one SNP among African-Americans were significantly (P < 0.05) associated with either risk of all lung cancer or non-small cell lung cancer (NSCLC). However, only the association between XRCC1 Arg399Gln (rs25487) and NSCLC among Latinos (odds ratio associated with every copy of Gln = 1.52; 95% confidence interval: 1.01-2.28) had a false-positive report probability of <0.5. Arg399Gln is a SNP with some functional evidence and has been shown previously to be an important SNP associated with lung cancer, mostly for Asians. Since the analyses were adjusted for genetic ancestry, the observed association between Arg399Gln and NSCLC among Latinos is unlikely to be confounded by population stratification; however, this result needs to be confirmed by additional studies among the Latino population. This study suggests that there are genetic differences in the association between BER pathway and lung cancer between Latinos and African-Americans.

Allergies and childhood leukemia

A majority of studies to date have reported an inversed association between allergies and childhood leukemia. However, this association is likely an indirect one and may represent some shared underlying immune mechanisms that have been explained in the context of the "hygiene hypothesis", which has been thought to play an important role in the development of both allergies and childhood leukemia. This review focuses on what we know so far about the role of various immune cells (Th1, Th2, T regulatory and Th17 cells) in the development of allergies and how they may potentially be related to the etiology of childhood leukemia. In addition, the utilities of genetic and molecular studies to disentangle the association between allergies and childhood leukemia and to elucidate the biological mechanisms are also discussed.

NQO1 polymorphisms and de novo childhood leukemia: a HuGE review and meta-analysis

Polymorphisms in NQO1, a gene coding for the phase II enzyme involved in the detoxification of quinone carcinogens, have been associated with childhood leukemia in some studies, although the observed direction and magnitude of effects have been inconsistent. Therefore, the authors systematically reviewed all published reports describing the effect of NQO1 in de novo childhood leukemia and conducted a meta-analysis of 7 case-control studies that examined the association between NQO1*2 and childhood leukemia. Although a family-based study previously demonstrated over-transmission of this allele among childhood acute lymphoblastic leukemia cases, the meta-analysis showed that the presence of a NQO1*2 variant allele, which reduces the activity of the enzyme NAD(P)H:quinone oxidoreductase 1 (NQO1), had no significant effect on childhood leukemia. However, there was an increased risk associated with having at least 1 copy of the NQO1*2 allele in a subset of cases with MLL translocations (summary odds ratio = 1.39, 95% confidence interval: 0.98, 1.97). Heterogeneity between studies may be due to differences in population exposures to NQO1 substrates and small sample sizes, as well as potential population stratification in non-family-based studies. Therefore, further research is warranted on the role of NQO1 polymorphisms in the etiology of childhood leukemia, especially among MLL-positive leukemias.

Distinguishing recurrent intra-axial metastatic tumor from radiation necrosis following gamma knife radiosurgery using dynamic susceptibility-weighted contrast-enhanced perfusion MR imaging

BACKGROUND AND PURPOSE

MR image-guided gamma knife radiosurgery is often used to treat intra-axial metastatic neoplasms. Following treatment, it is often difficult to determine whether a progressively enhancing lesion is due to metastatic tumor recurrence or radiation necrosis. The purpose of our study was to determine whether relative cerebral blood volume (rCBV), relative peak height (rPH), and percentage of signal-intensity recovery (PSR) derived from dynamic susceptibility-weighted contrast-enhanced perfusion MR imaging can distinguish recurrent metastatic tumor from radiation necrosis.

MATERIALS AND METHODS

Twenty-seven patients with systemic cancer underwent gamma knife radiosurgery for metastatic lesions of the brain and subsequently developed enlarging regions of enhancement within the radiation field. Subsequent surgical resection or clinicoradiologic follow-up established a diagnosis of recurrent metastatic tumor or radiation necrosis. Perfusion MR imaging datasets were retrospectively reprocessed, and regions of interest were drawn around the entire contrast-enhancing region. The resulting T2* signal-intensity time curves produced rCBV, rPH, and PSR values for each examination. A Welch t test was used to compare imaging values between groups.

RESULTS

The mean, minimum, and maximum PSR values were significantly lower (P < .01) in cases of recurrent metastatic tumor. The mean and maximum rCBV and rPH values were significantly higher (P < .02) in the recurrent metastatic tumor group.

CONCLUSIONS

The findings of our study suggest that perfusion MR imaging may be used to differentiate recurrent intra-axial metastatic tumor from gamma knife-induced radiation necrosis.

SNPLogic: an interactive single nucleotide polymorphism selection, annotation, and prioritization system

SNPLogic (http://www.snplogic.org) brings together single nucleotide polymorphism (SNP) information from numerous sources to provide a comprehensive SNP selection, annotation and prioritization system for design and analysis of genotyping projects. SNPLogic integrates information about the genetic context of SNPs (gene, chromosomal region, functional location, haplotypes tags and overlap with transcription factor binding sites, splicing sites, miRNAs and evolutionarily conserved regions), genotypic data (allele frequencies per population and validation method), coverage of commercial arrays (ParAllele, Affymetrix and Illumina), functional predictions (modeled on structure and sequence) and connections or established associations (biological pathways, gene ontology terms and OMIM disease terms). The SNPLogic web interface facilitates construction and annotation of user-defined SNP lists that can be saved, shared and exported. Thus, SNPLogic can be used to identify and prioritize candidate SNPs, assess custom and commercial arrays panels and annotate new SNP data with publicly available information. We have found integration of SNP annotation in the context of pathway information and functional prediction scores to be a powerful approach to the analysis and interpretation of SNP-disease association data.

Nucleotide excision repair genes and risk of lung cancer among San Francisco Bay Area Latinos and African Americans

Few studies on the association between nucleotide excision repair (NER) variants and lung cancer risk have included Latinos and African Americans. We examine variants in 6 NER genes (ERCC2, ERCC4, ERCC5, LIG1, RAD23B and XPC) in association with primary lung cancer risk among 113 Latino and 255 African American subjects newly diagnosed with primary lung cancer from 1998 to 2003 in the San Francisco Bay Area and 579 healthy controls (299 Latinos and 280 African Americans). Individual single nucleotide polymorphism and haplotype analyses, multifactor dimensionality reduction (MDR) and principal components analysis (PCA) were performed to assess the association between 6 genes in the NER pathway and lung cancer risk. Among Latinos, ERCC2 haplotype CGA (rs238406, rs11878644, rs6966) was associated with reduced lung cancer risk [odds ratio (OR) of 0.65 and 95% confidence interval (CI): 0.44-0.97], especially among nonsmokers (OR = 0.29; 95% CI: 0.12-0.67). From MDR analysis, in Latinos, smoking and 3 SNPs (ERCC2 rs171140, ERCC5 rs17655 and LIG1 rs20581) together had a prediction accuracy of 67.4% (p = 0.001) for lung cancer. Among African Americans, His/His genotype of ERCC5 His1104Asp (rs17655) was associated with increased lung cancer risk (OR = 1.78; 95% CI: 1.09-2.91), and LIG1 haplotype GGGAA (rs20581, rs156641, rs3730931, rs20579 and rs439132) was associated with reduced lung cancer risk (OR = 0.61; 95% CI: 0.42-0.88). Our study suggests different elements of the NER pathway may be important in the different ethnic groups resulting either from different linkage relationship, genetic backgrounds and/or exposure histories.

Pathway analysis of single-nucleotide polymorphisms potentially associated with glioblastoma multiforme susceptibility using random forests

Glioma is a complex disease that is unlikely to result from the effect of a single gene. Genetic analysis at the pathway level involving multiple genes may be more likely to capture gene-disease associations than analyzing genes one at a time. The current pilot study included 112 Caucasians with glioblastoma multiforme and 112 Caucasian healthy controls frequency matched to cases by age and gender. Subjects were genotyped using a commercially available (ParAllele/Affymetrix) assay panel of 10,177 nonsynonymous coding single-nucleotide polymorphisms (SNP) spanning the genome known at the time the panel was constructed. For this analysis, we selected 10 pathways potentially involved in gliomagenesis that had SNPs represented on the panel. We performed random forests (RF) analyses of SNPs within each pathway group and logistic regression to assess interaction among genes in the one pathway for which the RF prediction error was better than chance and the permutation P < 0.10. Only the DNA repair pathway had a better than chance classification of case-control status with a prediction error of 45.5% and P = 0.09. Three SNPs (rs1047840 of EXO1, rs12450550 of EME1, and rs799917 of BRCA1) of the DNA repair pathway were identified as promising candidates for further replication. In addition, statistically significant interactions (P < 0.05) between rs1047840 of EXO1 and rs799917 or rs1799966 of BRCA1 were observed. Despite less than complete inclusion of genes and SNPs relevant to glioma and a small sample size, RF analysis identified one important biological pathway and several SNPs potentially associated with the development of glioblastoma.

Macrobrachium rosenbergii nodavirus infection in M. rosenbergii (de Man) with white tail disease cultured in Taiwan

White tail disease (WTD) is a serious problem in Macrobrachium rosenbergii hatcheries and nursery ponds in Asia. The causative agents have been identified as M. rosenbergii nodavirus (MrNV) and its associated extra small virus. This is the first report demonstrating MrNV virus in M. rosenbergii displaying WTD signs in Taiwan by reverse transcriptase-polymerase chain reaction (RT-PCR). Amplified fragments of 850 and 425 bp for RNA-1 and RNA-2 of MrNV, respectively, were obtained by RT-PCR. RT-PCR products of about 850 and 1121 bp for RNA-1 and RNA-2 of MrNV were also obtained using different primer pairs. The amplicons were individually cloned into pGEM-T vector and sequenced. Using this recombinant plasmid of MrNV RNA-2 as DNA template, the non-radioactive DNA probes were prepared by PCR amplification with DIG-11-dUTP. The probes were used to successfully detect MrNV infection in the striated muscle tissues of WTD-diseased prawns using in situ hybridization. The 1121 bp genomic fragment of RNA-2 of MrNV consisted of a unique open reading frame with 1116 nucleotides, and it encoded a structural protein with 371 amino acids. The nucleotide sequence of the partial genome of MrNV RNA-2 revealed a 97% identity with an Indian isolate. A phylogenetic tree constructed using the nucleotide sequence of the viral capsid gene from insect and fish nodaviruses revealed that the MrNV Taiwan isolate could be interpreted as a new genus within the family Nodaviridae. However, its position showed more affinity with Alphanodavirus than with Betanodavirus. The study confirmed the presence of MrNV infection in freshwater prawns cultured in Taiwan suffering from WTD.

Parental social contact in the work place and the risk of childhood acute lymphoblastic leukaemia

To study the possible relation between parental social contact through occupation, a marker for a child's risk of infection, and childhood acute lymphoblastic leukaemia (ALL), the parents of 294 children with ALL aged 0-14.9 years and 376 matched controls were interviewed about their jobs after their child's birth up to the age of 3 years. Job titles were assigned to a level of social contact, and an index of occupational social contact months was created using the level and the job duration. Positive interactions between this index and rural residence associated with an increased risk of childhood ALL and common ALL (c-ALL) were observed (interaction P-value=0.02 for both, using tertiles of contact months; interaction P-value=0.05 and 0.02 for ALL and c-ALL, respectively, using continuous contact months); such findings were not observed when job durations were ignored. Our data suggest that duration of parental occupation may be important when examining the association between parental social contact in the workplace and childhood leukaemia.

Dysbindin gene variants are associated with bipolar I disorder in a Korean population

The dysbindin gene (DTNBP1) has been associated with schizophrenia in several populations. Because the clinical characteristics of schizophrenia and bipolar disorder overlap in many respects and findings from genetic studies have suggested common genes between them, we conducted a case control association study of bipolar disorder in Korea to investigate the genetic association between DTNBP1 and bipolar disorder. In total, 163 patients with bipolar disorder and 350 controls were evaluated. We genotyped three single nucleotide polymorphisms of DTNBP1 (SNP A, P1763, and P1320) and analyzed the allele, genotype, and haplotype associations with bipolar disorder. We found significant genotypic associations with P1763 and P1320, but no association with SNP A in the bipolar I group. When we included bipolar II and schizoaffective disorder in the affected phenotype, the significance decreased. A positive association was observed between the SNP A-P1763 haplotype and the bipolar I phenotype. This haplotype association was lost when we either broadened our phenotype or included P1320 in a haplotype. The positive results of the present study lost significance after a Bonferroni correction for multiple testing. These findings are consistent with previous findings that showed a positive association of DTNBP1 with bipolar disorders. Moreover, our results suggest that DTNBP1 may contribute more to bipolar I disorder than bipolar II disorder or schizoaffective disorder. Further comprehensive studies will be required to clarify these association, however, it seems likely that DTNBP1 is a susceptibility gene for bipolar disorder.