Comprehensive evaluation of one-carbon metabolism pathway gene variants and renal cell cancer risk

Introduction

Folate and one-carbon metabolism are linked to cancer risk through their integral role in DNA synthesis and methylation. Variation in one-carbon metabolism genes, particularly MTHFR, has been associated with risk of a number of cancers in epidemiologic studies, but little is known regarding renal cancer.

Methods

Tag single nucleotide polymorphisms (SNPs) selected to produce high genomic coverage of 13 gene regions of one-carbon metabolism (ALDH1L1, BHMT, CBS, FOLR1, MTHFR, MTR, MTRR, SHMT1, SLC19A1, TYMS) and the closely associated glutathione synthesis pathway (CTH, GGH, GSS) were genotyped for 777 renal cell carcinoma (RCC) cases and 1,035 controls in the Central and Eastern European Renal Cancer case-control study. Associations of individual SNPs (n = 163) with RCC risk were calculated using unconditional logistic regression adjusted for age, sex and study center. Minimum p-value permutation (Min-P) tests were used to identify gene regions associated with risk, and haplotypes were evaluated within these genes.

Results

The strongest associations with RCC risk were observed for SLC19A1 (P_min-P = 0.03) and MTHFR (P_min-P = 0.13). A haplotype consisting of four SNPs in SLC19A1 (rs12483553, rs2838950, rs2838951, and rs17004785) was associated with a 37% increased risk (p = 0.02), and exploratory stratified analysis suggested the association was only significant among those in the lowest tertile of vegetable intake.

Conclusions

To our knowledge, this is the first study to comprehensively examine variation in one-carbon metabolism genes in relation to RCC risk. We identified a novel association with SLC19A1, which is important for transport of folate into cells. Replication in other populations is required to confirm these findings.     

Comprehensive analysis of 5-aminolevulinic acid dehydrogenase (ALAD) variants and renal cell carcinoma risk among individuals exposed to lead

Background

Epidemiologic studies are reporting associations between lead exposure and human cancers. A polymorphism in the 5-aminolevulinic acid dehydratase (ALAD) gene affects lead toxicokinetics and may modify the adverse effects of lead.

Methods

The objective of this study was to evaluate single-nucleotide polymorphisms (SNPs) tagging the ALAD region among renal cancer cases and controls to determine whether genetic variation alters the relationship between lead and renal cancer. Occupational exposure to lead and risk of cancer was examined in a case-control study of renal cell carcinoma (RCC). Comprehensive analysis of variation across the ALAD gene was assessed using a tagging SNP approach among 987 cases and 1298 controls. Occupational lead exposure was estimated using questionnaire-based exposure assessment and expert review. Odds ratios (OR) and 95% confidence intervals (CI) were calculated using logistic regression.

Results

The adjusted risk associated with the ALAD variant rs8177796^CT/TT was increased (OR = 1.35, 95%CI = 1.05–1.73, p-value = 0.02) when compared to the major allele, regardless of lead exposure. Joint effects of lead and ALAD rs2761016 suggest an increased RCC risk for the homozygous wild-type and heterozygous alleles (^GGOR = 2.68, 95%CI = 1.17–6.12, p = 0.01; ^GAOR = 1.79, 95%CI = 1.06–3.04 with an interaction approaching significance (p_int = 0.06).. No significant modification in RCC risk was observed for the functional variant rs1800435^(K68N). Haplotype analysis identified a region associated with risk supporting tagging SNP results.

Conclusion

A common genetic variation in ALAD may alter the risk of RCC overall, and among individuals occupationally exposed to lead. Further work in larger exposed populations is warranted to determine if ALAD modifies RCC risk associated with lead exposure.     

Disclosure of personal medical information: differences among parents and affected adults for genetic and nongenetic conditions

Protecting the confidentiality of medical information has been an issue of great interest in the fields of bioethics, public policy, and law. Few empirical studies have addressed patient experiences and attitudes toward disclosure of private medical information in multiple contexts such as health insurance, employment, and the family. Furthermore, it is unclear whether differences exist in experiences and attitudes about privacy between those living with a serious medical condition versus those who have a child with a medical condition. The study sought to determine whether attitudes and experiences related to medical privacy and confidentiality differ between affected adults and parents of affected children. Interviews were conducted with 296 adults and parents of children with sickle cell disease (SCD), cystic fibrosis (CF), or diabetes mellitus (DM). This cross-sectional study collected data regarding their experiences, attitudes, and beliefs concerning medical privacy and confidentiality. Multinomial logistic regression analysis was conducted on quantitative data. Qualitative analysis was conducted on data from open-ended response items. Parents disclose their child's diagnosis to others more often than affected adults disclose their own disease status. Parents are less likely than affected adults to regret their disclosure, to hope others do not find out, to have been pressured to share information, and to be asked about their disease by employers. Affected adults express greater concern about disclosure, a greater prevalence and greater fear of discrimination, and experience greater pressure from family members to disclose. Clinicians and researchers working with these populations should consider these differences in privacy and disclosure. Further study is necessary to examine the implications of these differences in attitudes and experiences concerning insurance, employment, and social interactions among persons with these conditions.     

Inhibitors of V-ATPase proton transport reveal uncoupling functions of tether linking cytosolic and membrane domains of V0 subunit a (Vph1p)

Vacuolar ATPases (V-ATPases) are important for many cellular processes, as they regulate pH by pumping cytosolic protons into intracellular organelles. The cytoplasm is acidified when V-ATPase is inhibited; thus we conducted a high-throughput screen of a chemical library to search for compounds that acidify the yeast cytosol in vivo using pHluorin-based flow cytometry. Two inhibitors, alexidine dihydrochloride (EC(50) = 39 μM) and thonzonium bromide (EC(50) = 69 μM), prevented ATP-dependent proton transport in purified vacuolar membranes. They acidified the yeast cytosol and caused pH-sensitive growth defects typical of V-ATPase mutants (vma phenotype). At concentrations greater than 10 μM the inhibitors were cytotoxic, even at the permissive pH (pH 5.0). Membrane fractions treated with alexidine dihydrochloride and thonzonium bromide fully retained concanamycin A-sensitive ATPase activity despite the fact that proton translocation was inhibited by 80-90%, indicating that V-ATPases were uncoupled. Mutant V-ATPase membranes lacking residues 362-407 of the tether of Vph1p subunit a of V(0) were resistant to thonzonium bromide but not to alexidine dihydrochloride, suggesting that this conserved sequence confers uncoupling potential to V(1)V(0) complexes and that alexidine dihydrochloride uncouples the enzyme by a different mechanism. The inhibitors also uncoupled the Candida albicans enzyme and prevented cell growth, showing further specificity for V-ATPases. Thus, a new class of V-ATPase inhibitors (uncouplers), which are not simply ionophores, provided new insights into the enzyme mechanism and original evidence supporting the hypothesis that V-ATPases may not be optimally coupled in vivo. The consequences of uncoupling V-ATPases in vivo as potential drug targets are discussed.     

Improved modeling of side-chain--base interactions and plasticity in protein--DNA interface design

Combinatorial sequence optimization for protein design requires libraries of discrete side-chain conformations. The discreteness of these libraries is problematic, particularly for long, polar side chains, since favorable interactions can be missed. Previously, an approach to loop remodeling where protein backbone movement is directed by side-chain rotamers predicted to form interactions previously observed in native complexes (termed "motifs") was described. Here, we show how such motif libraries can be incorporated into combinatorial sequence optimization protocols and improve native complex recapitulation. Guided by the motif rotamer searches, we made improvements to the underlying energy function, increasing recapitulation of native interactions. To further test the methods, we carried out a comprehensive experimental scan of amino acid preferences in the I-AniI protein-DNA interface and found that many positions tolerated multiple amino acids. This sequence plasticity is not observed in the computational results because of the fixed-backbone approximation of the model. We improved modeling of this diversity by introducing DNA flexibility and reducing the convergence of the simulated annealing algorithm that drives the design process. In addition to serving as a benchmark, this extensive experimental data set provides insight into the types of interactions essential to maintain the function of this potential gene therapy reagent.     

Spatial Ecology of the Endangered Milne-Edwards’ Sifaka (Propithecus edwardsi): Do Logging and Season Affect Home Range and Daily Ranging Patterns?

Primates often live in human-altered habitats; Malagasy lemurs are no exception. It is important to understand if habitat alteration affects primates’ space use patterns across multiple spatial and temporal scales, as this drives population density. We quantified the daily, seasonal, and annual space-use of seven groups of Milne-Edwards’ sifaka (Propithecus edwardsi) living in unlogged and logged rain forest in Ranomafana National Park, Madagascar between December 2002 and November 2003. Concurrent data showed that sifakas consumed higher quality foods in the unlogged than in logged forests; thus we explored how space use patterns were related to energy use strategies. Sifaka groups in the logged rain forest traveled 7–13% less per day than groups in the unlogged rain forest, despite their larger home ranges (median: 46.12 and 23.52 ha, in the logged and unlogged forests, respectively). Sifakas may thus use an energy-minimizing strategy at the scale of the individual day but an energy-maximizing strategy at the annual home range scale. Sifakas exhibited fidelity to the home range across seasons, but their core area of use shifted considerably with season. We found no difference in population density between sites. However, given the interannual variability in sifaka foods, a multiyear study is needed to assess if energy strategies observed in this study are consistent across longer time periods. Our findings suggest that lemurs may persist in logged habitats by altering spatial use patterns; future work should attempt to quantify the threshold level of forest regeneration from logging that will allow lemurs to persist at similar densities as in unlogged forest.     

Pentoxifylline inhibits lipopolysaccharide-induced serum tumor necrosis factor and mortality

Tumor necrosis factor, a mononuclear phagocyte-derived peptide produced in response to lipopolysaccharide, has been shown to mediate certain aspects of septic shock and multiple organ failure resulting from gram-negative septicemia. In the present investigation, pretreatment of animals with pentoxifylline inhibited lipopolysaccharide-induced serum tumor necrosis factor in a dose-dependent fashion. Pentoxifylline prevented the sequestration of neutrophils seen in animals given intravenous lipopolysaccharide. Furthermore, pentoxifylline protected animals from the lethal effects of an intravenous challenge with lipopolysaccharide. These data indicate that pentoxifylline inhibits lipopolysaccharide-induced tumor necrosis factor and may be an effective agent in mitigating the lethal consequences of sepsis and other disease processes mediated by this cytokine.