Abstract 1833: Body mass index and physical activity in relation to risk of non-Hodgkin lymphoma (NHL)

Background: Obesity has been linked to NHL risk in some studies, and may be stronger for obesity in early adulthood (ages 18-20). There has only been limited evaluation of physical activity and risk of NHL, particularly physical activity earlier in life. The purpose of this study was to evaluate the association of body mass index (BMI), physical activity (PA), and NHL risk during adulthood and at age 18.

Methods: Self-reported anthropometrics and PA were collected in a clinic-based study of 954 newly diagnosed NHL cases and 1146 controls enrolled at the Mayo Clinic from 2002-2008. PA variables included duration and frequency of mild, moderate, and strenuous PA two years prior to case diagnosis or control selection, strenuous activity at age 18 (any vs. none), and height and weight at both time periods. An overall PA index was estimated by weighting the reported duration and frequency of each PA intensity by the average energy requirement (defined in METs) to obtain an average MET-minutes/week for each participant. BMI was calculated as weight (kg) divided by height (m) squared. Odds Ratios (OR), 95% confidence intervals (CI), and test for trend were estimated using unconditional logistic regression adjusted for the age, gender, and residence. Continuous variables were divided into quartiles according to the distribution among the controls; results are reported for the highest vs. lowest category or quartile unless otherwise specified.

Results: The mean age at diagnosis/enrollment was 61 for both cases and controls; 47% and 43% of the cases and controls, respectively, were female. The most common NHL subtypes were CLL/SLL (32%), follicular lymphoma (FL; 26%), and diffuse large B-cell lymphoma (DLBCL; 21%). BMI 2 years prior to diagnosis was not associated with NHL risk (OR=1.21, p-trend=0.13), while there was a positive association with BMI at age 18 (OR=1.40, p-trend=0.001). There was no association of the PA index with risk (OR=0.91, p-trend=0.29). Furthermore, frequency of walking (OR=0.71, p-trend 0.43), mild (OR=1.30, p-trend=0.64), moderate (OR=0.99, p-trend=0.75), and strenuous (OR=0.77, p-trend=0.20) PA were not associated with NHL risk when evaluated individually. However, there was a suggestive weak inverse association between strenuous activity at age 18 and NHL risk (OR=0.85, 95% CI 0.71-1.05). On exploratory analysis, the association of BMI at age 18 with NHL risk was specific to DLBCL (OR=1.84, p-trend=0.002) and CLL/SLL (OR=1.25, p-trend=0.044) but not FL; all other results were similar across these subtypes.

Conclusions: We did not observe an association between adult BMI and NHL risk; however a higher BMI in early adulthood was associated with NHL risk, consistent with limited prior reports. We found little evidence to support an association between PA in either early adulthood or later in life and NHL risk.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 1833.

Abstract 2811: Vitamin K intake and risk of non-Hodgkin lymphoma (NHL)

Background. Vitamin K1 (phylloquinone) is a fat soluble vitamin found mainly in green leafy vegetables, with smaller amounts found in other vegetables, vegetable oils, and some fruits. Vitamin K-dependent gamma-carboxylation of specific glumatic acid residues is critical to the functioning of several key proteins in the coagulation cascade. Vitamin K compounds also inhibit IL-6 and other inflammatory cytokines and serve as transcription factors that foster cell-cycle arrest and apoptosis, pathways relevant to lymphomagenesis. We tested the hypothesis that dietary and supplemental intake of Vitamin K was inversely associated with risk of NHL and the common subtypes of diffuse large B cell, follicular, and chronic lymphocytic leukemia/small lymphocytic lymphomas.

Methods. We evaluated dietary and supplemental intake of vitamin K and NHL risk in a clinic-based study of 603 newly diagnosed NHL cases and 1007 frequency-matched controls enrolled at the Mayo Clinic from 2002-2008. Usual diet two years before case diagnosis or control enrollment was assessed using a self-administered, 128-item food frequency questionnaire. Dietary intake of vitamin K was estimated using the Food Processor SQL system. Unconditional logistic regression was used to estimate odds ratios (ORs) and 95% confidence intervals (CI), adjusted for age, sex, residence, and total energy. NHL subtypes were centrally reviewed, and subtype-specific risks were estimated using polychotomous logistic regression.

Results. The mean age at diagnosis was 60.8 years for cases and 57% were male; for controls, the mean age at enrollment was 60.1 years and 53% were male. Median intake of vitamin K from diet among controls was 63.5 ug/day; 16% used a multivitamin supplement that included vitamin K. NHL risk was inversely associated with intake of dietary vitamin K (p-trend=0.001); compared to intake <39.3 ug/d, risk was decreased for intakes of 39.3-63.4 ug/d (OR=0.76; 95% CI 0.57-1.02), 63.5-107.7 ug/d (OR=0.74; 95% CI 0.55-1.00), and >107.7 (OR=0.56; 95% CI 0.40-0.77). There was an U-shaped association for supplemental intake of Vitamin K and NHL risk; compared to no use, supplemental intake of <5.9 ug/d (OR=0.63; 95% CI 0.37-1.08) and 5.9-17.6 ug/d (OR=0.53; 95% CI 0.30-0.93) were inversely associated with NHL risk, while intake of >17.6 ug/d (OR=1.13; 95% CI 0.73-1.74) showed no association. There was no evidence of heterogeneity by NHL subtype (p=0.4). Further adjustment for education, family history of NHL, pack-years of smoking, body mass index, and alcohol consumption did not alter these results, nor did adjustment for a food-frequency questionnaire-based estimate of total antioxidant intake.

Conclusion: Higher intake of vitamin K from the diet was inversely associated with risk of NHL overall and for the major subtypes. These first results, which require replication, suggest that the coagulation pathway or other biologic effects of vitamin K may play a role in lymphomagenesis.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 2811.

Experience-dependent plasticity in hypocretin/orexin neurones: re-setting arousal threshold

The neuropeptide hypocretin is synthesized exclusively in the lateral hypothalamus and participates in many brain functions critical for animal survival, particularly in the promotion and maintenance of arousal in animals - a core process in animal behaviours. Consistent with its arousal-promoting role in animals, the neurones synthesizing hypocretin receive extensive innervations encoding physiological, psychological and environmental cues and send final outputs to key arousal-promoting brain areas. The activity in hypocretin neurones fluctuates and correlates with the behavioural state of animals and intensive activity has been detected in hypocretin neurones during wakefulness, foraging for food and craving for addictive drugs. Therefore, it is likely that hypocretin neurones undergo experience-dependent changes resulting from intensive activations by stimuli encoding changes in the internal and external environments. This review summarizes the most recent evidence supporting experience-dependent plasticity in hypocretin neurones. Current data suggest that nutritional and behavioural factors lead to synaptic plasticity and re-organization of synaptic architecture in hypocretin neurones. This may be the substrate of enhanced levels of arousal resulting from behavioural changes in animals and may help to explain the mechanisms underlying the changes in arousal levels induced by physiological, psychological and environmental factors.

Antioxidant intake from fruits, vegetables and other sources and risk of non-Hodgkin's lymphoma: the Iowa Women's Health Study

Antioxidant nutrients found in fruits, vegetables and other foods are thought to inhibit carcinogenesis and to influence immune status. We evaluated the association of these factors with risk of non-Hodgkin's lymphoma (NHL) overall and for diffuse large B-cell lymphoma (DLBCL) and follicular lymphoma specifically in a prospective cohort of 35,159 Iowa women aged 55-69 years when enrolled at baseline in 1986. Diet was ascertained using a validated semiquantitative food frequency questionnaire. Through 2005, 415 cases of NHL (including 184 DLBCL and 90 follicular) were identified. Relative risks (RRs) and 95% confidence intervals (CIs) were estimated using Cox regression, adjusting for age and total energy. The strongest associations of antioxidants with risk of NHL (RR for highest versus lowest quartile; p for trend) were observed for dietary vitamin C (RR = 0.78; p = 0.044), alpha-carotene (RR = 0.71; p = 0.015), proanthocyanidins (RR = 0.70; p = 0.0024) and dietary manganese (RR = 0.62; p = 0.010). There were no associations with multivitamin use or supplemental intake of vitamins C, E, selenium, zinc, copper or manganese. From a food perspective, greater intake of total fruits and vegetables (RR = 0.69; p = 0.011), yellow/orange (RR = 0.72; p = 0.015) and cruciferous (RR = 0.82; p = 0.017) vegetables, broccoli (RR = 0.72; p = 0.018) and apple juice/cider (RR = 0.65; p = 0.026) were associated with lower NHL risk; there were no strong associations for other antioxidant-rich foods, including whole grains, chocolate, tea or nuts. Overall, these associations were mainly observed for follicular lymphoma and were weaker or not apparent for DLBCL. In conclusion, these results support a role for vegetables, and perhaps fruits and associated antioxidants from food sources, as protective factors against the development of NHL and follicular lymphoma in particular.

Abstract A115: Alcohol use and molecularly defined colorectal cancer risks in a prospective study of older women

Background: Colorectal cancer (CRC) is the third most common incident cancer among women in the United States. Alcohol use has been proposed as a CRC risk factor, but existing observational data remain inconsistent. To date, relatively few studies have examined associations between alcohol use and CRC risk based on molecularly-defined subtypes.

Aim: To evaluate associations between alcohol use and incident CRC overall, as well as by molecularly-defined subtypes including microsatellite instability (MSI), CpG island methylator phenotype (CIMP) and BRAF mutation status in the prospective, population-based, Iowa Women's Health Study (IWHS).

Methods: The IWHS recruited 41,836 randomly selected Iowa women, ages 55–69 years at enrollment, in 1986. Women with prevalent cancers or no follow-up were excluded, leaving 38,001 eligible for this study. Alcohol use was obtained from a self-administered food frequency questionnaire at study baseline. Incident CRCs were identified through annual linkage with the State Health Registry of Iowa. Archived, paraffin-embedded tissue specimens were recently requested for incident CRC cases diagnosed through December 31, 2002. In the present study, useable tissue specimens were obtained and molecularly characterized for 563/1,255 cases (45%), whose baseline age, body mass index, physical activity level, total energy intake and alcohol use were similar to non-retrieved cases (p > 0.05 for each comparison). Alcohol use was categorized as never (n=21,464), < 3.4 g/day (n=8,313) and > 3.4 g/day (n=8,224), based on the median split among users. Molecularly-defined CRC subtypes were categorized as MSI-high (MSIH; n=148), MSI-low or microsatellite stable (MSI-L/MSS; n=400); CIMP-positive (n=167) or CIMP-negative (n=368); and BRAF-mutation (n=154) or BRAF-wildtype (n=391). Relative risks (RRs) and 95% confidence intervals (95% CIs) were estimated for alcohol use compared to never drinkers, using multivariable Cox regression models adjusted for body mass index, waist-to-hip ratio, smoking status, physical activity level, exogenous estrogen use, and daily intakes of total energy, total fat, red meat, sucrose, calcium, folate, methionine and vitamin E.

Results: There was no statistically significant association between alcohol use and overall CRC risk (RR=1.00; 95% CI = 0.86–1.15 for < 3.4 g/day versus none; RR=1.06; 95% CI=0.91–1.24 for >3.4 g/day versus none). Further, there were no associations with alcohol use for specific, molecularly-defined CRC subtypes (RRs shown for > 3.4 g/day versus none): MSI-H (RR=1.07; 95% CI=0.70–1.64); MSI-L or MSS (RR=1.12; 95% CI=0.85–1.47); CIMP-positive (RR=0.97; 95% CI=0.64–1.47); CIMP-negative (RR=1.13; 95% CI=0.85–1.50); BRAF-mutation (RR=0.94; 95% CI=0.61–1.45); and BRAF-wildtype (RR=1.20; 95% CI=0.91–1.57).

Conclusion: In this cohort of older women, alcohol use did not appear to be a risk factor for incident CRC, overall or by the defined molecular subtypes.

Citation Information: Cancer Prev Res 2010;3(1 Suppl):A115.

Characterization, physicochemical properties and biocompatibility of La-incorporated apatites

In this study, the physicochemical properties and biocompatibilities of La-containing apatites were intensively investigated together with their characterizations in terms of composition, structure, valent state and morphology using X-ray diffraction, Fourier-transform infrared spectra, X-ray photoelectron spectroscopy, scanning electron microscopy and energy dispersive X-ray spectroscopy, respectively. The results indicate that the La(3+) ion can be incorporated into the crystal lattice of hydroxyapatite resulting in the production of La-incorporated apatites (La(x)Ca(10-x)(PO(4))(6)(OH)(2+x-2y)O(y square y-x) (x> or =0.5, y<1+x/2) or La(x)Ca(10-x)(PO(4))(6)O(y square y-x) (0.5<x<2, y=1+x/2)) by high-temperature solid phase synthesis. For La content <20%, the product is composed of the major phase, La(x)-OAP, as well as a small amount of tricalcium phosphate, but for a La content of 20%, the product is pure La-incorporated oxyapatite with the formula La(2)Ca(8)(PO(4))(6)O(2) (La(2)-OAP, x=2, y=2). It is also found that the La content plays important roles in both the physicochemical properties and biocompatibilities of the La-incorporated apatites. In contrast to La-free apatite, La-incorporated apatites possess a series of attractive properties, including higher thermal stability, higher flexural strength, lower dissolution rate, larger alkaline phosphatase activity, preferable osteoblast morphology and comparable cytotoxicity. In particular, the sintered La-incorporated apatite block achieves a maximal flexure strength of 66.69+/-0.98 MPa at 5% La content (confidence coefficient 0.95), increased 320% in comparison with the La-free apatite. The present study suggests that the La-incorporated apatite possesses application potential in developing a new type of bioactive coating material for metal implants and also as a promising La carrier for further exploring the beneficial functions of La in the human body.

A new cell culture system for infection with hepatitis B virus that fuses HepG2 cells with primary human hepatocytes

Hepatitis B virus (HBV) infection exhibits a very narrow host range and shows a strong tropism for liver parenchymal cells, however none of the previously established experimental models can reproduce the natural process of HBV infection. In the present study, primary human hepatocytes were fused with HepG2 cells to establish the hybrid HepCHLine-4 cell line with high susceptibility to HBV. The HepCHLine-4 cells expressed HBV-specific antigen when co-incubated with HBV-positive serum from a hepatitis B patient. Post-infection, HBV relaxed circular DNA and covalently closed circular DNA were detected in HepCHLine-4 cells using a nested polymerase chain reaction, and HBV-specific particles were visualized by electron microscopy of the culture media of HepCHLine-4 cells. HepG2 cells were not susceptible to HBV infection under the same conditions. The HepCHLine-4 cells can be sub-cultured for > 12 months while maintaining susceptibility to HBV and may, therefore, be useful for studying HBV infection and the viral life cycle in human hepatocytes.

Genetic variation in B-cell-activating factor is associated with an increased risk of developing B-cell non-Hodgkin lymphoma

Elevated B-cell-activating factor (BAFF; TNFSF13B) levels have been found in patients with B-cell malignancies and autoimmune diseases, suggesting that it may play a pathogenic role. We previously found that a single nucleotide polymorphism (SNP) in the TNFSF13B promoter resulted in increased transcription, suggesting that genetic variation in TNFSF13B may influence its expression. We therefore wanted to determine if genetic variation in TNFSF13B is associated with high BAFF levels and non-Hogkin lymphoma (NHL) risk. We genotyped 9 tagSNPs within TNFSF13B in a clinic-based study of 441 NHL cases and 475 matched controls and evaluated the association of individual SNPs with risk of NHL; 3 tagSNPs were significant (P < 0.05). When categorized into low-, moderate-, and high-risk groups based on risk alleles, we found the permutation-corrected odds ratio for the trend to be 1.43 (P = 0.0019) for risk of B-cell NHL, 1.69 (P = 0.0093) for diffuse large B-cell lymphoma, 1.43 (P = 0.029) for follicular lymphoma, and 1.06 (P = 0.21) for chronic lymphocytic leukemia/small lymphocytic lymphoma. The mean serum BAFF level in those who carried the low-risk alleles was 2 ng/mL compared with 4.3 ng/mL in those with the high-risk alleles (P = 0.02). Taken together, our data suggest that genetic variation in the TNFSF13B gene is significantly associated with NHL risk and elevated serum BAFF levels.

Risk of non-Hodgkin lymphoma in association with germline variation in complement genes

Germline mutations in complement genes have been associated with susceptibility to infections and autoimmune diseases, conditions that are associated with non-Hodgkin lymphoma (NHL) risk. To test the hypothesis that common genetic variation in complement genes affect risk of NHL, we genotyped 167 single nucleotide polymorphisms (SNPs) from 31 genes in 441 NHL cases and 475 controls. Principal components (PC) and haplotype analyses were used for gene-level tests of NHL risk, while individual SNPs were modelled as having a log-additive effect. In gene level PC analyses, C2 (P = 0.023), C5 (P = 0.0032) and C9 (P = 0.020) were associated with NHL risk; haplotype analyses showed similar results, as well as a haplotype association for C7 (P = 0.046). When all four genes were considered simultaneously, only C5 and C9 remained significant (P < 0.05). In SNP level results from these genes, 10 SNPs had a P < 0.05. However, after correcting for multiple testing, only the C5 SNPs rs7026551 (q = 0.015; OR = 1.54, 95% CI 1.21-1.95) and rs2416810 (q = 0.015; OR = 1.57; 95% CI 1.22-2.01), and the C9 SNP rs187875 (q = 0.015; OR = 0.68; 95% 0.56-0.84) remained noteworthy. Associations were similar for the common NHL subtypes. In summary, we provide evidence for a role of genetic variation in complement genes, particularly C5 and C9, and NHL risk.

Genetic variation in tumor necrosis factor and the nuclear factor-kappaB canonical pathway and risk of non-Hodgkin's lymphoma

Non-Hodgkin's lymphoma (NHL) is a cancer closely associated with immune function, and the tumor necrosis factor (TNF) G-308A promoter polymorphism, which influences immune function and regulation, was recently reported by the InterLymph Consortium to be associated with NHL risk. TNF signaling activates the nuclear factor-kappaB (NF-kappaB) canonical pathway, leading to transcriptional activation of multiple genes that influence inflammation and immune response. We hypothesized that, in addition to TNF signaling, common genetic variation in genes from the NF-kappaB canonical pathway may affect risk of NHL. We genotyped 54 single nucleotide polymorphisms (SNP) within TNF, lymphotoxin A LTA, and nine NF-kappaB genes from the canonical pathway (TNFRSF1A, TRADD, TRAF2, TRAF5, RIPK1, CHUK, IKBKB, NFKB1, and REL) in a clinic-based study of 441 incident cases and 475 frequency-matched controls. Tagging SNPs were selected from HapMap supplemented by putative functional SNPs for LTA/TNF. We used principal components and haplo.stats to model gene-level associations and logistic regression to model SNP-level associations. Compared with the wild-type (GG), the AA genotype for the TNF promoter polymorphism G-308A (rs1800629) was associated with increased risk of NHL [odds ratio (OR), 2.14; 95% confidence interval (95% CI), 0.94-4.85], whereas the GA genotype was not (OR, 1.00; 95% CI, 0.74-1.34). This association was similar for follicular lymphoma and diffuse large B-cell lymphoma. A previously reported LTA/TNF haplotype was also associated with NHL risk. In gene-level analysis of the NF-kappaB pathway, only NFKB1 showed a statistically significant association with NHL (P = 0.049), and one NFKB1 tagSNP (rs4648022) was associated with NHL risk overall (ordinal OR, 0.59; 95% CI, 0.41-0.84; Ptrend = 0.0037) and for each of the common subtypes. In conclusion, we provide additional evidence for the role of genetic variation in TNF and LTA SNPs and haplotypes with risk of NHL and also provide some of the first preliminary evidence for an association of genetic variation in NFKB1, a downstream target of TNF signaling, with risk of NHL.

No interaction of body mass index and smoking on diabetes mellitus risk in elderly women

OBJECTIVE

We sought to assess the interaction of smoking and body mass index (BMI) on diabetes risk.

METHODS

We analyzed data from a community-based prospective cohort of 41,836 women from Iowa who completed a baseline survey in 1986 and five subsequent surveys through 2004. The final analysis included 36,839 participants.

RESULTS

At baseline (1986), there were 66% never smokers, 20% former smokers, and 14% current smokers. Subjects represented 40% normal weight, 38% overweight, and 22% obese individuals. Compared to normal weight women, the hazard ratio (HR) for diabetes was increased in overweight (HR 1.96; 95% CI 1.75-2.19) and obese subjects (HR 3.58; 95% CI 3.19-4.02). The hazard ratio for diabetes increased in a dose-dependent manner with smoking intensity. Compared to never smokers, former smokers had a higher risk for diabetes (HR 1.22; 95% CI 1.11-1.34). Among current smokers, the hazard ratio for diabetes was 1.21 (95% CI 0.95-1.53) for 1-19 pack-year smokers, 1.33 (95% CI 1.12-1.57) for 20-39 pack-year smokers, and 1.45 (95% CI 1.23-1.71) for > or =40 pack-year smokers. Similar trends were observed when the results were stratified by BMI. A test of interaction between BMI and smoking on diabetes risk was not statistically significant.

CONCLUSIONS

Our findings suggest that smoking increases diabetes risk through a BMI-independent mechanism.

Prospective evaluation of trans-fatty acid intake and colorectal cancer risk in the Iowa Women's Health Study

Concerns regarding the safety of dietary trans-fatty acids (tFAs) have generated recent public interest, scientific discussion and legislative action. Although most widely recognized as a risk factor for cardiovascular disease, associations between tFA intake and incident cancer have also been proposed. With respect to colorectal cancer (CRC), existing observational data remain limited and inconclusive. Therefore, we conducted a prospective evaluation of tFA intake and CRC risk, overall and by anatomic subsite, among participants in the Iowa Women's Health Study (IWHS), a population-based cohort of older women (ages 55-69 years at enrollment). Exposure data were collected at baseline using a semiquantitative food-frequency questionnaire. Incident CRC cases were identified through annual linkage to the Iowa Cancer Registry. CRC risks were estimated using Cox proportional hazards regression models. In total, 35,216 women met our inclusion criteria and 1,229 CRC cases (631 proximal, 571 distal, 27 site not specified) were observed through 18 years of follow-up. Adjusting for age and total energy consumption, tFA intake in the 4th versus 1st quartile was not significantly associated with overall CRC risk [relative risk (RR) = 1.12; 95% confidence interval (CI) = 0.96-1.32]. Similarly, risk estimates based on proximal (RR = 1.09; 95% CI = 0.87-1.37) and distal (RR = 1.18; 95% CI = 0.93-1.49) CRC subsites did not differ from unity. Multivariable adjustment yielded slightly attenuated risk estimates, but the observed associations were not meaningfully altered. Given these findings, tFA intake does not appear to be a major CRC risk factor, at least among older women.

Susceptibility genes and B-chronic lymphocytic leukaemia

Common genetic variants are thought to increase the risk of chronic lymphocytic leukaemia (CLL), and case-control studies provide an approach to detect these variants. There have been multiple candidate gene studies published to date, but relatively few disease pathway studies or large genomic association studies. We summarize the results of these previous studies, as well as present results from our recent large pathway study of 9412 single nucleotide polymorphisms from 1253 immunity and inflammation genes in a study of 126 CLL cases and 484 frequency-matched controls. Several promising genes have been identified as susceptibility genes for risk of CLL across all of these association studies. However, a number of candidate gene studies have not been replicated in follow-up studies, whereas the results from disease pathway and large genomic studies have yet to be replicated in an independent sample. The challenge of future studies of this type will be overcoming study design issues, including definition of CLL, sample size limitations and multiple testing issues.

Unpasteurized milk consumption and subsequent risk of cancer

Concerns have been raised regarding the possible adverse health effects of consumption of unpasteurized milk and risk of cancer. We examined the association of self-reported intake of unpasteurized milk with subsequent risk of cancer in a large population-based cohort study. The Iowa Women's Health Study is a prospective cohort study of 55-69 year old women at baseline in 1986. Of the 41,836 women in the cohort at baseline, 22,808 cancer-free women completed the fourth follow-up questionnaire in 1997. Risk ratios (RR) and 95% confidence intervals (CI) were calculated using Cox proportional hazards regression analysis. Reported intake of unpasteurized milk was high: 59.2% consumed only as a child, 2.5% consumed only as an adult, and 16.5% consumed as a child and an adult. A total of 2,379 cancers were identified in the cohort at risk. Overall, the age-adjusted risk of cancer was lower among women who reported consumption of unpasteurized milk only as a child (RR = 0.90, 95% CI: 0.82-0.99) or as a child and an adult (RR = 0.85; 95% CI: 0.75-0.97). Adjustment for confounding factors attenuated these associations (RR = 0.92, 95% CI: 0.83-1.02 for consumption only as a child, and RR = 0.91; 95% CI: 0.79-1.04 for consumption as a child and an adult). These data suggest that consumption of unpasteurized milk does not increase risk of cancer.

Relative weight at age 12 and risk of postmenopausal breast cancer

BACKGROUND

Early adolescent weight may affect the risk of postmenopausal breast cancer, and this association may be modified by a family history of breast or ovarian cancer in a first-degree relative, and/or estrogen (ER) and progesterone (PR) receptor status of the disease.

METHODS

Relative weight at age 12 years (above, below, or average weight compared with peers) and family history were ascertained using a mailed questionnaire in 1986, in the Iowa Women's Health Study, a prospective cohort study of postmenopausal women. Incident breast cancer cases (including ER and PR status) were identified using the Iowa Surveillance, Epidemiology, and End Results Cancer Registry. Relative risks (RR) and 95% confidence intervals (95% CI) were estimated using Cox proportional hazards regression, and were adjusted for breast cancer risk factors, including body mass index at age 18 years and body mass index at study baseline.

RESULTS

Through 2003, 2,503 cases of postmenopausal breast cancer were identified among 35,941 women in the analytic cohort. Compared with women with average weight at age 12 years, there was no association of below average weight with risk of breast cancer (RR, 1.02; 95% CI, 0.92-1.13), whereas women with above average weight had a lower risk (RR, 0.85; 95% CI, 0.74-0.98). There was no evidence of an interaction between weight at age 12 years and family history (P = 0.44). The inverse association of above average weight with risk of breast cancer was strongest for PR- tumors (RR, 0.62; 95% CI, 0.43-0.89), intermediate for ER+ (RR, 0.80; 95% CI, 0.67-0.96) and ER- (RR, 0.77; 95% CI, 0.50-1.19) tumors, and weakest for PR+ tumors (RR, 0.90; 95% CI, 0.74-1.09). These associations were not modified by a family history (all P > 0.18). In a joint ER/PR analyses, the strongest inverse association with above average weight at age 12 years was seen for ER+/PR- (RR, 0.49; 95% CI, 0.29-0.85).

CONCLUSION

Above average weight at age 12 years was inversely associated with risk of postmenopausal breast cancer, and was not modified by a family history of the disease. The inverse association was strongest for ER+/PR- tumors.

Genetic variation in 1253 immune and inflammation genes and risk of non-Hodgkin lymphoma

Smaller-scale evaluations suggest that common genetic variation in candidate genes related to immune function may predispose to the development of non-Hodgkin lymphoma (NHL). We report an analysis of variants within genes associated with immunity and inflammation and risk of NHL using a panel of 9412 single-nucleotide polymorphisms (SNPs) from 1253 genes in a study of 458 patients with NHL and 484 frequency-matched controls. We modeled haplotypes and risk of NHL, as well as the main effects for all independent SNPs from a gene in multivariate logistic regression models; we separately report results for nonsynonymous (ns) SNPs. In gene-level analyses, the strongest findings (P < or = .001) were for CREB1, FGG, MAP3K5, RIPK3, LSP1, TRAF1, DUSP2, and ITGB3. In nsSNP analyses, the strongest findings (P < or = .01) were for ITGB3 L59P (odds ratio [OR] = 0.66; 95% confidence interval [CI] 0.52-0.85), TLR6 V427A (OR = 5.20; CI 1.77-15.3), SELPLG M264V (OR = 3.20; CI 1.48-6.91), UNC84B G671S (OR = 1.50; CI 1.12-2.00), B3GNT3 H328R (OR = 0.74; CI 0.59-0.93), and BAT2 V1883L (OR = 0.64; CI 0.45-0.90). Our results suggest that genetic variation in genes associated with immune response (TRAF1, RIPK3, BAT2, and TLR6), mitogen-activated protein kinase (MAPK) signaling (MAP3K5, DUSP2, and CREB1), lymphocyte trafficking and migration (B3GNT3, SELPLG, and LSP1), and coagulation pathways (FGG and ITGB3) may be important in the etiology of NHL, and should be prioritized in replication studies.

Association of Aspirin and Nonaspirin Nonsteroidal Anti-inflammatory Drugs With Cancer Incidence and Mortality

BACKGROUND

The cancer chemopreventive benefits of aspirin and nonaspirin nonsteroidal anti-inflammatory drugs (NSAIDs) are incompletely defined and may vary by smoking history. We evaluated associations between aspirin and nonaspirin NSAID use with cancer incidence and mortality stratified by smoking history in the Iowa Women's Health Study, a prospective cohort of postmenopausal women.

METHODS

Aspirin and nonaspirin NSAID use was self-reported by questionnaire in 1992. Cancer incidence and mortality were ascertained by annual linkage to the Iowa Surveillance, Epidemiology, and End Results Cancer Registry and death certificates. Cox proportional hazards models were used to estimate multivariable relative risks (RRs) and 95% confidence intervals (CIs). All statistical tests were two-sided.

RESULTS

During an average of 10 years of follow-up, 3487 incident cancer cases and 3581 deaths were observed in the cohort of 22,507 women. Compared with nonuse, aspirin use was inversely associated with total cancer incidence (multivariable-adjusted RR = 0.84, 95% CI = 0.77 to 0.90), with age-adjusted incidence rates of 147 and 170 per 10,000 person-years for ever and never users, respectively, and was inversely associated with cancer mortality (multivariable-adjusted RR = 0.87, 95% CI = 0.76 to 0.99), with age-adjusted rates of 47 and 52 per 10,000 person-years. The inverse relationship was stronger among former and never smokers than current smokers, although not statistically significantly (P = .28). Aspirin use was also inversely associated with coronary heart disease mortality (multivariable-adjusted RR = 0.75, 95% CI = 0.64 to 0.89), with age-adjusted rates of 23 and 30 per 10,000 person-years for ever and never users, respectively, and with all-cause mortality (multivariable-adjusted RR = 0.82, 95% CI = 0.76 to 0.89), with age-adjusted rates of 126 and 155 per 10,000 person-years. Nonaspirin NSAID use was not associated with cancer incidence or mortality, coronary heart disease mortality, or all-cause mortality.

CONCLUSIONS

Aspirin use, but not nonaspirin NSAID use, was associated with lower risks of cancer incidence and mortality, which was more pronounced among former and never smokers than current smokers.

Recreational Physical Activity and Risk of Postmenopausal Breast Cancer Based on Hormone Receptor Status

BACKGROUND

Physical activity is a potentially modifiable breast cancer risk factor. There is considerable recent evidence to suggest that risk factors for breast cancer differ based on its subtype, particularly estrogen receptor (ER)/progesterone receptor (PR) status, but this has been less well studied for physical activity. The objective of this study was to examine the association of physical activity with breast cancer incidence based on ER/PR status of the tumor.

METHODS

The Iowa Women's Health Study is a prospective cohort study of 41 836 postmenopausal women. Recreational physical activity was self-reported on the baseline questionnaire, and 3 levels (high, medium, and low) were defined. Breast cancer incidence and ER/PR status, through 18 years of follow-up, were ascertained by linkage with the Iowa Surveillance, Epidemiology, and End Results Cancer Registry. Cox proportional hazards models were used to estimate multivariate relative risks (RRs) and 95% confidence intervals (CIs) of breast cancer, adjusting for other breast cancer risk factors.

RESULTS

During 554 819 person-years of follow-up, 2548 incident cases of breast cancer were observed. Compared with low physical activity, high physical activity levels were inversely associated with risk of breast cancer (RR, 0.86; 95% CI, 0.78-0.96), and there were inverse associations for ER-positive (ER+)/PR-positive (RR, 0.87; 95% CI, 0.75-1.00), ER+/PR-negative (PR-) (RR, 0.67; 95% CI, 0.47-0.96), and ER-negative/PR- (RR, 0.80; 95% CI, 0.56-1.14) tumors. Further adjustment for body mass index attenuated the overall association with breast cancer (RR, 0.91; 95% CI, 0.82-1.01) and for ER+/PR-positive tumors (RR, 0.94; 95% CI, 0.81-1.08), while there was no change for ER+/PR- tumors (RR, 0.66; 95% CI, 0.46-0.94).

CONCLUSIONS

Higher recreational physical activity might reduce the risk of postmenopausal breast cancer overall. Risk reduction varies by ER/PR status of the tumor, being most marked for ER+/PR- tumors, which, in general, have been associated with a clinically more aggressive tumor phenotype. If confirmed in additional studies, these results would suggest that additional mechanisms, besides an effect on body mass, may account for observed protective effects of physical activity in reducing breast cancer.

Image segmentation feature selection and pattern classification for mammographic microcalcifications

Since microcalcifications in X-ray mammograms are the primary indicator of breast cancer, detection of microcalcifications is central to the development of an effective diagnostic system. This paper proposes a two-stage detection procedure. In the first stage, a data driven, closed form mathematical model is used to calculate the location and shape of suspected microcalcifications. When tested on the Nijmegen University Hospital (Netherlands) database, data analysis shows that the proposed model can effectively detect the occurrence of microcalcifications. The proposed mathematical model not only eliminates the need for system training, but also provides information on the borders of suspected microcalcifications for further feature extraction. In the second stage, 61 features are extracted for each suspected microcalcification, representing texture, the spatial domain and the spectral domain. From these features, a sequential forward search (SFS) algorithm selects the classification input vector, which consists of features sensitive only to microcalcifications. Two types of classifiers-a general regression neural network (GRNN) and a support vector machine (SVM)--are applied, and their classification performance is compared using the Az value of the Receiver Operating Characteristic curve. For all 61 features used as input vectors, the test data set yielded Az values of 97.01% for the SVM and 96.00% for the GRNN. With input features selected by SFS, the corresponding Az values were 98.00% for the SVM and 97.80% for the GRNN. The SVM outperformed the GRNN, whether or not the input vectors first underwent SFS feature selection. In both cases, feature selection dramatically reduced the dimension of the input vectors (82% for the SVM and 59% for the GRNN). Moreover, SFS feature selection improved the classification performance, increasing the Az value from 97.01 to 98.00% for the SVM and from 96.00 to 97.80% for the GRNN.

Class II histone deacetylases: structure, function, and regulation

Acetylation of histones, as well as non-histone proteins, plays important roles in regulating various cellular processes. Dynamic control of protein acetylation levels in vivo occurs through the opposing actions of histone acetyltransferases and histone deacetylases (HDACs). In the past few years, distinct classes of HDACs have been identified in mammalian cells. Class I members, such as HDAC1, HDAC2, HDAC3, and HDAC8, are well-known enzymatic transcriptional corepressors homologous to yeast Rpd3. Class II members, including HDAC4, HDAC5, HDAC6, HDAC7, and HDAC9, possess domains similar to the deacetylase domain of yeast Hdal. HDAC4, HDAC5, and HDAC7 function as transcriptional corepressors that interact with the MEF2 transcription factors and the N-CoR, BCoR, and CtBP corepressors. Intriguingly, HDAC4, HDAC5, and probably HDAC7 are regulated through subcellular compartmentalization controlled by site-specific phosphorylation and binding of 14-3-3 proteins; the regulation of these HDACs is thus directly linked to cellular signaling networks. Both HDAC6 and HDAC9 possess unique structural modules, so they may have special biological functions. Comprehension of the structure, function, and regulation of class II deacetylases is important for elucidating how acetylation regulates functions of histones and other proteins in vivo.

Effects of polyamines on the thermal stability and formation kinetics of DNA duplexes with abnormal structure

The effects of ions (i.e. Na+, Mg2+ and polyamines including spermidine and spermine) on the stability of various DNA oligonucleotides in solution were studied. These synthetic DNA molecules contained sequences that mimic various cellular DNA structures, such as duplexes, bulged loops, hairpins and/or mismatched base pairs. Melting temperature curves obtained from the ultraviolet spectroscopic experiments indicated that the effectiveness of the stabilization of cations on the duplex formation follows the order of spermine > spermidine > Mg2+ > Na+ > Tris-HCl buffer alone at pH 7.3. Circular dichroism spectra showed that salts and polyamines did not change the secondary structures of those DNA molecules under study. Surface plasmon resonance (SPR) observations suggested that the rates of duplex formation are independent of the kind of cations used or the structure of the duplexes. However, the rate constants of DNA duplex dissociation decrease in the same order when those cations are involved. The enhancement of the duplex stability by polyamines, especially spermine, can compensate for the instability caused by abnormal structures (e.g. bulged loops, hairpins or mismatches). The effects can be so great as to make the abnormal DNAs as stable as the perfect duplex, both kinetically and thermodynamically. Our results may suggest that the interconversion of various DNA structures can be accomplished readily in the presence of polyamine. This may be relevant in understanding the role of DNA polymorphism in cells.

Mechanism of product chain length determination and the role of a flexible loop in Escherichia coli undecaprenyl-pyrophosphate synthase catalysis

The Escherichia coli undecaprayl-pyrophosphate synthase (UPPs) structure has been solved using the single wavelength anomalous diffraction method. The putative substrate-binding site is located near the end of the betaA-strand with Asp-26 playing a critical catalytic role. In both subunits, an elongated hydrophobic tunnel is found, surrounded by four beta-strands (betaA-betaB-betaD-betaC) and two helices (alpha2 and alpha3) and lined at the bottom with large residues Ile-62, Leu-137, Val-105, and His-103. The product distributions formed by the use of the I62A, V105A, and H103A mutants are similar to those observed for wild-type UPPs. Catalysis by the L137A UPPs, on the other hand, results in predominantly the formation of the C(70) polymer rather than the C(55) polymer. Ala-69 and Ala-143 are located near the top of the tunnel. In contrast to the A143V reaction, the C(30) intermediate is formed to a greater extent and is longer lived in the process catalyzed by the A69L mutant. These findings suggest that the small side chain of Ala-69 is required for rapid elongation to the C(55) product, whereas the large hydrophobic side chain of Leu-137 is required to limit the elongation to the C(55) product. The roles of residues located on a flexible loop were investigated. The S71A, N74A, or R77A mutants displayed 25-200-fold decrease in k(cat) values. W75A showed an 8-fold increase of the FPP K(m) value, and 22-33-fold increases in the IPP K(m) values were observed for E81A and S71A. The loop may function to bridge the interaction of IPP with FPP, needed to initiate the condensation reaction and serve as a hinge to control the substrate binding and product release.

Histone deacetylase 4 possesses intrinsic nuclear import and export signals

Nucleocytoplasmic trafficking of histone deacetylase 4 (HDAC4) plays an important role in regulating its function, and binding of 14-3-3 proteins is necessary for its cytoplasmic retention. Here, we report the identification of nuclear import and export sequences of HDAC4. While its N-terminal 118 residues modulate the nuclear localization, residues 244 to 279 constitute an authentic, strong nuclear localization signal. Mutational analysis of this signal revealed that three arginine-lysine clusters are necessary for its nuclear import activity. As for nuclear export, leucine-rich sequences located in the middle part of HDAC4 do not function as nuclear export signals. By contrast, a hydrophobic motif (MXXLXVXV) located at the C-terminal end serves as a nuclear export signal that is necessary for cytoplasmic retention of HDAC4. This motif is required for CRM1-mediated nuclear export of HDAC4. Furthermore, binding of 14-3-3 proteins promotes cytoplasmic localization of HDAC4 by both inhibiting its nuclear import and stimulating its nuclear export. Unlike wild-type HDAC4, a point mutant with abrogated MEF2-binding ability remains cytoplasmic upon exogenous expression of MEF2C, supporting the notion that direct MEF2 binding targets HDAC4 to the nucleus. Therefore, HDAC4 possesses intrinsic nuclear import and export signals for its dynamic nucleocytoplasmic shuttling, and association with 14-3-3 and MEF2 proteins affects such shuttling and thus directs HDAC4 to the cytoplasm and the nucleus, respectively.

Crystallographic analysis of a novel complex of actinomycin D bound to the DNA decamer CGATCGATCG

The potent anticancer drug actinomycin D (ActD) acts by binding to DNA, thereby interfering with replication and transcription. ActD inhibits RNA polymerase far more specifically than DNA polymerase. Such discrimination is not easily understood by the conventional DNA binding mode of ActD. We have solved and refined at 1.7 A resolution the crystal structure of ActD complexed to CGATCGATCG, which contains no canonical GpC binding sequence. The crystal data are space group P4(3)2(1)2, a = b = 47.01 A, and c = 160.37 A. The structure was solved by the multiple wavelength anomalous diffraction method using a 5-bromo-U DNA. The asymmetric unit of the unit cell contains two independent dimers of a novel slipped duplex complex consisting of two decamer DNA strands bound with two ActD drug molecules. (The DNA in one dimer is numbered C1 to G10 in one strand and C11 to G20 in the complementary strand and in the second dimer, C101 to G110 and C111 to G120, respectively.) The structure reveals a highly unusual ActD binding mode in which the DNA adopts a slipped duplex with the A3-T4/A13-T14 dinucleotides looped out. ActD intercalates between G2-C11* (C11* being from a symmetry-related molecule) and C5-G20 base pairs. Two such slipped duplex-ActD complexes bound to each other by mutually intercalating their T4/T14 bases into the helix cavities (located between C5-G20 and G6-C19 base pairs) of neighboring complexes, forming a dimer of drug-DNA complexes. The binding site mimics the drug binding at the elongation point during transcription. Modeling studies show that the ActD-DNA complex fits snugly in the active site cavity in RNA polymerase but not in DNA polymerase. This may explain the strong preference of ActD inhibition toward transcription.

Ramosetron for the management of chemotherapy-induced gastrointestinal events in patients with hematological malignancies

The objective of this study was to evaluate the efficacy and safety of ramosetron hydrochloride for the management of nausea and vomiting induced by chemotherapy in patients with hematological malignancies. A total of 30 patients with hematological malignancies were included in the ramosetron group. Ramosetron (0.3 mg i.v.) was administered 0.5 h before chemotherapy. The impact of ramosetron on anorexia, nausea and vomiting as well as other adverse effects were assessed. Meanwhile, another 39 patients received tropisetron (o.d. for 3 days). As compared to the tropisetron group, the response rate of the ramosetron group in controlling anorexia within 18-24 h after chemotherapy was higher (p < 0.05); within 18-24 h after chemotherapy, the complete response rate and effective rate in controlling nausea was higher (p < 0.05); within 12-18 h and 18-24 h after chemotherapy, the complete response rate and effective rate in controlling vomiting was higher (p < 0.05). The incidence of adverse effects was similar in both groups. We conclude that ramosetron belongs to a new generation of 5-HT3 receptor antagonists and that it is a safe, economic and effective antiemetic drug.

Histone deacetylase 4 associates with extracellular signal-regulated kinases 1 and 2, and its cellular localization is regulated by oncogenic Ras

Histone deacetylase 4 (HDAC4) is a member of a family of enzymes that catalyze the removal of acetyl groups from core histones, resulting in a compact chromatin structure that is generally associated with repressed gene transcription. Protein phosphorylation has been implicated in the regulation of the corepressor activity of the deacetylase. Here we report that serine/threonine kinases are found in association with HDAC4 and phosphorylate HDAC4 in vitro, and HDAC4 is phosphorylated in cells. The extracellular signal-regulated kinases 1 and 2 (ERK1/2), also known as p44(MAPK) and p42(MAPK), respectively, are two of the kinases associated with HDAC4. ERK1/2 are components of the Ras-mitogen-activated protein kinase (MAPK) signal transduction pathway. Activation of the Ras-MAPK pathway by expression of oncogenic Ras or constitutively active MAPK/ERK kinase 1 results in an increased percentage of cells (from approximately 10% to approximately 70%) that express HDAC4 in the nucleus in C2C12 myoblast cells. In cells transfected with oncogenic Ras, nuclear HDAC4 is associated with kinase activity. Our results provide evidence that protein kinase activity is present in a protein complex with HDAC4 and directly links the Ras-MAPK signal transduction pathway to a mechanism for chromatin remodeling (i.e., histone deacetylation).

The structure of aspartyl dipeptidase reveals a unique fold with a Ser-His-Glu catalytic triad

The three-dimensional structure of Salmonella typhimurium aspartyl dipeptidase, peptidase E, was solved crystallographically and refined to 1.2-A resolution. The structure of this 25-kDa enzyme consists of two mixed beta-sheets forming a V, flanked by six alpha-helices. The active site contains a Ser-His-Glu catalytic triad and is the first example of a serine peptidase/protease with a glutamate in the catalytic triad. The active site Ser is located on a strand-helix motif reminiscent of that found in alpha/beta-hydrolases, but the polypeptide fold and the organization of the catalytic triad differ from those of the known serine proteases. This enzyme is a member of a family of serine hydrolases and appears to represent a new example of convergent evolution of peptidase activity.

Crystal structures of the chromosomal proteins Sso7d/Sac7d bound to DNA containing T-G mismatched base-pairs

Sso7d and Sac7d are two small chromatin proteins from the hyperthermophilic archaeabacterium Sulfolobus solfataricus and Sulfolobus acidocaldarius, respectively. The crystal structures of Sso7d-GTGATCGC, Sac7d-GTGATCGC and Sac7d-GTGATCAC have been determined and refined at 1.45 A, 2.2 A and 2.2 A, respectively, to investigate the DNA binding property of Sso7d/Sac7d in the presence of a T-G mismatch base-pair. Detailed structural analysis revealed that the intercalation site includes the T-G mismatch base-pair and Sso7d/Sac7d bind to that mismatch base-pair in a manner similar to regular DNA. In the Sso7d-GTGATCGC complex, a new inter-strand hydrogen bond between T2O4 and C14N4 is formed and well-order bridging water molecules are found. The results suggest that the less stable DNA stacking site involving a T-G mismatch may be a preferred site for protein side-chain intercalation.

Binding of a macrocyclic bisacridine and ametantrone to CGTACG involves similar unusual intercalation platforms

The binding of a macrocyclic bisacridine and an antitumor intercalator ametantrone to DNA has been studied. We carried out X-ray diffraction analyses of the complexes between both intercalators and CGTACG. We have determined the crystal structure, by the multiple-wavelength anomalous diffraction (MAD) method, of bisacridine complexed with CGTA[br(5)C]G at 1.8 A resolution. The refined native crystal structure at 1.1 A resolution (space group C222, a = 29.58 A, b = 54.04 A, c = 40.22 A, and R-factor = 0.163) revealed that only one acridine of the bisacridine drug binds at the C5pG6 step of the DNA, with the other acridine plus both linkers completely disordered. Surprisingly, both terminal G.C base pairs are unraveled. The C1 nucleotide is disordered, and the G2 base is bridged to its own phosphate P2 through a hydrated Co(2+) ion. G12 is swung toward the minor groove with its base stacked over the backbone. The C7 nucleotide is flipped away from the duplex part and base paired to a 2-fold symmetry-related G6. The central four base pairs adopt the B-DNA conformation. An unusual intercalator platform is formed by bringing four complexes together (involving the 222 symmetry) such that the intercalator cavity is flanked by two sets of G x C base pairs (i.e., C5 x G8 and G6 x C7) on each side, joined together by G6 x G8 tertiary base pairing interactions. In the bisacridine-CGTACG complex, the intercalation platform is intercalated with two acridines, whereas in the ametantrone-CGTACG complex, only one ametantrone is bound. NMR titration of the bisacridine to AACGATCGTT suggests that the bisacridine prefers to bridge more than one DNA duplex by intercalating each acridine to different duplexes. The results may be relevant in understanding binding of certain intercalators to DNA structure associated with the quadruplet helix and Holliday junction.

Regulation of histone deacetylase 4 by binding of 14-3-3 proteins

Histone (de)acetylation is important for the regulation of fundamental biological processes such as gene expression and DNA recombination. Distinct classes of histone deacetylases (HDACs) have been identified, but how they are regulated in vivo remains largely unexplored. Here we describe results demonstrating that HDAC4, a member of class II human HDACs, is localized in the cytoplasm and/or the nucleus. Moreover, we have found that HDAC4 interacts with the 14-3-3 family of proteins that are known to bind specifically to conserved phosphoserine-containing motifs. Deletion analyses suggested that S246, S467, and S632 of HDAC4 mediate this interaction. Consistent with this, alanine substitutions of these serine residues abrogated 14-3-3 binding. Although these substitutions had minimal effects on the deacetylase activity of HDAC4, they stimulated its nuclear localization and thus led to enhanced transcriptional repression. These results indicate that 14-3-3 proteins negatively regulate HDAC4 by preventing its nuclear localization and thereby uncover a novel regulatory mechanism for HDACs.

Ultra-high resolution DNA structures

This paper describes the progress in our efforts at producing ultra-high resolution (< 0.8 A) DNA structures using advanced cryo-crystallography and synchrotron. Our work is aimed at providing reliable geometric (bond length and bond angle), electronic and motional information of DNA molecules in different conformational contexts. These highly-reliable, new structures will be the basis for constructing better DNA force-field parameters, which will benefit the structural refinement of DNA, protein-DNA complexes, and ligand-DNA complexes.

Photoreactivity of 5-iodouracil-containing DNA-Sso7d complex

X-ray structure of DNA-Sso7d complex indicated that binding of this protein causes sharp DNA bending. In order to examine whether this protein also causes DNA bending in solution, photoreactions of 1U-substituted DNA in the presence and the absence of Sso7d protein were investigated. It was found that the unusual intrastrand hydrogen abstraction at methyl of adjacent thymine occurred efficiently at the observed bending site of crystal structure.

Crystallization of peptidase T from Salmonella typhimurium

Aminotripeptidase (peptidase T) from Salmonella typhimurium and a derivative carrying a C-terminal His tag have been crystallized. In both cases, the space group was found to be C2, with a single molecule in the asymmetric unit. Crystals of the native peptidase T diffract to 2.9 A, but a selenomethionine derivative of this protein did not yield good crystals. Crystals of the His-tag peptidase T diffracted to 2.6 A, however, and could be used for the production of good-quality selenomethionine crystals. All 15 methionines, a native metal ion and two mercury reactive sites could be located and crystals suitable for MAD data collection have been produced.

Hexahydrated magnesium ions bind in the deep major groove and at the outer mouth of A-form nucleic acid duplexes

Magnesium ions play important roles in the structure and function of nucleic acids. Whereas the tertiary folding of RNA often requires magnesium ions binding to tight places where phosphates are clustered, the molecular basis of the interactions of magnesium ions with RNA helical regions is less well understood. We have refined the crystal structures of four decamer oligonucleotides, d(ACCGGCCGGT), r(GCG)d(TATACGC), r(GC)d(GTATACGC) and r(G)d(GCGTATACGC) with bound hexahydrated magnesium ions at high resolution. The structures reveal that A-form nucleic acid has characteristic [Mg(H(2)O)(6)](2+)binding modes. One mode has the ion binding in the deep major groove of a GpN step at the O6/N7 sites of guanine bases via hydrogen bonds. Our crystallographic observations are consistent with the recent NMR observations that in solution [Co(NH(3))(6)](3+), a model ion of [Mg(H(2)O)(6)](2+), binds in an identical manner. The other mode involves the binding of the ion to phosphates, bridging across the outer mouth of the narrow major groove. These [Mg(H(2)O)(6)](2+)ions are found at the most negative electrostatic potential regions of A-form duplexes. We propose that these two binding modes are important in the global charge neutralization, and therefore stability, of A-form duplexes.

The genome sequence of Drosophila melanogaster

The fly Drosophila melanogaster is one of the most intensively studied organisms in biology and serves as a model system for the investigation of many developmental and cellular processes common to higher eukaryotes, including humans. We have determined the nucleotide sequence of nearly all of the approximately 120-megabase euchromatic portion of the Drosophila genome using a whole-genome shotgun sequencing strategy supported by extensive clone-based sequence and a high-quality bacterial artificial chromosome physical map. Efforts are under way to close the remaining gaps; however, the sequence is of sufficient accuracy and contiguity to be declared substantially complete and to support an initial analysis of genome structure and preliminary gene annotation and interpretation. The genome encodes approximately 13,600 genes, somewhat fewer than the smaller Caenorhabditis elegans genome, but with comparable functional diversity.

Structure and recognition of sheared tandem G x A base pairs associated with human centromere DNA sequence at atomic resolution

G x A mismatched base pairs are frequently found in nucleic acids. Human centromere DNA sequences contain unusual repeating motifs, e.g. , (GAATG)n x (CATTC)n found in the human chromosome. The purine-rich strand of this repeating pentamer sequence forms duplex and hairpin structures with unusual stability. The high stability of these structures is contributed by the "sheared" G x A base pairs which present a novel recognition surface for ligands and proteins. We have solved the crystal structure, by the multiple-wavelength anomalous diffraction (MAD) method of d(CCGAATGAGG) in which the centromere core sequence motif GAATG is embedded. Three crystal forms were refined to near-atomic resolution. The structures reveal the detailed conformation of tandem G x A base pairs whose unique hydrogen-bonding surface has interesting interactions with bases, hydrated magnesium ions, cobalt(III)hexaammine, spermine, and water molecules. The results are relevant in understanding the structure associated with human centromere sequence in particular and G x A base pairs in nucleic acids (including RNA, like ribozyme) in general.

Imidazole-imidazole pair as a minor groove recognition motif for T:G mismatched base pairs

The T:G mismatched base pair is associated with many genetic mutations. Understanding its biological consequences may be aided by studying the structural perturbation of DNA caused by a T:G base pair and by specific probing of the mismatch using small molecular ligands. We have shown previously that AR-1-144, a tri-imidazole (Im-Im-Im) minor groove binder, recognizes the sequence CCGG. NMR structural analysis of the symmetric 2:1 complex of AR-1-144 and GAACCGGTTC revealed that each AR-1-144 binds to four base pairs with the guanine N2 amino group forming a bifurcated hydrogen bond to a side-by-side Im/Im pair. We predicted that the free G-N2 amino group in a T:G wobble base pair can form two individual hydrogen bonds to a side-by-side Im/Im pair. Thus an Im/Im pair may be a good recognition motif for a T:G base pair in DNA. Cooperative and tight binding of an AR-1-144 homodimer to GAACTGGTTC permits a detailed structural analysis by 2D NOE NMR refinement and the refined structure confirms our prediction. Surprisingly, AR-1-144 does not bind to GAATCGGTTC. We further show that both the Im-Im-Im/Im-Py-Im heterodimer and the Im-Im-Im/Im-Im-Im homodimer bind strongly to the CACGGGTC + GACTCGTG duplex. These results together suggest that an Im/Im pair can specifically recognize a single T:G mismatch. Our results may be useful in future design of molecules (e.g. linked dimers) that can recognize a single T:G mismatch with specificity.

HDAC4, a human histone deacetylase related to yeast HDA1, is a transcriptional corepressor

Histone acetylation plays an important role in regulating chromatin structure and thus gene expression. Here we describe the functional characterization of HDAC4, a human histone deacetylase whose C-terminal part displays significant sequence similarity to the deacetylase domain of yeast HDA1. HDAC4 is expressed in various adult human tissues, and its gene is located at chromosome band 2q37. HDAC4 possesses histone deacetylase activity intrinsic to its C-terminal domain. When tethered to a promoter, HDAC4 represses transcription through two independent repression domains, with repression domain 1 consisting of the N-terminal 208 residues and repression domain 2 containing the deacetylase domain. Through a small region located at its N-terminal domain, HDAC4 interacts with the MADS-box transcription factor MEF2C. Furthermore, HDAC4 and MEF2C individually upregulate but together downmodulate c-jun promoter activity. These results suggest that HDAC4 interacts with transcription factors such as MEF2C to negatively regulate gene expression.

Binocular depth-from-motion in infantile and late-onset esotropia patients with poor stereopsis

PURPOSE

There are at least two possible ways to detect motion-in-depth binocular without monocular cues: the binocular disparities at different times and a mechanism that detects interocular velocity differences. The perception of interocular velocity differences (Binocular depth-from-motion [BDFM]) depends on the relative velocity of the images on the retina of the left and right eyes, and this information can be experienced by normal and some strabismic patients. The purpose of this study was to determine the characteristics of esotropic patients who have BDFM but have poor stereopsis.

METHODS

Forty-one infantile and 28 late-onset esotropia patients with poor stereopsis were studied. Dynamic stereopsis and BDFM were tested with computer-generated random dot stereograms and kinematograms. The correlations between BDFM and other binocular functional tests were determined.

RESULTS

A total of 31 (44.9%) patients, 15 (36.5%) of the infantile and 16 (57.1%) of the late-onset esotropia group, passed the BDFM test. None of these patients passed the random dot stereo test under static or dynamic conditions. Fusion of the Worth four dot test at near 0.3 m was correlated with the presence of BDFM. Three of the 15 infantile and 10 of the 16 late-onset esotropic patients with positive BDFM showed gross stereopsis as measured by the Titmus Fly. The angle of strabismus was significantly smaller in the patients with positive BDFM for the infantile and the late-onset esotropia groups.

CONCLUSIONS

BDFM was present in about half of the esotropic patients who do not have fine stereopsis. Ocular alignment within 10 to 15 prism diopters is an important factor in obtaining BDFM. Strabismus surgery still provides some binocular benefit for infantile esotropia patients who were bypassed for early surgery. Separate mechanisms may underlie static stereopsis and BDFM.

Identification of a human histone acetyltransferase related to monocytic leukemia zinc finger protein

We describe here the identification and functional characterization of a novel human histone acetyltransferase, termed MORF (monocytic leukemia zinc finger protein-related factor). MORF is a 1781-residue protein displaying significant sequence similarity to MOZ (monocytic leukemia zinc finger protein). MORF is ubiquitously expressed in adult human tissues, and its gene is located at human chromosome band 10q22. MORF has intrinsic histone acetyltransferase activity. In addition to its histone acetyltransferase domain, MORF possesses a strong transcriptional repression domain at its N terminus and a highly potent activation domain at its C terminus. Therefore, MORF is a novel histone acetyltransferase that contains multiple functional domains and may be involved in both positive and negative regulation of transcription.

Solution structure of a DNA duplex containing a cis-diammineplatinum(II) 1,3-d(GTG) intrastrand cross-link, a major adduct in cells treated with the anticancer drug carboplatin

The platinum 1,3-d(GXG) intrastrand cross-link is one of the adducts formed in the reaction of the antitumor drug cisplatin with DNA, and in fact the major adduct found in cells treated with the cisplatin analogue carboplatin. To determine the 3D structure of this adduct, the duplex d(CTCTGTGTCTC).d(GAGACACAGAG)], where GTG denotes a platinum 1,3-intrastrand cross-link, was prepared and studied with high-resolution (1)H NMR. The solution structure was determined using the SPEDREF protocol, which includes an iterative NOE-restrained refinement procedure. Calculated and recorded NOE spectra were found to be in good agreement (NMR R factor 22%). The studied duplex is more distorted from B-DNA than previously determined structures of the 1,2-d(GG) intrastrand adducts. The base pairing is lost for the 5'G-C and the central T-A base pair in the GTG lesion, and the central thymine is extruded from the minor groove. To accommodate this lesion, the minor groove is widened, and the 5'-guanine ribose adopts an N-type conformation. The helix is unwound locally and is significantly bent toward the major groove. Significant difference between the structural distortion of the 1, 3-d(GTG) cross-link and other Pt-DNA cross-links sheds new light on the observed differences in protein recognition of these lesions, and thus on the possible differences in mechanisms of action of the various Pt-DNA adducts formed in treatment with platinum anticancer complexes.

Structural studies of atom-specific anticancer drugs acting on DNA

The interactions of many important anticancer drugs with DNA play important roles in their biological functions. In fact, DNA can be considered as a macromolecular receptor for those drugs. There are several classes of DNA-acting anticancer drugs. Some form noncovalent complexes with DNA by either intercalation (such as daunorubicin and doxorubicin) or groove-binding (such as distamycin A). Others, such as cisplatin, mitomycin C, and ecteinascidins, form covalent linkages with DNA. Finally, some (e.g., duocarmycin/CC-1065, bleomycin/pepleomycin, and enediyne antibiotics) cause DNA backbone cleavages. During the past decade, the detailed molecular interactions of several DNA-acting anticancer drugs with DNA have been studied with structural tools, including high resolution X-ray diffraction and NMR spectroscopy. These results have provided useful insights into DNA conformation and drug-DNA interactions. In particular, it was found that specific atomic sites on DNA are often the targets for drug covalent actions. Here we review the structural aspects of the interactions of several anticancer drugs acting on: (1) the N2 amino group of guanine in the minor groove, (2) the N3 atom of guanine and adenine in the minor groove, (3) the N7 atom of guanine and adenine in the major groove, and finally, (4) the C4', C5', and C1' atoms of the deoxyribose in the backbone of B-DNA double-helix. Understanding the underlying mechanism of the drug action at the cellular and molecular levels through those structural studies should be useful in the development of new anticancer drugs.

The solution structure of the Sac7d/DNA complex: a small-angle X-ray scattering study

Small-angle X-ray scattering has been used to study the structure of the multimeric complexes that form between double-stranded DNA and the archaeal chromatin protein Sac7d from Sulfolobus acidocaldarius. Scattering data from complexes of Sac7d with a defined 32-mer oligonucleotide, with poly[d(GC)], and with E. coli DNA indicate that the protein binds along the surface of an extended DNA structure. Molecular models of fully saturated Sac7d/DNA complexes were constructed using constraints from crystal structure and solution binding data. Conformational space was searched systematically by varying the parameters of the models within the constrained set to find the best fits between the X-ray scattering data and simulated scattering curves. The best fits were obtained for models composed of repeating segments of B-DNA with sharp kinks at contiguous protein binding sites. The results are consistent with extrapolation of the X-ray crystal structure of a 1:1 Sac7d/octanucleotide complex [Robinson, H., et al. (1998) Nature 392, 202-205] to polymeric DNA. The DNA conformation in our multimeric Sac7d/DNA model has the base pairs tilted by about 35 degrees and displaced 3 A from the helix axis. There is a large roll between two base pairs at the protein-induced kink site, resulting in an overall bending angle of about 70 degrees for Sac7d binding. Regularly repeating bends in the fully saturated complex result in a zigzag structure with negligible compaction of DNA. The Sac7d molecules in the model form a unique structure with two left-handed helical ribbons winding around the outside of the right-handed duplex DNA.

Binding of AR-1-144, a tri-imidazole DNA minor groove binder, to CCGG sequence analyzed by NMR spectroscopy

The interactions of N-[2-(dimethylamino)ethyl]-1-methyl-4-[1-methyl-4-[4-formamido-1-meth ylimidazole-2-carboxamido]imidazole-2-carboxamido]imidazole-2-c arboxa mide (AR-1-144), a tri-imidazole polyamide minor groove binder, with DNA have been investigated by NMR and CD spectroscopy. A series of DNA oligonucleotides with a C/G-containing four-bp core, i.e. CCGG, CGCG, GGCC, and GCGC, have been titrated with AR-1-144 at different ratios. AR-1-144 favors the CCGG sequence. The flanking sequence of the CCGG core also influences the binding preference, with a C or T being favored on the 3'-side of the CCGG core. The three-dimensional structure of the symmetric 2:1 side-by-side complex of AR-1-144 and GAACCGGTTC, determined by NOE-constrained NMR refinement, reveals that each AR-1-144 binds to four base pairs, i.e. at C5-G6-G7-T8, with every amide-imidazole unit forming two potential hydrogen bonds with DNA. The same DNA binding preference of AR-1-144 was also confirmed by circular dichroism spectroscopy, indicating that the DNA binding preference of AR-1-144 is independent of concentration. The cooperative binding of an AR-1-144 homodimer to the (purine)CCGG(pyrimidine) core sequence appears to be weaker than that of the distamycin A homodimer to A/T sequences, most likely due to the diminished hydrophobic interactions between AR-1-144 and DNA. Our results are consistent with previous footprinting data and explain the binding pattern found in the crystal structure of a di-imidazole drug bound to CATGGCCATG.

Structural basis of electron transfer modulation in the purple CuA center

The X-ray structure of an engineered purple CuA center in azurin from Pseudomonas aeruginosa has been determined and refined at 1.65 A resolution. Two independent purple CuA azurin molecules are in the asymmetric unit of a new P21 crystal, and they have nearly identical conformations (rmsd of 0.27 A for backbone atoms). The purple CuA azurin was produced by the loop-engineering strategy, and the resulting overall structure is unperturbed. The insertion of a slightly larger Cu-binding loop into azurin causes the two structural domains of azurin to move away from each other. The high-resolution structure reveals the detailed environment of the delocalized mixed-valence [Cu(1.5).Cu(1.5)] binuclear purple CuA center, which serves as a useful reference model for other native proteins, and provides a firm basis for understanding results from spectroscopic and functional studies of this class of copper center in biology. The two independent Cu-Cu distances of 2.42 and 2.35 A (with respective concomitant adjustments of ligand-Cu distances) are consistent with that (2.39 A) obtained from X-ray absorption spectroscopy with the same molecule, and are among the shortest Cu-Cu bonds observed to date in proteins or inorganic complexes. A comparison of the purple CuA azurin structure with those of other CuA centers reveals an important relationship between the angular position of the two His imidazole rings with respect to the Cu2S2(Cys) core plane and the distance between the Cu and the axial ligand. This relationship strongly suggests that the fine structural variation of different CuA centers can be correlated with the angular positions of the two histidine rings because, from these positions, one can predict the relative axial ligand interactions, which are responsible for modulating the Cu-Cu distance and the electron transfer properties of the CuA centers.

High-resolution A-DNA crystal structures of d(AGGGGCCCCT). An A-DNA model of poly(dG) x poly(dC)

A-DNA conformation is favored by guanine-rich sequences, such as (dG)n x (dC)n, or under low-humidity conditions. Earlier A-DNA crystal structures revealed some conformational variations which may be the result of sequence-dependent effects and/or crystal packing forces. Here we report the high-resolution crystal structure of d(AGGGGCCCCT) in two crystal forms (either in the P212121 or the P6122 space group) to gain insights into the conformation and dynamics of the (dG)n x (dC)n sequence. The P212121 form has been analyzed using data to 1.1 A resolution by the anisotropic temperature factor refinement procedure of the SHELX97 program. Such analysis affords us with the detailed geometric, conformational and motional property of an A-DNA structure. The backbone torsional angles fall in a narrow range, except for the alpha/gamma angles which have two distinct combinations (gauche-/gauche+ or trans/trans). An A-DNA model of poly(dG) x poly(dC) has been constructed using the conformational parameters derived from the crystal structure of the P212121 form. In the crystal structure of the P6122 space group, the central eight base pairs of the decamer adopt A-DNA conformation with the two terminal nucleotides flipped out to form base pairs with the neighboring nucleotides. Comparison of the A-DNA structure of the same sequence from two different crystal forms, reinforced the conclusion that molecules crystallized in the same space group have a more similar conformation, whereas the same molecule crystallized in different space groups has different (local) conformations.