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1.  Exome-Wide Association Study of Endometrial Cancer in a Multiethnic Population 
PLoS ONE  2014;9(5):e97045.
Endometrial cancer (EC) contributes substantially to total burden of cancer morbidity and mortality in the United States. Family history is a known risk factor for EC, thus genetic factors may play a role in EC pathogenesis. Three previous genome-wide association studies (GWAS) have found only one locus associated with EC, suggesting that common variants with large effects may not contribute greatly to EC risk. Alternatively, we hypothesize that rare variants may contribute to EC risk. We conducted an exome-wide association study (EXWAS) of EC using the Infinium HumanExome BeadChip in order to identify rare variants associated with EC risk. We successfully genotyped 177,139 variants in a multiethnic population of 1,055 cases and 1,778 controls from four studies that were part of the Epidemiology of Endometrial Cancer Consortium (E2C2). No variants reached global significance in the study, suggesting that more power is needed to detect modest associations between rare genetic variants and risk of EC.
doi:10.1371/journal.pone.0097045
PMCID: PMC4014590  PMID: 24810602
2.  A genome-wide association study of breast cancer in women of African ancestry 
Human genetics  2012;132(1):39-48.
Genome-wide association studies (GWAS) in diverse populations are needed to reveal variants that are more common and/or limited to defined populations. We conducted a GWAS of breast cancer in women of African ancestry, with genotyping of > 1,000,000 SNPs in 3,153 African American cases and 2,831 controls, and replication testing of the top 66 associations in an additional 3,607 breast cancer cases and 11,330 controls of African ancestry. Two of the 66 SNPs replicated (p < 0.05) in stage 2, which reached statistical significance levels of 10−6 and 10−5 in the stage 1 and 2 combined analysis (rs4322600 at chromosome 14q31: OR = 1.18, p = 4.3×10−6; rs10510333 at chromosome 3p26: OR = 1.15, p = 1.5×10−5). These suggestive risk loci have not been identified in previous GWAS in other populations and will need to be examined in additional samples. Identification of novel risk variants for breast cancer in women of African ancestry will demand testing of a substantially larger set of markers from stage 1 in a larger replication sample.
doi:10.1007/s00439-012-1214-y
PMCID: PMC3749077  PMID: 22923054
GWAS; breast cancer; African ancestry; common genetic variation
3.  Genome-wide association study of endometrial cancer in E2C2 
Human Genetics  2013;133(2):211-224.
Endometrial cancer (EC), a neoplasm of the uterine epithelial lining, is the most common gynecological malignancy in developed countries and the fourth most common cancer among US women. Women with a family history of EC have an increased risk for the disease, suggesting that inherited genetic factors play a role. We conducted a two-stage genome-wide association study of Type I EC. Stage 1 included 5,472 women (2,695 cases and 2,777 controls) of European ancestry from seven studies. We selected independent single-nucleotide polymorphisms (SNPs) that displayed the most significant associations with EC in Stage 1 for replication among 17,948 women (4,382 cases and 13,566 controls) in a multiethnic population (African America, Asian, Latina, Hawaiian and European ancestry), from nine studies. Although no novel variants reached genome-wide significance, we replicated previously identified associations with genetic markers near the HNF1B locus. Our findings suggest that larger studies with specific tumor classification are necessary to identify novel genetic polymorphisms associated with EC susceptibility.
Electronic supplementary material
The online version of this article (doi:10.1007/s00439-013-1369-1) contains supplementary material, which is available to authorized users.
doi:10.1007/s00439-013-1369-1
PMCID: PMC3898362  PMID: 24096698
4.  Antiviral therapy for hepatitis B virus-related hepatocellular carcinoma after radical hepatectomy 
Cancer Biology & Medicine  2013;10(3):158-164.
Objective
To assess the effect of antiviral therapy for hepatitis B virus (HBV)-related hepatocellular carcinoma (HCC) after radical hepatectomy.
Methods
A total of 478 HBV-related HCC patients treated by radical hepatectomy were retrospectively collected. Patients in the treatment group (n=141) received postoperative lamivudine treatment (100 mg/d), whereas patients in the control group (n=337) did not. Recurrence-free survival (RFS) rates, overall survival (OS) rates, treatments for recurrent HCC and cause of death were compared between the two groups. Propensity score matching (PSM) analysis was also conducted to reduce confounding bias between the two groups.
Results
The 1-, 3-, and 5-year RFS rates didn't significantly differ between the two groups (P=0.778); however, the 1-, 3-, and 5-year OS rates in the treatment group were significantly higher than those in the control group (P=0.002). Similar results were observed in the matched data. Subgroup analysis showed that antiviral treatment conferred a significant survival benefit for Barcelona Clinical Liver Cancer stage A/B patients. Following HCC recurrence, more people in the treatment group were able to choose curative treatments than those in the control group (P=0.031). For cause of death, fewer people in the treatment group died of liver failure than those in the control group (P=0.041).
Conclusion
Postoperative antiviral therapy increases chances of receiving curative treatments for recurrent HCC and prevents death because of liver failure, thereby significantly prolonging OS, especially in early- or intermedian-stage tumors.
doi:10.7497/j.issn.2095-3941.2013.03.006
PMCID: PMC3860342  PMID: 24379991
Antiviral therapy; hepatocellular carcinoma; propensity score matching; recurrence-free survival rate
5.  HGPGD: The Human Gene Population Genetic Difference Database 
PLoS ONE  2013;8(5):e64150.
Demographic events such as migration, and evolutionary events like mutation and recombination, have contributed to the genetic variations that are found in the human genome. During the evolution and differentiation of human populations, different functional genes and pathways (a group of genes that act together to perform specific biological tasks) would have displayed different degrees of genetic diversity or evolutionary conservatism. To query the genetic differences of functional genes or pathways in populations, we have developed the human gene population genetic difference (HGPGD) database. Currently, 11 common population genetic features, 18,158 single human genes, 220 KEGG (Kyoto Encyclopedia of Genes and Genomes) human pathways and 4,639 Gene Ontology (GO) categories (3,269 in biological process; 862 in molecular function; and 508 in cellular component) are available in the HGPGD database. The 11 population genetic features are related mainly to three aspects: allele frequency, linkage disequilibrium pattern, and transferability of tagSNPs. By entering a list of Gene IDs, KEGG pathway IDs or GO category IDs and selecting a population genetic feature, users can search the genetic differences between pairwise HapMap populations. We hope that, when the researchers carry out gene-based, KEGG pathway-based or GO category-based research, they can take full account of the genetic differences between populations. The HGPGD database (V1.0) is available at http://www.bioapp.org/hgpgd.
doi:10.1371/journal.pone.0064150
PMCID: PMC3661546  PMID: 23717556
6.  Evaluating genetic risk for prostate cancer among Japanese and Latinos 
Background
There have been few genome-wide association studies (GWAS) of prostate cancer among diverse populations. To search for novel prostate cancer risk variants, we conducted GWAS of prostate cancer in Japanese and Latinos. In addition, we tested prostate cancer risk variants and developed genetic risk models of prostate cancer for Japanese and Latinos.
Methods
Our first stage GWAS of prostate cancer included Japanese (cases/controls=1,033/1,042) and Latino (cases/controls=1,043/1,057) from the Multiethnic Cohort. Significant associations from stage 1 (P < 1.0×10−4) were examined in silico in GWAS of prostate cancer (stage 2) in Japanese (cases/controls=1,583/3,386) and Europeans (cases/controls=1,854/1,894).
Results
No novel stage 1 SNPs outside of known risk regions reached genome-wide significance. For Japanese, in stage 1, the most notable putative novel association was seen with 10 SNPs (P<8.0. x10−6) at chromosome 2q33; however, this was not replicated in stage 2. For Latinos, the most significant association was observed with rs17023900 at the known 3p12 risk locus (stage 1: OR=1.45; P=7.01×10−5 and stage 2: OR=1.58; P =3.05×10−7). The majority of the established risk variants for prostate cancer, 79% and 88%, were positively associated with prostate cancer in Japanese and Latinos (stage I), respectively. The cumulative effects of these variants significantly influence prostate cancer risk (OR per allele=1.10; P = 2.71×10−25 and OR=1.07; P = 1.02×10−16 for Japanese and Latinos, respectively).
Conclusion and Impact
Our GWAS of prostate cancer did not identify novel genome-wide significant variants. However, our findings demonstrate that established risk variants for prostate cancer significantly contribute to risk among Japanese and Latinos.
doi:10.1158/1055-9965.EPI-12-0598
PMCID: PMC3494732  PMID: 22923026
7.  Genome-Wide Testing of Putative Functional Exonic Variants in Relationship with Breast and Prostate Cancer Risk in a Multiethnic Population 
PLoS Genetics  2013;9(3):e1003419.
Rare variation in protein coding sequence is poorly captured by GWAS arrays and has been hypothesized to contribute to disease heritability. Using the Illumina HumanExome SNP array, we successfully genotyped 191,032 common and rare non-synonymous, splice site, or nonsense variants in a multiethnic sample of 2,984 breast cancer cases, 4,376 prostate cancer cases, and 7,545 controls. In breast cancer, the strongest associations included either SNPs in or gene burden scores for genes LDLRAD1, SLC19A1, FGFBP3, CASP5, MMAB, SLC16A6, and INS-IGF2. In prostate cancer, one of the most associated SNPs was in the gene GPRC6A (rs2274911, Pro91Ser, OR = 0.88, P = 1.3×10−5) near to a known risk locus for prostate cancer; other suggestive associations were noted in genes such as F13A1, ANXA4, MANSC1, and GP6. For both breast and prostate cancer, several of the most significant associations involving SNPs or gene burden scores (sum of minor alleles) were noted in genes previously reported to be associated with a cancer-related phenotype. However, only one of the associations (rs145889899 in LDLRAD1, p = 2.5×10−7 only seen in African Americans) for overall breast or prostate cancer risk was statistically significant after correcting for multiple comparisons. In addition to breast and prostate cancer, other cancer-related traits were examined (body mass index, PSA level, and alcohol drinking) with a number of known and potentially novel associations described. In general, these findings do not support there being many protein coding variants of moderate to high risk for breast and prostate cancer with odds ratios over a range that is probably required for protein coding variation to play a truly outstanding role in risk heritability. Very large sample sizes will be required to better define the role of rare and less penetrant coding variation in prostate and breast cancer disease genetics.
Author Summary
For breast and prostate cancer, GWAS have revealed many risk variants (>70 for each cancer as of this report). All together the common variants in these regions explain only a minority of familial risk of these cancers. Using the Illumina HumanExome SNP array, we explored the hypothesis of rare coding variation contributing to breast and prostate cancer risk in a sample of African American, Latino, Japanese, Native Hawaiian, and European American breast and prostate cancer cases and controls from the Multiethnic Cohort study. While only one association exceeded significance thresholds after correcting for multiple comparisons, a number of suggestive associations involving genes previously reported to be associated with a cancer-related phenotype were noted. Our results do not generally support a major role of protein-coding variants with odds ratios over a range that is probably required for protein coding variation to play a truly outstanding role in risk heritability. If very rare and/or less penetrant coding variants underlie disease heritability of these cancers, then very large sample sizes (i.e. consortia) will be required for their discovery.
doi:10.1371/journal.pgen.1003419
PMCID: PMC3610631  PMID: 23555315
8.  A Genome-Wide Scan for Breast Cancer Risk Haplotypes among African American Women 
PLoS ONE  2013;8(2):e57298.
Genome-wide association studies (GWAS) simultaneously investigating hundreds of thousands of single nucleotide polymorphisms (SNP) have become a powerful tool in the investigation of new disease susceptibility loci. Haplotypes are sometimes thought to be superior to SNPs and are promising in genetic association analyses. The application of genome-wide haplotype analysis, however, is hindered by the complexity of haplotypes themselves and sophistication in computation. We systematically analyzed the haplotype effects for breast cancer risk among 5,761 African American women (3,016 cases and 2,745 controls) using a sliding window approach on the genome-wide scale. Three regions on chromosomes 1, 4 and 18 exhibited moderate haplotype effects. Furthermore, among 21 breast cancer susceptibility loci previously established in European populations, 10p15 and 14q24 are likely to harbor novel haplotype effects. We also proposed a heuristic of determining the significance level and the effective number of independent tests by the permutation analysis on chromosome 22 data. It suggests that the effective number was approximately half of the total (7,794 out of 15,645), thus the half number could serve as a quick reference to evaluating genome-wide significance if a similar sliding window approach of haplotype analysis is adopted in similar populations using similar genotype density.
doi:10.1371/journal.pone.0057298
PMCID: PMC3585353  PMID: 23468962
9.  The Glutathione S-Transferase P1 341C>T Polymorphism and Cancer Risk: A Meta-Analysis of 28 Case-Control Studies 
PLoS ONE  2013;8(2):e56722.
Background
GSTP1, which is one major group of the glutathione S-transferase family, plays an important role in the metabolism of carcinogens and toxins, reducing damage of DNA as a suppressor of carcinogenesis. The 341C>T polymorphism of the GSTP1 has been implicated in cancer risk through cutting down its metabolic detoxification activities. However, results from previous studies remain conflicting rather than conclusive. To clarify the correlation and provide more statistical evidence for detecting the significance of 341C>T, a meta-analysis was conducted.
Methodology/Principal Findings
The relevant studies were identified through searching of PubMed, Embase, ISI Web of Knowledge and China National Knowledge Infrastructure in August 2012, and selected based on the established inclusion criteria for publications, then a meta-analysis was performed to quantitatively summarize the association of GSTP1 341C>T polymorphism with cancer susceptibility. Stratified analyses were employed to identify the source of heterogeneity. Publication bias was evaluated as well as sensitivity analysis. Based on 28 case-control studies with 13249 cases and 16798 controls, the pooled results indicated that the variant genotypes significantly increased the risk of cancer in homozygote comparison (TT versus CC: P = 0.012, OR = 1.40, 95% CI: 1.08–1.81, Phet. = 0.575), and recessive model (TT versus CT/CC: P = 0.012, OR = 1.40, 95% CI: 1.08–1.81, Phet. = 0.562). This was confirmed when stratified analyses were conducted according to ethnicity, source of control, matched control, quality score and cancer types. Moreover, significantly increased risk of cancer was also found in lung cancer (heterozygote comparison and dominant model). The stability of these observations was confirmed by a sensitivity analysis. Begger's funnel plot and Egger's test did not reveal any publication bias.
Conclusions/Significance
This meta-analysis suggests that the GSTP1 341C>T polymorphism may contribute to genetic susceptibility to cancer, especially to lung cancer, and in Asian population. Nevertheless, additional well-designed studies focusing on different ethnicity and cancer types are needed to provide a more exact and comprehensive conclusion.
doi:10.1371/journal.pone.0056722
PMCID: PMC3578943  PMID: 23437223
10.  Discovery and verification of gelsolin as a potential biomarker of colorectal adenocarcinoma in a Chinese population: Examining differential protein expression using an iTRAQ labelling-based proteomics approach 
Despite the wide range of available colorectal cancer (CRC) screening tests, less than 50% of cases are detected at early stages. However, the identification of differentially expressed proteins or novel protein biomarkers in CRC may have some utility and, ultimately, improve patient care and survival. Proteomics combined with mass spectroscopy and liquid chromatography are emerging as powerful tools that have led to the discovery of potential markers in cancer biomarker discovery in several types of cancers. This article describes a novel technology that uses isotopic reagents to tag selected proteins that show a consistent pattern of differential expression in CRC.
OBJECTIVE:
To identify and validate potential biomarkers of colorectal adenocarcinoma using a proteomic approach.
METHODS:
Multidimensional liquid chromatography/mass spectrometry was used to analyze biological samples labelled with isobaric mass tags for relative and absolute quantitation to identify differentially expressed proteins in human colorectal adenocarcinoma and paired normal mucosa for the discovery of cancerous biomarkers. Cancerous and noncancerous samples were compared using online and offline separation. Protein identification was performed using mass spectrometry. The downregulation of gelsolin protein in colorectal adenocarcinoma samples was confirmed by Western blot analysis and validated using immunohistochemistry.
RESULTS:
A total of 802 nonredundant proteins were identified in colorectal adenocarcinoma samples, 82 of which fell outside the expression range of 0.8 to 1.2, and were considered to be potential cancer-specific proteins. Immunohistochemistry revealed a complete absence of gelsolin expression in 86.89% of samples and a reduction of expression in 13.11% of samples, yielding a sensitivity of 86.89% and a specificity of 100% for distinguishing colorectal adenocarcinoma from normal tissue.
CONCLUSIONS:
These findings suggest that decreased expression of gelsolin is a potential biomarker of colorectal adenocarcinoma.
PMCID: PMC3275404  PMID: 22288069
Biomarker; Colorectal cancer; Gelsolin; Proteomic
11.  A common variant at the TERT-CLPTM1L locus is associated with estrogen receptor–negative breast cancer 
Haiman, Christopher A | Chen, Gary K | Vachon, Celine M | Canzian, Federico | Dunning, Alison | Millikan, Robert C | Wang, Xianshu | Ademuyiwa, Foluso | Ahmed, Shahana | Ambrosone, Christine B | Baglietto, Laura | Balleine, Rosemary | Bandera, Elisa V | Beckmann, Matthias W | Berg, Christine D | Bernstein, Leslie | Blomqvist, Carl | Blot, William J | Brauch, Hiltrud | Buring, Julie E | Carey, Lisa A | Carpenter, Jane E | Chang-Claude, Jenny | Chanock, Stephen J | Chasman, Daniel I | Clarke, Christine L | Cox, Angela | Cross, Simon S | Deming, Sandra L | Diasio, Robert B | Dimopoulos, Athanasios M | Driver, W Ryan | Dünnebier, Thomas | Durcan, Lorraine | Eccles, Diana | Edlund, Christopher K | Ekici, Arif B | Fasching, Peter A | Feigelson, Heather S | Flesch-Janys, Dieter | Fostira, Florentia | Försti, Asta | Fountzilas, George | Gerty, Susan M | Giles, Graham G | Godwin, Andrew K | Goodfellow, Paul | Graham, Nikki | Greco, Dario | Hamann, Ute | Hankinson, Susan E | Hartmann, Arndt | Hein, Rebecca | Heinz, Judith | Holbrook, Andrea | Hoover, Robert N | Hu, Jennifer J | Hunter, David J | Ingles, Sue A | Irwanto, Astrid | Ivanovich, Jennifer | John, Esther M | Johnson, Nicola | Jukkola-Vuorinen, Arja | Kaaks, Rudolf | Ko, Yon-Dschun | Kolonel, Laurence N | Konstantopoulou, Irene | Kosma, Veli-Matti | Kulkarni, Swati | Lambrechts, Diether | Lee, Adam M | Le Marchand, Loïc | Lesnick, Timothy | Liu, Jianjun | Lindstrom, Sara | Mannermaa, Arto | Margolin, Sara | Martin, Nicholas G | Miron, Penelope | Montgomery, Grant W | Nevanlinna, Heli | Nickels, Stephan | Nyante, Sarah | Olswold, Curtis | Palmer, Julie | Pathak, Harsh | Pectasides, Dimitrios | Perou, Charles M | Peto, Julian | Pharoah, Paul D P | Pooler, Loreall C | Press, Michael F | Pylkäs, Katri | Rebbeck, Timothy R | Rodriguez-Gil, Jorge L | Rosenberg, Lynn | Ross, Eric | Rüdiger, Thomas | Silva, Isabel dos Santos | Sawyer, Elinor | Schmidt, Marjanka K | Schulz-Wendtland, Rüdiger | Schumacher, Fredrick | Severi, Gianluca | Sheng, Xin | Signorello, Lisa B | Sinn, Hans-Peter | Stevens, Kristen N | Southey, Melissa C | Tapper, William J | Tomlinson, Ian | Hogervorst, Frans B L | Wauters, Els | Weaver, JoEllen | Wildiers, Hans | Winqvist, Robert | Van Den Berg, David | Wan, Peggy | Xia, Lucy Y | Yannoukakos, Drakoulis | Zheng, Wei | Ziegler, Regina G | Siddiq, Afshan | Slager, Susan L | Stram, Daniel O | Easton, Douglas | Kraft, Peter | Henderson, Brian E | Couch, Fergus J
Nature Genetics  2011;43(12):1210-1214.
Estrogen receptor (ER)-negative breast cancer shows a higher incidence in women of African ancestry compared to women of European ancestry. In search of common risk alleles for ER-negative breast cancer, we combined genome-wide association study (GWAS) data from women of African ancestry (1,004 ER-negative cases and 2,745 controls) and European ancestry (1,718 ER-negative cases and 3,670 controls), with replication testing conducted in an additional 2,292 ER-negative cases and 16,901 controls of European ancestry. We identified a common risk variant for ER-negative breast cancer at the TERT-CLPTM1L locus on chromosome 5p15 (rs10069690: per-allele odds ratio (OR) = 1.18 per allele, P = 1.0 × 10−10). The variant was also significantly associated with triple-negative (ER-negative, progesterone receptor (PR)-negative and human epidermal growth factor-2 (HER2)-negative) breast cancer (OR = 1.25, P = 1.1 × 10−9), particularly in younger women (<50 years of age) (OR = 1.48, P = 1.9 × 10−9). Our results identify a genetic locus associated with estrogen receptor negative breast cancer subtypes in multiple populations.
doi:10.1038/ng.985
PMCID: PMC3279120  PMID: 22037553
12.  Genome-wide association study of prostate cancer in men of African ancestry identifies a susceptibility locus at 17q21 
Nature genetics  2011;43(6):570-573.
In search of common risk alleles for prostate cancer that could contribute to high rates of the disease in men of African ancestry, we conducted a genome-wide association study (GWAS), with 1,047,986 single nucleotide polymorphism (SNP) markers examined in 3,425 African American prostate cancer cases and 3,290 African American male controls. The most significant 17 novel associations in stage 1 were followed-up in 1,844 cases and 3,269 controls of African ancestry. We identified a novel risk variant on chromosome 17q21 (rs7210100; odds ratio per allele=1.51; p=3.4×10−13). The frequency of the risk allele is ~5% in men of African descent while it is rare in other populations (<1%). Further studies are needed to investigate the biological contribution of this allele to prostate cancer risk. These findings emphasize the importance of conducting GWAS in diverse populations.
doi:10.1038/ng.839
PMCID: PMC3102788  PMID: 21602798
13.  Low Temperature Photo-Oxidation of Chloroperoxidase Compound II 
Journal of inorganic biochemistry  2010;104(11):1156-1163.
Oxidation of the heme-thiolate enzyme chloroperoxidase (CPO) from Caldariomyces fumago with peroxynitrite (PN) gave the Compound II intermediate, which was photo-oxidized with 365 nm light to give a reactive oxidizing species. Cryo-solvents at pH ≈ 6 were employed, and reactions were conducted at temperatures as low as −50 °C. The activity of CPO as evaluated by the chlorodimedone assay was unaltered by treatment with PN or by production of the oxidizing transient and subsequent reaction with styrene. EPR spectra at 77 K gave the amount of ferric protein at each stage in the reaction sequence. The PN oxidation step gave a 6:1 mixture of Compound II and ferric CPO, the photolysis step gave an approximate 1:1 mixture of active oxidant and ferric CPO, and the final mixture after reaction with excess styrene contained ferric CPO in 80% yield. In single turnover reactions at −50 °C, styrene was oxidized to styrene oxide in high yield. Kinetic studies of styrene oxidation at −50 °C displayed saturation kinetics with an equilibrium constant for formation of the complex of Kbind = 3.8 × 104 M−1 and an oxidation rate constant of kox = 0.30 s−1. UV-visible spectra of mixtures formed in the photo-oxidation sequence at ca. −50 °C did not contain the signature Q-band absorbance at 690 nm ascribed to CPO Compound I prepared by chemical oxidation of the enzyme, indicating that different species were formed in the chemical oxidation and the photo-oxidation sequence.
doi:10.1016/j.jinorgbio.2010.07.004
PMCID: PMC2963949  PMID: 20674981
chloroperoxidase; Compound I; UV-visible spectrum; EPR spectrum; kinetics; oxidation
14.  Characterizing Genetic Risk at Known Prostate Cancer Susceptibility Loci in African Americans 
PLoS Genetics  2011;7(5):e1001387.
GWAS of prostate cancer have been remarkably successful in revealing common genetic variants and novel biological pathways that are linked with its etiology. A more complete understanding of inherited susceptibility to prostate cancer in the general population will come from continuing such discovery efforts and from testing known risk alleles in diverse racial and ethnic groups. In this large study of prostate cancer in African American men (3,425 prostate cancer cases and 3,290 controls), we tested 49 risk variants located in 28 genomic regions identified through GWAS in men of European and Asian descent, and we replicated associations (at p≤0.05) with roughly half of these markers. Through fine-mapping, we identified nearby markers in many regions that better define associations in African Americans. At 8q24, we found 9 variants (p≤6×10−4) that best capture risk of prostate cancer in African Americans, many of which are more common in men of African than European descent. The markers found to be associated with risk at each locus improved risk modeling in African Americans (per allele OR = 1.17) over the alleles reported in the original GWAS (OR = 1.08). In summary, in this detailed analysis of the prostate cancer risk loci reported from GWAS, we have validated and improved upon markers of risk in some regions that better define the association with prostate cancer in African Americans. Our findings with variants at 8q24 also reinforce the importance of this region as a major risk locus for prostate cancer in men of African ancestry.
Author Summary
Prostate cancer is one of the most common cancers in men and is especially frequent in men of African origin, as incidence rates in African Americans in the United States are >1.5–fold greater than rates in European Americans. In order to gain a more complete understanding of the genetic basis of inherited susceptibility to prostate cancer in men of African origin, we examined the associations at risk loci identified in men of European and Asian descent in a large African American sample of 3,425 cases of prostate cancer and 3,290 male controls. In testing 49 known risk variants, we were able to demonstrate that at least half of these variants also contribute to risk in African American men. We were able to find additional risk variants in many of the previously reported regions that better captured the pattern of risk in African American men. In addition, we verified and improved upon the evidence we previously reported that there are multiple risk variants in a region of 8q24 that are important in men of African origin.
doi:10.1371/journal.pgen.1001387
PMCID: PMC3102736  PMID: 21637779
15.  Kinetics and Activation Parameters for Oxidations of Styrene by Compounds I from Cytochrome P450BM-3 (CYP102A1) Heme Domain and from CYP119† 
Biochemistry  2009;48(38):9140-9146.
Cytochrome P450 (CYP or P450) enzymes are ubiquitous in nature where they catalyze a vast array of oxidation reactions. The active oxidants in P450s have long been assumed to be iron(IV)-oxo porphyrin radical cations termed Compounds I, but P450 Compounds I have proven difficult to prepare. The recent development of an entry to these transients by photo-oxidation of the corresponding iron(IV)-oxo neutral porphyrin species (Compounds II) permits spectroscopic and kinetic studies. We report here application of the photo-oxidation method for production of Compound I from the heme domain of CYP102A1 (cytochrome P450BM-3), and product and kinetic studies of reactions of styrene with this Compound I transient and also Compound I from CYP119. The studies were performed at low temperatures in 1:1 (v:v) mixtures of glycerol--phosphate buffer. Single turnover reactions at 0 °C gave styrene oxide in good yields. In kinetic studies conducted between −10 and −50 °C, both Compounds I displayed saturation kinetics permitting determinations of binding constants and first-order oxidation rate constants. Temperature-dependent functions for the binding constants and rate constants were determined for both Compounds I. In the temperature range studied, the Compound I transient from CYP102A1 heme domain bound styrene more strongly than Compound I from CYP119, but the rate constants for oxidations of styrene by the latter were somewhat larger than those for the former. The temperature dependent functions for the first-order oxidation reactions are log k = 13.2 – 15.2/2.303RT and log k = 13.3 – 14.6/2.303RT (kcal/mol) for Compounds I from CYP102A1 heme domain and CYP119, respectively.
doi:10.1021/bi901258m
PMCID: PMC2755501  PMID: 19708688
16.  Quantitative Production of Compound I from a Cytochrome P450 Enzyme at Low Temperatures. Kinetics, Activation Parameters, and Kinetic Isotope Effects for Oxidation of Benzyl Alcohol 
Journal of the American Chemical Society  2009;131(30):10629-10636.
Cytochrome P450 enzymes are commonly thought to oxidize substrates via an iron(IV)-oxo porphyrin radical cation transient termed Compound I, but kinetic studies of P450 Compounds I are essentially non-existent. We report production of Compound I from cytochrome P450 119 (CYP119) in high conversion from the corresponding Compound II species at low temperatures in buffer mixtures containing 50% glycerol by photolysis with 365 nm light from a pulsed lamp. Compound I was studied as a reagent in oxidations of benzyl alcohol and its benzylic mono- and dideuterio isotopomers. Pseudo-first-order rate constants obtained at −50 °C with concentrations of substrates between 1.0 and 6.0 mM displayed saturation kinetics that gave binding constants for the substrate in the Compound I species (Kbind) and first-order rate constants for the oxidation reactions (kox). Representative results are Kbind = 214 M−1 and kox = 0.48 s−1 for oxidation of benzyl alcohol. For the dideuterated substrate C6H5CD2OH, kinetics were studied between −50 °C and −25 °C, and a van't Hoff plot for complexation and an Arrhenius plot for the oxidation reaction were constructed. The H/D kinetic isotope effects (KIEs) at −50 °C were resolved into a large primary KIE (P = 11.9) and a small, inverse secondary KIE (S = 0.96). Comparison of values extrapolated to 22 °C of both the rate constant for oxidation of C6H5CD2OH and the KIE for the non-deuterated and dideuterated substrates to values obtained previously in laser flash photolysis experiments suggested that tunneling could be a significant component of the total rate constant at −50 °C.
doi:10.1021/ja9031105
PMCID: PMC2737099  PMID: 19572732
17.  Spectra and Kinetic Studies of the Compound I Derivative of Cytochrome P450 119 (CYP119) 
Journal of the American Chemical Society  2008;130(40):13310-13320.
The Compound I derivative of cytochrome P450 119 (CYP119) was produced by laser flash photolysis of the corresponding Compound II derivative, which, in turn, was prepared by reaction of the resting enzyme with peroxynitrite. The UV-visible spectrum of the Compound I species contains an asymmetric Soret band that can be resolved into overlapping transitions centered at ca. 367 and 416 nm and a Q-band with λmax ≈ 650 nm. Reactions of the Compound I derivative with organic substrates gave epoxideized (alkene oxidations) and hydroxylated (C-H oxidations) products as demonstrated by product studies and oxygen-18 labeling studies. The kinetics of oxidations by CYP119 Compound I were measured directly; the reactions included hydroxylations of benzyl alcohol, ethylbenzene, Tris buffer, lauric acid, and methyl laurate, and epoxidations of styrene and 10-undecenoic acid. Apparent second-order rate constants, equal to the product of the equilibrium binding constant (Kbind) times the first-order oxidation rate constant (kox), were obtained for all substrates. The oxidations of lauric acid and methyl laurate displayed saturation kinetic behavior, which permitted solution of both Kbind and kox for these substrates. The unactivated C-H positions of lauric acid reacted with a rate constant of kox = 0.8 s−1 at room temperature. The CYP119 Compound I derivative is more reactive than model Compound I species, iron(IV)-oxo porphyrin radical cations, and similar in reactivity to the Compound I derivative of the heme-thiolate enzyme chloroperoxidase. Kinetic isotope effects (kH/kD) for oxidations of benzyl alcohol and ethylbenzene were small, reflecting the increased reactivity of the Compound I derivative in comparison to models. Nonetheless, CYP119 Compound I apparently is much less reactive than the oxidizing species formed in the P450cam reaction cycle. Competition kinetic studies employing CYP119 activated by hydrogen peroxide indicate that the same oxidizing transient is formed in the photochemical reaction and in the hydrogen peroxide shunt reaction.
doi:10.1021/ja802652b
PMCID: PMC2907162  PMID: 18788736
18.  Kinetics of Oxidation of Benzphetamine by Compounds I of Cytochrome P450 2B4 and Its Mutants 
Cytochromes P450 are ubiquitous heme-containing enzymes that catalyze a wide range of reactions in nature including many oxidation reactions. The active oxidant species in P450 enzymes are widely thought to be iron(IV)-oxo porphyrin radical cations, termed Compound I species, but these intermediates have not been observed under turnover conditions. We prepared Compounds I of the mammalian hepatic P450 enzyme CYP2B4 and three mutants (E301Q, T302A, and F429H) by laser flash photolysis of the Compound II species that, in turn, were prepared by reaction of the resting enzymes with peroxynitrite. The PN treatment resulted in a small amount of nitration of the P450 as determined by mass spectrometry, but no change in reactivity of the P450 in a test reaction. CYP2B4 Compound I oxidized benzphetamine to norbenzphetamine in high yield in bulk studies. In direct kinetic studies of benzphetamine oxidations, Compounds I displayed saturation kinetics with similar binding equilibrium constants (Kbind) for each. The first-order oxidation rate constants (kox) were comparable for Compounds I of CYP2B4, the E301Q mutant, and the T302A mutant, whereas the kox for Compound I of the F429H mutant was reduced by a factor of two. CYP119 Compound I, studied for comparison purposes, reacted with benzphetamine with a binding constant that was nearly an order of magnitude smaller than that of CYP2B4 but a rate constant that was similar. Substrate binding constants for P450 Compound I are important for controlling overall rates of oxidation reactions, and the intrinsic reactivities of Compounds I from various P450 enzymes are comparable.
doi:10.1021/ja808982g
PMCID: PMC2765530  PMID: 19209859
19.  Highly Reactive Porphyrin-Iron-Oxo Derivatives Produced by Photolyses of Metastable Porphyrin-Iron(IV) Diperchlorates 
Photolyses of metastable porphyrin-iron(IV) diperchlorates in laser flash photolysis reactions gave highly reactive transients. The systems studied were 5,10,15,20-tetraphenylporphyrin (TPP), 5,10,15,20-tetramesitylporphyrin (TMP), and 2,3,7,8,12,13,17,18-octaethylporphyrin (OEP). The new species, which decayed within milliseconds in acetonitrile solutions, were shown to react with organic substrates by oxo-transfer reactions involving insertions into carbon-carbon double bonds of alkenes and styrenes or benzylic carbon-hydrogen bonds of arenes. The order of reactivity was OEP > TPP > TMP. Second-order rate constants for reactions with several substrates at 22°C were determined; representative values of rate constants for the TPP derivative were k = 8.6 × 105 M−1 s−1 for styrene, k = 2.5 × 106 M−1 s−1 for cyclohexene, and k = 7.7 × 104 M−1 s−1 for ethylbenzene. These porphyrin-iron-oxo transients reacted 4 to 5 orders of magnitude faster than the corresponding iron(IV)-oxo porphyrin radical cations with rate constants similar to those of porphyrin-manganese(V)-oxo derivatives. Rate constants for oxidations of benzylic C-H positions of arenes correlated with the C-H bond dissociation energies, and Hammett correlations for reactions with substituted styrenes had ρ+ values ranging from −0.5 to −0.7 reflecting electrophilic character of the oxidants and their high reactivity. On the basis of their unique UV-visible spectra, high reactivities, and oxo-transfer properties, the new transients are tentatively identified as porphyrin-iron(V)-oxo perchlorates, electronic isomers (or valence tautomers) of well known iron(IV)-oxo porphyrin radical cations.
doi:10.1021/ja807847q
PMCID: PMC2664257  PMID: 19193008
20.  Kinetic Isotope Effects in Hydroxylation Reactions Effected by Cytochrome P450 Compounds I Implicate Multiple Electrophilic Oxidants for P450-Catalyzed Oxidations† 
Biochemistry  2009;48(7):1620-1627.
Kinetic isotope effects were measured for oxidations of (S,S)-2-(p-trifluoromethylphenyl)cyclopropylmethane containing zero, two, and three deuterium atoms on the methyl group by Compounds I from the cytochrome P450 enzymes CYP119 and CYP2B4 at 22 °C. The oxidations displayed saturation kinetics, which permitted solution of both binding constants (Kbind) and first-order oxidation rate constants (kox) for both enzymes with the three substrates. The binding constant for CYP2B4 Compound I was about one order of magnitude greater than that for CYP119 Compound I, but the oxidation rate constants were similar for the two. In oxidations of 1-d0, kox = 10.4 s−1 for CYP119 Compound I, and kox = 12.4 s−1 for CYP2B4 Compound I. Primary kinetic isotope effects (P) and secondary kinetic isotope effects (S) were obtained from the results with the three isotopomers. The primary KIEs were large, P = 9.8 and P = 8.9 for CYP119 and CYP2B4 Compounds I, respectively, and the secondary KIEs were small and normal, S = 1.07 and S = 1.05, respectively. Large intermolecular KIEs for 1-d0 and 1-d3 of kH/kD = 11.2 and 9.8 found for the two Compounds I contrast with small intermolecular KIEs obtained previously for the same substrate in P450-catalyzed oxidations; these differences suggest that a second electrophilic oxidant, presumably iron-complexed hydrogen peroxide, is important in cytochromes P450 oxidations under turnover conditions.
doi:10.1021/bi802279d
PMCID: PMC2664160  PMID: 19182902
21.  Haplotypes of DNMT1 and DNMT3B are associated with mutagen sensitivity induced by benzo[a]pyrene diol epoxide among smokers 
Carcinogenesis  2008;29(7):1380-1385.
The mutagen sensitivity assay is an in vitro measure of DNA repair capacity used to evaluate intrinsic susceptibility for cancer. The high heritability of mutagen sensitivity to different mutagens validates the use of this phenotype to predict cancer susceptibility. However, genetic determinants of mutagen sensitivity have not been fully characterized. Recently, several studies found that three major cytosine DNA methyltransferases (DNMTs), especially DNMT1, have a direct role in the DNA damage response, independent of their methyltransferase activity. This study evaluated the hypothesis that sequence variants in DNMT1, DNMT3A and DNMT3B are associated with mutagen sensitivity induced by the tobacco carcinogen benzo[a]pyrene diol epoxide (BPDE) in 278 cancer-free smokers. Single-nucleotide polymorphisms (n = 134) dispersed over the entire gene and regulatory regions of these DNMTs were genotyped by the Illumina Golden Gate Assay. DNA sequence variation in the DNMT1 and DNMT3B loci was globally associated with breaks per cell (P < 0.04 for both). No global association between DNMT3A and breaks per cell was seen (P = 0.09). Two haplotypes in block1 of DNMT1 (H284) and 3B (H70) were associated with 16 and 24% increase in breaks per cell, respectively. Subjects with three or four adverse haplotypes of both DNMT1 and 3B had a 50% elevation in mean level of breaks per cell compared with persons without adverse alleles (P = 0.004). The association between sequence variants of DNMT1 and 3B and mutagen sensitivity induced by BPDE supports the involvement of these DNMTs in protecting the cell from DNA damage.
doi:10.1093/carcin/bgn121
PMCID: PMC2899849  PMID: 18499700
22.  Double-strand break damage and associated DNA repair genes predispose smokers to gene methylation 
Cancer research  2008;68(8):3049-3056.
Gene promoter hypermethylation in sputum is a promising biomarker for predicting lung cancer. Identifying factors that predispose smokers to methylation of multiple gene promoters in the lung could impact strategies for early detection and chemoprevention. This study evaluated the hypothesis that double-strand break repair capacity and sequence variation in genes in this pathway are associated with a high methylation index in a cohort of current and former cancer-free smokers. A 50% reduction in the mean level of double-strand break repair capacity was seen in lymphocytes from smokers with a high methylation index, defined as ≥ 3 of 8 genes methylated in sputum, compared to smokers with no genes methylated. The classification accuracy for predicting risk for methylation was 88%. Single nucleotide polymorphisms within the MRE11A, CHEK2, XRCC3, DNA-Pkc, and NBN DNA repair genes were highly associated with the methylation index. A 14.5-fold increased odds for high methylation was seen for persons with ≥ 7 risk alleles of these genes. Promoter activity of the MRE11A gene that plays a critical role in recognition of DNA damage and activation of ATM was reduced in persons with the risk allele. Collectively, ours is the first population-based study to identify double-strand break DNA repair capacity and specific genes within this pathway as critical determinants for gene methylation in sputum, that is, in turn, associated with elevated risk for lung cancer.
doi:10.1158/0008-5472.CAN-07-6344
PMCID: PMC2483467  PMID: 18413776
promoter methylation; DNA double strand break; single nucleotide polymorphism; DNA repair capacity; association study
23.  Screening and association testing of common coding variation in steroid hormone receptor co-activator and co-repressor genes in relation to breast cancer risk: the Multiethnic Cohort 
BMC Cancer  2009;9:43.
Background
Only a limited number of studies have performed comprehensive investigations of coding variation in relation to breast cancer risk. Given the established role of estrogens in breast cancer, we hypothesized that coding variation in steroid receptor coactivator and corepressor genes may alter inter-individual response to estrogen and serve as markers of breast cancer risk.
Methods
We sequenced the coding exons of 17 genes (EP300, CCND1, NME1, NCOA1, NCOA2, NCOA3, SMARCA4, SMARCA2, CARM1, FOXA1, MPG, NCOR1, NCOR2, CALCOCO1, PRMT1, PPARBP and CREBBP) suggested to influence transcriptional activation by steroid hormone receptors in a multiethnic panel of women with advanced breast cancer (n = 95): African Americans, Latinos, Japanese, Native Hawaiians and European Americans. Association testing of validated coding variants was conducted in a breast cancer case-control study (1,612 invasive cases and 1,961 controls) nested in the Multiethnic Cohort. We used logistic regression to estimate odds ratios for allelic effects in ethnic-pooled analyses as well as in subgroups defined by disease stage and steroid hormone receptor status. We also investigated effect modification by established breast cancer risk factors that are associated with steroid hormone exposure.
Results
We identified 45 coding variants with frequencies ≥ 1% in any one ethnic group (43 non-synonymous variants). We observed nominally significant positive associations with two coding variants in ethnic-pooled analyses (NCOR2: His52Arg, OR = 1.79; 95% CI, 1.05–3.05; CALCOCO1: Arg12His, OR = 2.29; 95% CI, 1.00–5.26). A small number of variants were associated with risk in disease subgroup analyses and we observed no strong evidence of effect modification by breast cancer risk factors. Based on the large number of statistical tests conducted in this study, the nominally significant associations that we observed may be due to chance, and will need to be confirmed in other studies.
Conclusion
Our findings suggest that common coding variation in these candidate genes do not make a substantial contribution to breast cancer risk in the general population. Cataloging and testing of coding variants in coactivator and corepressor genes should continue and may serve as a valuable resource for investigations of other hormone-related phenotypes, such as inter-individual response to hormonal therapies used for cancer treatment and prevention.
doi:10.1186/1471-2407-9-43
PMCID: PMC2637888  PMID: 19183483
24.  A common genetic risk factor for colorectal and prostate cancer 
Nature genetics  2007;39(8):954-956.
Variants on chromosome 8q24 contribute risk for prostate cancer; here, we tested whether they also modulate risk for colorectal cancer. We studied 1,807 affected individuals and 5,511 controls and found that one variant, rs6983267, is also significantly associated with colorectal cancer (odds ratio = 1.22; P = 4.4 × 10−6) and that the apportionment of risk among the variants differs significantly between the two cancers. Comprehensive testing in the region uncovered variants capturing significant additional risk. Our results show that variants at 8q24 have different effects on cancer development that depend on the tissue type.
doi:10.1038/ng2098
PMCID: PMC2391283  PMID: 17618282
25.  FIMM, a database of functional molecular immunology 
Nucleic Acids Research  2000;28(1):222-224.
FIMM database (http://sdmc.krdl.org.sg:8080/fimm ) contains data relevant to functional molecular immunology, focusing on cellular immunology. It contains fully referenced data on protein antigens, major histocompatibility complex (MHC) molecules, MHC-associated peptides and relevant disease associations. FIMM has a set of search tools for extraction of information and results are presented as lists or as reports.
PMCID: PMC102489  PMID: 10592231

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