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2. Functional analysis and fine mapping of the 9p22.2 ovarian cancer susceptibility locus

Author

Buckley, Melissa A, Woods, Nicholas T, Tyrer, Jonathan P, Mendoza-Fandiño, Gustavo, Lawrenson, Kate, Hazelett, Dennis J, Najafabadi, Hamed S, Gjyshi, Anxhela, Carvalho, Renato S, Lyra, Paulo C, Coetzee, Simon G, Shen, Howard C, Yang, Ally W, Earp, Madalene A, Yoder, Sean J, Risch, Harvey, Chenevix-Trench, Georgia, Ramus, Susan J, Phelan, Catherine M, Coetzee, Gerhard A, Noushmehr, Houtan, Hughes, Timothy R, Sellers, Thomas A, Goode, Ellen L, Pharoah, Paul D, Gayther, Simon A, and Monteiro, Alvaro NA

Subjects
Biological Sciences, Biomedical and Clinical Sciences, Oncology and Carcinogenesis, Genetics, Prevention, Human Genome, Cancer, Rare Diseases, Biotechnology, Ovarian Cancer, 2.1 Biological and endogenous factors, Aetiology, Base Sequence, Carcinoma, Ovarian Epithelial, Cell Cycle Proteins, Cell Line, Tumor, Chromosome Mapping, Chromosomes, Human, Pair 9, Cystadenocarcinoma, Serous, DNA, Neoplasm, DNA-Binding Proteins, Female, Genetic Predisposition to Disease, Genome-Wide Association Study, HEK293 Cells, Humans, Linkage Disequilibrium, Ovarian Neoplasms, Polymorphism, Single Nucleotide, Ovarian Cancer Association Consortium, Oncology & Carcinogenesis, Biochemistry and cell biology, Oncology and carcinogenesis
Abstract

Genome-wide association studies have identified 40 ovarian cancer risk loci. However, the mechanisms underlying these associations remain elusive. In this study, we conducted a two-pronged approach to identify candidate causal SNPs and assess underlying biological mechanisms at chromosome 9p22.2, the first and most statistically significant associated locus for ovarian cancer susceptibility. Three transcriptional regulatory elements with allele-specific effects and a scaffold/matrix attachment region were characterized and, through physical DNA interactions, BNC2 was established as the most likely target gene. We determined the consensus binding sequence for BNC2 in vitro, verified its enrichment in BNC2 ChIP-seq regions, and validated a set of its downstream target genes. Fine-mapping by dense regional genotyping in over 15,000 ovarian cancer cases and 30,000 controls identified SNPs in the scaffold/matrix attachment region as among the most likely causal variants. This study reveals a comprehensive regulatory landscape at 9p22.2 and proposes a likely mechanism of susceptibility to ovarian cancer. SIGNIFICANCE: Mapping the 9p22.2 ovarian cancer risk locus identifies BNC2 as an ovarian cancer risk gene.See related commentary by Choi and Brown, p. 439.

Published
2019

4. Cell-type-specific enrichment of risk-associated regulatory elements at ovarian cancer susceptibility loci

Author

Coetzee, Simon G, Shen, Howard C, Hazelett, Dennis J, Lawrenson, Kate, Kuchenbaecker, Karoline, Tyrer, Jonathan, Rhie, Suhn K, Levanon, Keren, Karst, Alison, Drapkin, Ronny, Ramus, Susan J, Consortium, The Consortium of Investigators of Modifiers of BRCA1 2 The Ovarian Cancer Association, Couch, Fergus J, Offit, Kenneth, Chenevix-Trench, Georgia, Monteiro, Alvaro NA, Antoniou, Antonis, Freedman, Matthew, Coetzee, Gerhard A, Pharoah, Paul DP, Noushmehr, Houtan, Gayther, Simon A, Anton-Culver, Hoda, Antonenkova, Natalia, Baker, Helen, Bandera, Elisa V, Bean, Yukie, Beckmann, Matthias W, Berchuck, Andrew, Bisogna, Maria, Bjorge, Line, Bogdanova, Natalia, Brinton, Louise A, Brooks-Wilson, Angela, Bruinsma, Fiona, Butzow, Ralf, Campbell, Ian G, Carty, Karen, Chang-Claude, Jenny, Chen, Ann, Chen, Zhihua, Cook, Linda S, Cramer, Daniel W, Cunningham, Julie M, Cybulski, Cezary, Dansonka-Mieszkowska, Agnieszka, Dennis, Joe, Dicks, Ed, Doherty, Jennifer A, Dörk, Thilo, du Bois, Andreas, Dürst, Matthias, Eccles, Diana, Easton, Douglas F, Edwards, Robert P, Eilber, Ursula, Ekici, Arif B, Fasching, Peter A, Fridley, Brooke L, Gao, Yu-Tang, Gentry-Maharaj, Aleksandra, Giles, Graham G, Glasspool, Rosalind, Goode, Ellen L, Goodman, Marc T, Grownwald, Jacek, Harrington, Patricia, Harter, Philipp, Hasmad, Hanis Nazihah, Hein, Alexander, Heitz, Florian, Hildebrandt, Michelle AT, Hillemanns, Peter, Hogdall, Estrid, Hogdall, Claus, Hosono, Satoyo, Iversen, Edwin S, Jakubowska, Anna, James, Paul, Jensen, Allan, Ji, Bu-Tian, Karlan, Beth Y, Kjaer, Susanne Kruger, Kelemen, Linda E, Kellar, Melissa, Kelley, Joseph L, Kiemeney, Lambertus A, Krakstad, Camilla, Kupryjanczyk, Jolanta, Lambrechts, Diether, Lambrechts, Sandrina, Le, Nhu D, Lele, Shashi, Leminen, Arto, Lester, Jenny, Levine, Douglas A, Liang, Dong, and Lissowska, Jolanta

Subjects
Biological Sciences, Genetics, Rare Diseases, Prevention, Human Genome, Ovarian Cancer, Biotechnology, Cancer, 2.1 Biological and endogenous factors, Underpinning research, Aetiology, 1.1 Normal biological development and functioning, Chromatin, Female, Genetic Predisposition to Disease, Genome-Wide Association Study, Histones, Humans, Organ Specificity, Ovarian Neoplasms, Polymorphism, Single Nucleotide, Regulatory Sequences, Nucleic Acid, Ovarian Cancer Association Consortium, The Consortium of Investigators of Modifiers of BRCA1/2, Ovarian Cancer Association Consortium The Consortium of Investigators of Modifiers of BRCA1/2, Medical and Health Sciences, Genetics & Heredity
Abstract

Understanding the regulatory landscape of the human genome is a central question in complex trait genetics. Most single-nucleotide polymorphisms (SNPs) associated with cancer risk lie in non-protein-coding regions, implicating regulatory DNA elements as functional targets of susceptibility variants. Here, we describe genome-wide annotation of regions of open chromatin and histone modification in fallopian tube and ovarian surface epithelial cells (FTSECs, OSECs), the debated cellular origins of high-grade serous ovarian cancers (HGSOCs) and in endometriosis epithelial cells (EECs), the likely precursor of clear cell ovarian carcinomas (CCOCs). The regulatory architecture of these cell types was compared with normal human mammary epithelial cells and LNCaP prostate cancer cells. We observed similar positional patterns of global enhancer signatures across the three different ovarian cancer precursor cell types, and evidence of tissue-specific regulatory signatures compared to non-gynecological cell types. We found significant enrichment for risk-associated SNPs intersecting regulatory biofeatures at 17 known HGSOC susceptibility loci in FTSECs (P = 3.8 × 10(-30)), OSECs (P = 2.4 × 10(-23)) and HMECs (P = 6.7 × 10(-15)) but not for EECs (P = 0.45) or LNCaP cells (P = 0.88). Hierarchical clustering of risk SNPs conditioned on the six different cell types indicates FTSECs and OSECs are highly related (96% of samples using multi-scale bootstrapping) suggesting both cell types may be precursors of HGSOC. These data represent the first description of regulatory catalogues of normal precursor cells for different ovarian cancer subtypes, and provide unique insights into the tissue specific regulatory variation with respect to the likely functional targets of germline genetic susceptibility variants for ovarian cancer.

Published
2015

5. Identification of six new susceptibility loci for invasive epithelial ovarian cancer.

Author

Kuchenbaecker, Karoline B, Ramus, Susan J, Tyrer, Jonathan, Lee, Andrew, Shen, Howard C, Beesley, Jonathan, Lawrenson, Kate, McGuffog, Lesley, Healey, Sue, Lee, Janet M, Spindler, Tassja J, Lin, Yvonne G, Pejovic, Tanja, Bean, Yukie, Li, Qiyuan, Coetzee, Simon, Hazelett, Dennis, Miron, Alexander, Southey, Melissa, Terry, Mary Beth, Goldgar, David E, Buys, Saundra S, Janavicius, Ramunas, Dorfling, Cecilia M, van Rensburg, Elizabeth J, Neuhausen, Susan L, Ding, Yuan Chun, Hansen, Thomas VO, Jønson, Lars, Gerdes, Anne-Marie, Ejlertsen, Bent, Barrowdale, Daniel, Dennis, Joe, Benitez, Javier, Osorio, Ana, Garcia, Maria Jose, Komenaka, Ian, Weitzel, Jeffrey N, Ganschow, Pamela, Peterlongo, Paolo, Bernard, Loris, Viel, Alessandra, Bonanni, Bernardo, Peissel, Bernard, Manoukian, Siranoush, Radice, Paolo, Papi, Laura, Ottini, Laura, Fostira, Florentia, Konstantopoulou, Irene, Garber, Judy, Frost, Debra, Perkins, Jo, Platte, Radka, Ellis, Steve, EMBRACE, Godwin, Andrew K, Schmutzler, Rita Katharina, Meindl, Alfons, Engel, Christoph, Sutter, Christian, Sinilnikova, Olga M, GEMO Study Collaborators, Damiola, Francesca, Mazoyer, Sylvie, Stoppa-Lyonnet, Dominique, Claes, Kathleen, De Leeneer, Kim, Kirk, Judy, Rodriguez, Gustavo C, Piedmonte, Marion, O'Malley, David M, de la Hoya, Miguel, Caldes, Trinidad, Aittomäki, Kristiina, Nevanlinna, Heli, Collée, J Margriet, Rookus, Matti A, Oosterwijk, Jan C, Breast Cancer Family Registry, Tihomirova, Laima, Tung, Nadine, Hamann, Ute, Isaccs, Claudine, Tischkowitz, Marc, Imyanitov, Evgeny N, Caligo, Maria A, Campbell, Ian G, Hogervorst, Frans BL, HEBON, Olah, Edith, Diez, Orland, Blanco, Ignacio, Brunet, Joan, Lazaro, Conxi, Pujana, Miquel Angel, Jakubowska, Anna, Gronwald, Jacek, Lubinski, Jan, and Sukiennicki, Grzegorz

Subjects
EMBRACE, GEMO Study Collaborators, Breast Cancer Family Registry, HEBON, KConFab Investigators, Australian Cancer Study, Australian Ovarian Cancer Study Group, Consortium of Investigators of Modifiers of BRCA1 and BRCA2, Humans, Neoplasms, Glandular and Epithelial, Ovarian Neoplasms, Genetic Predisposition to Disease, BRCA1 Protein, BRCA2 Protein, Risk, Genotype, Heterozygote, Mutation, Polymorphism, Single Nucleotide, Alleles, Genes, Reporter, Quantitative Trait Loci, Adolescent, Adult, Female, Genome-Wide Association Study, Young Adult, Carcinoma, Ovarian Epithelial, Human Genome, Rare Diseases, Genetics, Cancer, Prevention, Ovarian Cancer, 2.1 Biological and endogenous factors, Aetiology, Biological Sciences, Medical and Health Sciences, Developmental Biology
Abstract

Genome-wide association studies (GWAS) have identified 12 epithelial ovarian cancer (EOC) susceptibility alleles. The pattern of association at these loci is consistent in BRCA1 and BRCA2 mutation carriers who are at high risk of EOC. After imputation to 1000 Genomes Project data, we assessed associations of 11 million genetic variants with EOC risk from 15,437 cases unselected for family history and 30,845 controls and from 15,252 BRCA1 mutation carriers and 8,211 BRCA2 mutation carriers (3,096 with ovarian cancer), and we combined the results in a meta-analysis. This new study design yielded increased statistical power, leading to the discovery of six new EOC susceptibility loci. Variants at 1p36 (nearest gene, WNT4), 4q26 (SYNPO2), 9q34.2 (ABO) and 17q11.2 (ATAD5) were associated with EOC risk, and at 1p34.3 (RSPO1) and 6p22.1 (GPX6) variants were specifically associated with the serous EOC subtype, all with P < 5 × 10(-8). Incorporating these variants into risk assessment tools will improve clinical risk predictions for BRCA1 and BRCA2 mutation carriers.

Published
2015

6. Multiple independent variants at the TERT locus are associated with telomere length and risks of breast and ovarian cancer.

Author

Bojesen, Stig E, Pooley, Karen A, Johnatty, Sharon E, Beesley, Jonathan, Michailidou, Kyriaki, Tyrer, Jonathan P, Edwards, Stacey L, Pickett, Hilda A, Shen, Howard C, Smart, Chanel E, Hillman, Kristine M, Mai, Phuong L, Lawrenson, Kate, Stutz, Michael D, Lu, Yi, Karevan, Rod, Woods, Nicholas, Johnston, Rebecca L, French, Juliet D, Chen, Xiaoqing, Weischer, Maren, Nielsen, Sune F, Maranian, Melanie J, Ghoussaini, Maya, Ahmed, Shahana, Baynes, Caroline, Bolla, Manjeet K, Wang, Qin, Dennis, Joe, McGuffog, Lesley, Barrowdale, Daniel, Lee, Andrew, Healey, Sue, Lush, Michael, Tessier, Daniel C, Vincent, Daniel, Bacot, Françis, Australian Cancer Study, Australian Ovarian Cancer Study, Kathleen Cuningham Foundation Consortium for Research into Familial Breast Cancer (kConFab), Gene Environment Interaction and Breast Cancer (GENICA), Swedish Breast Cancer Study (SWE-BRCA), Hereditary Breast and Ovarian Cancer Research Group Netherlands (HEBON), Epidemiological study of BRCA1 & BRCA2 Mutation Carriers (EMBRACE), Genetic Modifiers of Cancer Risk in BRCA1/2 Mutation Carriers (GEMO), Vergote, Ignace, Lambrechts, Sandrina, Despierre, Evelyn, Risch, Harvey A, González-Neira, Anna, Rossing, Mary Anne, Pita, Guillermo, Doherty, Jennifer A, Alvarez, Nuria, Larson, Melissa C, Fridley, Brooke L, Schoof, Nils, Chang-Claude, Jenny, Cicek, Mine S, Peto, Julian, Kalli, Kimberly R, Broeks, Annegien, Armasu, Sebastian M, Schmidt, Marjanka K, Braaf, Linde M, Winterhoff, Boris, Nevanlinna, Heli, Konecny, Gottfried E, Lambrechts, Diether, Rogmann, Lisa, Guénel, Pascal, Teoman, Attila, Milne, Roger L, Garcia, Joaquin J, Cox, Angela, Shridhar, Vijayalakshmi, Burwinkel, Barbara, Marme, Frederik, Hein, Rebecca, Sawyer, Elinor J, Haiman, Christopher A, Wang-Gohrke, Shan, Andrulis, Irene L, Moysich, Kirsten B, Hopper, John L, Odunsi, Kunle, Lindblom, Annika, Giles, Graham G, Brenner, Hermann, Simard, Jacques, Lurie, Galina, Fasching, Peter A, Carney, Michael E, Radice, Paolo, Wilkens, Lynne R, Swerdlow, Anthony, Goodman, Marc T, Brauch, Hiltrud, Garcia-Closas, Montserrat, and Hillemanns, Peter

Subjects
Australian Cancer Study, Australian Ovarian Cancer Study, Kathleen Cuningham Foundation Consortium for Research into Familial Breast Cancer, Gene Environment Interaction and Breast Cancer, Swedish Breast Cancer Study, Hereditary Breast and Ovarian Cancer Research Group Netherlands, Epidemiological study of BRCA1 & BRCA2 Mutation Carriers, Genetic Modifiers of Cancer Risk in BRCA1/2 Mutation Carriers, Chromatin, Telomere, Humans, Breast Neoplasms, Ovarian Neoplasms, Genetic Predisposition to Disease, Luciferases, Telomerase, RNA, Messenger, Oligonucleotide Array Sequence Analysis, Risk Factors, Case-Control Studies, Gene Expression Profiling, Reverse Transcriptase Polymerase Chain Reaction, DNA Methylation, Alternative Splicing, Genotype, Polymorphism, Single Nucleotide, Female, Genome-Wide Association Study, Genetic Loci, Real-Time Polymerase Chain Reaction, Biomarkers, Tumor, Genetics, Breast Cancer, Cancer, Ovarian Cancer, Rare Diseases, Prevention, 2.1 Biological and endogenous factors, Aetiology, Biological Sciences, Medical and Health Sciences, Developmental Biology
Abstract

TERT-locus SNPs and leukocyte telomere measures are reportedly associated with risks of multiple cancers. Using the Illumina custom genotyping array iCOGs, we analyzed ∼480 SNPs at the TERT locus in breast (n = 103,991), ovarian (n = 39,774) and BRCA1 mutation carrier (n = 11,705) cancer cases and controls. Leukocyte telomere measurements were also available for 53,724 participants. Most associations cluster into three independent peaks. The minor allele at the peak 1 SNP rs2736108 associates with longer telomeres (P = 5.8 × 10(-7)), lower risks for estrogen receptor (ER)-negative (P = 1.0 × 10(-8)) and BRCA1 mutation carrier (P = 1.1 × 10(-5)) breast cancers and altered promoter assay signal. The minor allele at the peak 2 SNP rs7705526 associates with longer telomeres (P = 2.3 × 10(-14)), higher risk of low-malignant-potential ovarian cancer (P = 1.3 × 10(-15)) and greater promoter activity. The minor alleles at the peak 3 SNPs rs10069690 and rs2242652 increase ER-negative (P = 1.2 × 10(-12)) and BRCA1 mutation carrier (P = 1.6 × 10(-14)) breast and invasive ovarian (P = 1.3 × 10(-11)) cancer risks but not via altered telomere length. The cancer risk alleles of rs2242652 and rs10069690, respectively, increase silencing and generate a truncated TERT splice variant.

Published
2013

7. Identification and molecular characterization of a new ovarian cancer susceptibility locus at 17q21.31

Author

Permuth-Wey, Jennifer, Lawrenson, Kate, Shen, Howard C, Velkova, Aneliya, Tyrer, Jonathan P, Chen, Zhihua, Lin, Hui-Yi, Ann Chen, Y, Tsai, Ya-Yu, Qu, Xiaotao, Ramus, Susan J, Karevan, Rod, Lee, Janet, Lee, Nathan, Larson, Melissa C, Aben, Katja K, Anton-Culver, Hoda, Antonenkova, Natalia, Antoniou, Antonis C, Armasu, Sebastian M, Bacot, François, Baglietto, Laura, Bandera, Elisa V, Barnholtz-Sloan, Jill, Beckmann, Matthias W, Birrer, Michael J, Bloom, Greg, Bogdanova, Natalia, Brinton, Louise A, Brooks-Wilson, Angela, Brown, Robert, Butzow, Ralf, Cai, Qiuyin, Campbell, Ian, Chang-Claude, Jenny, Chanock, Stephen, Chenevix-Trench, Georgia, Cheng, Jin Q, Cicek, Mine S, Coetzee, Gerhard A, Cook, Linda S, Couch, Fergus J, Cramer, Daniel W, Cunningham, Julie M, Dansonka-Mieszkowska, Agnieszka, Despierre, Evelyn, Doherty, Jennifer A, Dörk, Thilo, du Bois, Andreas, Dürst, Matthias, Easton, Douglas F, Eccles, Diana, Edwards, Robert, Ekici, Arif B, Fasching, Peter A, Fenstermacher, David A, Flanagan, James M, Garcia-Closas, Montserrat, Gentry-Maharaj, Aleksandra, Giles, Graham G, Glasspool, Rosalind M, Gonzalez-Bosquet, Jesus, Goodman, Marc T, Gore, Martin, Górski, Bohdan, Gronwald, Jacek, Hall, Per, Halle, Mari K, Harter, Philipp, Heitz, Florian, Hillemanns, Peter, Hoatlin, Maureen, Høgdall, Claus K, Høgdall, Estrid, Hosono, Satoyo, Jakubowska, Anna, Jensen, Allan, Jim, Heather, Kalli, Kimberly R, Karlan, Beth Y, Kaye, Stanley B, Kelemen, Linda E, Kiemeney, Lambertus A, Kikkawa, Fumitaka, Konecny, Gottfried E, Krakstad, Camilla, Krüger Kjaer, Susanne, Kupryjanczyk, Jolanta, Lambrechts, Diether, Lambrechts, Sandrina, Lancaster, Johnathan M, Le, Nhu D, Leminen, Arto, Levine, Douglas A, Liang, Dong, Kiong Lim, Boon, Lin, Jie, Lissowska, Jolanta, Lu, Karen H, and Lubiński, Jan

Subjects
Biological Sciences, Biomedical and Clinical Sciences, Genetics, Rare Diseases, Biotechnology, Ovarian Cancer, Cancer, Human Genome, 2.1 Biological and endogenous factors, Aetiology, Carcinoma, Ovarian Epithelial, Chromosomes, Human, Pair 17, Female, Genetic Predisposition to Disease, Humans, Neoplasms, Glandular and Epithelial, Ovarian Neoplasms, Polymorphism, Single Nucleotide, Australian Cancer Study, Australian Ovarian Cancer Study, Consortium of Investigators of Modifiers of BRCA1/2
Abstract

Epithelial ovarian cancer (EOC) has a heritable component that remains to be fully characterized. Most identified common susceptibility variants lie in non-protein-coding sequences. We hypothesized that variants in the 3' untranslated region at putative microRNA (miRNA)-binding sites represent functional targets that influence EOC susceptibility. Here, we evaluate the association between 767 miRNA-related single-nucleotide polymorphisms (miRSNPs) and EOC risk in 18,174 EOC cases and 26,134 controls from 43 studies genotyped through the Collaborative Oncological Gene-environment Study. We identify several miRSNPs associated with invasive serous EOC risk (odds ratio=1.12, P=10(-8)) mapping to an inversion polymorphism at 17q21.31. Additional genotyping of non-miRSNPs at 17q21.31 reveals stronger signals outside the inversion (P=10(-10)). Variation at 17q21.31 is associated with neurological diseases, and our collaboration is the first to report an association with EOC susceptibility. An integrated molecular analysis in this region provides evidence for ARHGAP27 and PLEKHM1 as candidate EOC susceptibility genes.

Published
2013

9. Supplementary Table 5 from Functional Analysis and Fine Mapping of the 9p22.2 Ovarian Cancer Susceptibility Locus

Author

Buckley, Melissa A., primary, Woods, Nicholas T., primary, Tyrer, Jonathan P., primary, Mendoza-Fandiño, Gustavo, primary, Lawrenson, Kate, primary, Hazelett, Dennis J., primary, Najafabadi, Hamed S., primary, Gjyshi, Anxhela, primary, Carvalho, Renato S., primary, Lyra, Paulo C., primary, Coetzee, Simon G., primary, Shen, Howard C., primary, Yang, Ally W., primary, Earp, Madalene A., primary, Yoder, Sean J., primary, Risch, Harvey, primary, Chenevix-Trench, Georgia, primary, Ramus, Susan J., primary, Phelan, Catherine M., primary, Coetzee, Gerhard A., primary, Noushmehr, Houtan, primary, Hughes, Timothy R., primary, Sellers, Thomas A., primary, Goode, Ellen L., primary, Pharoah, Paul D., primary, Gayther, Simon A., primary, and Monteiro, Alvaro N.A., primary

Published
2023
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10. Supplementary Figures 1-4 and extended methods from Functional Analysis and Fine Mapping of the 9p22.2 Ovarian Cancer Susceptibility Locus

Author

Buckley, Melissa A., primary, Woods, Nicholas T., primary, Tyrer, Jonathan P., primary, Mendoza-Fandiño, Gustavo, primary, Lawrenson, Kate, primary, Hazelett, Dennis J., primary, Najafabadi, Hamed S., primary, Gjyshi, Anxhela, primary, Carvalho, Renato S., primary, Lyra, Paulo C., primary, Coetzee, Simon G., primary, Shen, Howard C., primary, Yang, Ally W., primary, Earp, Madalene A., primary, Yoder, Sean J., primary, Risch, Harvey, primary, Chenevix-Trench, Georgia, primary, Ramus, Susan J., primary, Phelan, Catherine M., primary, Coetzee, Gerhard A., primary, Noushmehr, Houtan, primary, Hughes, Timothy R., primary, Sellers, Thomas A., primary, Goode, Ellen L., primary, Pharoah, Paul D., primary, Gayther, Simon A., primary, and Monteiro, Alvaro N.A., primary

Published
2023
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11. Supplementary Table 3 from Functional Analysis and Fine Mapping of the 9p22.2 Ovarian Cancer Susceptibility Locus

Author

Buckley, Melissa A., primary, Woods, Nicholas T., primary, Tyrer, Jonathan P., primary, Mendoza-Fandiño, Gustavo, primary, Lawrenson, Kate, primary, Hazelett, Dennis J., primary, Najafabadi, Hamed S., primary, Gjyshi, Anxhela, primary, Carvalho, Renato S., primary, Lyra, Paulo C., primary, Coetzee, Simon G., primary, Shen, Howard C., primary, Yang, Ally W., primary, Earp, Madalene A., primary, Yoder, Sean J., primary, Risch, Harvey, primary, Chenevix-Trench, Georgia, primary, Ramus, Susan J., primary, Phelan, Catherine M., primary, Coetzee, Gerhard A., primary, Noushmehr, Houtan, primary, Hughes, Timothy R., primary, Sellers, Thomas A., primary, Goode, Ellen L., primary, Pharoah, Paul D., primary, Gayther, Simon A., primary, and Monteiro, Alvaro N.A., primary

Published
2023
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12. Data from Functional Analysis and Fine Mapping of the 9p22.2 Ovarian Cancer Susceptibility Locus

Author

Buckley, Melissa A., primary, Woods, Nicholas T., primary, Tyrer, Jonathan P., primary, Mendoza-Fandiño, Gustavo, primary, Lawrenson, Kate, primary, Hazelett, Dennis J., primary, Najafabadi, Hamed S., primary, Gjyshi, Anxhela, primary, Carvalho, Renato S., primary, Lyra, Paulo C., primary, Coetzee, Simon G., primary, Shen, Howard C., primary, Yang, Ally W., primary, Earp, Madalene A., primary, Yoder, Sean J., primary, Risch, Harvey, primary, Chenevix-Trench, Georgia, primary, Ramus, Susan J., primary, Phelan, Catherine M., primary, Coetzee, Gerhard A., primary, Noushmehr, Houtan, primary, Hughes, Timothy R., primary, Sellers, Thomas A., primary, Goode, Ellen L., primary, Pharoah, Paul D., primary, Gayther, Simon A., primary, and Monteiro, Alvaro N.A., primary

Published
2023
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13. Supplementary Table 1 from Functional Analysis and Fine Mapping of the 9p22.2 Ovarian Cancer Susceptibility Locus

Author

Buckley, Melissa A., primary, Woods, Nicholas T., primary, Tyrer, Jonathan P., primary, Mendoza-Fandiño, Gustavo, primary, Lawrenson, Kate, primary, Hazelett, Dennis J., primary, Najafabadi, Hamed S., primary, Gjyshi, Anxhela, primary, Carvalho, Renato S., primary, Lyra, Paulo C., primary, Coetzee, Simon G., primary, Shen, Howard C., primary, Yang, Ally W., primary, Earp, Madalene A., primary, Yoder, Sean J., primary, Risch, Harvey, primary, Chenevix-Trench, Georgia, primary, Ramus, Susan J., primary, Phelan, Catherine M., primary, Coetzee, Gerhard A., primary, Noushmehr, Houtan, primary, Hughes, Timothy R., primary, Sellers, Thomas A., primary, Goode, Ellen L., primary, Pharoah, Paul D., primary, Gayther, Simon A., primary, and Monteiro, Alvaro N.A., primary

Published
2023
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14. Supplementary Table 2 from Functional Analysis and Fine Mapping of the 9p22.2 Ovarian Cancer Susceptibility Locus

Author

Buckley, Melissa A., primary, Woods, Nicholas T., primary, Tyrer, Jonathan P., primary, Mendoza-Fandiño, Gustavo, primary, Lawrenson, Kate, primary, Hazelett, Dennis J., primary, Najafabadi, Hamed S., primary, Gjyshi, Anxhela, primary, Carvalho, Renato S., primary, Lyra, Paulo C., primary, Coetzee, Simon G., primary, Shen, Howard C., primary, Yang, Ally W., primary, Earp, Madalene A., primary, Yoder, Sean J., primary, Risch, Harvey, primary, Chenevix-Trench, Georgia, primary, Ramus, Susan J., primary, Phelan, Catherine M., primary, Coetzee, Gerhard A., primary, Noushmehr, Houtan, primary, Hughes, Timothy R., primary, Sellers, Thomas A., primary, Goode, Ellen L., primary, Pharoah, Paul D., primary, Gayther, Simon A., primary, and Monteiro, Alvaro N.A., primary

Published
2023
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15. Supplementary Table 4 from Functional Analysis and Fine Mapping of the 9p22.2 Ovarian Cancer Susceptibility Locus

Author

Buckley, Melissa A., primary, Woods, Nicholas T., primary, Tyrer, Jonathan P., primary, Mendoza-Fandiño, Gustavo, primary, Lawrenson, Kate, primary, Hazelett, Dennis J., primary, Najafabadi, Hamed S., primary, Gjyshi, Anxhela, primary, Carvalho, Renato S., primary, Lyra, Paulo C., primary, Coetzee, Simon G., primary, Shen, Howard C., primary, Yang, Ally W., primary, Earp, Madalene A., primary, Yoder, Sean J., primary, Risch, Harvey, primary, Chenevix-Trench, Georgia, primary, Ramus, Susan J., primary, Phelan, Catherine M., primary, Coetzee, Gerhard A., primary, Noushmehr, Houtan, primary, Hughes, Timothy R., primary, Sellers, Thomas A., primary, Goode, Ellen L., primary, Pharoah, Paul D., primary, Gayther, Simon A., primary, and Monteiro, Alvaro N.A., primary

Published
2023
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18. Amyloid conformation-dependent disaggregation revealed by a reconstituted yeast prion system

Author

Tanaka, Motomasa, primary, Nakagawa, Yoshiko, additional, Shen, Howard C.-H., additional, Sugiyama, Shinju, additional, Tomabechi, Yuri, additional, Krayukhina, Elena, additional, Okamoto, Kenji, additional, Yokoyama, Takeshi, additional, Shirouzu, Mikako, additional, Uchiyama, Susumu, additional, Inaba, Megumi, additional, Niwa, Tatsuya, additional, Sako, Yasushi, additional, and Taguchi, Hideki, additional

Published
2020
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22. Functional Analysis and Fine Mapping of the 9p22.2 Ovarian Cancer Susceptibility Locus

Author

Buckley, Melissa A, Woods, Nicholas T, Tyrer, Jonathan P, Mendoza-Fandiño, Gustavo, Lawrenson, Kate, Hazelett, Dennis J, Najafabadi, Hamed S, Gjyshi, Anxhela, Carvalho, Renato S, Lyra, Paulo C, Coetzee, Simon G, Shen, Howard C, Yang, Ally W, Earp, Madalene A, Yoder, Sean J, Risch, Harvey, Chenevix-Trench, Georgia, Ramus, Susan J, Phelan, Catherine M, Coetzee, Gerhard A, Noushmehr, Houtan, Hughes, Timothy R, Sellers, Thomas A, Goode, Ellen L, Pharoah, Paul D, Gayther, Simon A, Monteiro, Alvaro NA, Ovarian Cancer Association Consortium, Lawrenson, Kate [0000-0002-6469-2515], Hazelett, Dennis J [0000-0003-0749-9935], Najafabadi, Hamed S [0000-0003-2735-4231], Coetzee, Simon G [0000-0003-4267-5930], Yoder, Sean J [0000-0003-0005-7798], Coetzee, Gerhard A [0000-0003-4267-5930], Noushmehr, Houtan [0000-0003-4051-8114], and Apollo - University of Cambridge Repository

Subjects
Ovarian Cancer Association Consortium, Oncology and Carcinogenesis, Cystadenocarcinoma, Cell Cycle Proteins, Carcinoma, Ovarian Epithelial, Polymorphism, Single Nucleotide, Chromosomes, Linkage Disequilibrium, Cell Line, Rare Diseases, Ovarian Epithelial, Cell Line, Tumor, Genetics, 2.1 Biological and endogenous factors, Humans, Genetic Predisposition to Disease, Oncology & Carcinogenesis, Polymorphism, Aetiology, Cancer, Ovarian Neoplasms, Tumor, Base Sequence, Prevention, Carcinoma, Human Genome, Serous, Chromosome Mapping, DNA, Single Nucleotide, DNA, Neoplasm, Ovarian Cancer, Cystadenocarcinoma, Serous, DNA-Binding Proteins, HEK293 Cells, Neoplasm, Female, Chromosomes, Human, Pair 9, Human, Pair 9, Biotechnology, Genome-Wide Association Study
Abstract

Genome-wide association studies have identified 40 ovarian cancer risk loci. However, the mechanisms underlying these associations remain elusive. In this study, we conducted a two-pronged approach to identify candidate causal SNPs and assess underlying biological mechanisms at chromosome 9p22.2, the first and most statistically significant associated locus for ovarian cancer susceptibility. Three transcriptional regulatory elements with allele-specific effects and a scaffold/matrix attachment region were characterized and, through physical DNA interactions, BNC2 was established as the most likely target gene. We determined the consensus binding sequence for BNC2 in vitro, verified its enrichment in BNC2 ChIP-seq regions, and validated a set of its downstream target genes. Fine-mapping by dense regional genotyping in over 15,000 ovarian cancer cases and 30,000 controls identified SNPs in the scaffold/matrix attachment region as among the most likely causal variants. This study reveals a comprehensive regulatory landscape at 9p22.2 and proposes a likely mechanism of susceptibility to ovarian cancer. SIGNIFICANCE: Mapping the 9p22.2 ovarian cancer risk locus identifies BNC2 as an ovarian cancer risk gene.See related commentary by Choi and Brown, p. 439.

Published
2018
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30. Identification of six new susceptibility loci for invasive epithelial ovarian cancer

Author

Kuchenbaecker, Karoline B., Ramus, Susan J., Tyrer, Jonathan, Lee, Andrew, Shen, Howard C., Beesley, Jonathan, Lawrenson, Kate, McGuffog, Lesley, Healey, Sue, Lee, Janet M., Spindler, Tassja J., Lin, Yvonne G., Pejovic, Tanja, Bean, Yukie, Li, Qiyuan, Coetzee, Simon, Hazelett, Dennis, Miron, Alexander, Southey, Melissa, Terry, Mary Beth, Goldgar, David E., Buys, Saundra S., Janavicius, Ramunas, Dorfling, Cecilia M., van Rensburg, Elizabeth J., Neuhausen, Susan L., Ding, Yuan Chun, Hansen, Thomas V. O., Jønson, Lars, Gerdes, Anne-Marie, Ejlertsen, Bent, Barrowdale, Daniel, Dennis, Joe, Benitez, Javier, Osorio, Ana, Garcia, Maria Jose, Komenaka, Ian, Weitzel, Jeffrey N., Ganschow, Pamela, Peterlongo, Paolo, Bernard, Loris, Viel, Alessandra, Bonanni, Bernardo, Peissel, Bernard, Manoukian, Siranoush, Radice, Paolo, Papi, Laura, Ottini, Laura, Fostira, Florentia, Konstantopoulou, Irene, Garber, Judy, Frost, Debra, Perkins, Jo, Platte, Radka, Ellis, Steve, Godwin, Andrew K., Schmutzler, Rita Katharina, Meindl, Alfons, Engel, Christoph, Sutter, Christian, Sinilnikova, Olga M., Damiola, Francesca, Mazoyer, Sylvie, Stoppa-Lyonnet, Dominique, Claes, Kathleen, De Leeneer, Kim, Kirk, Judy, Rodriguez, Gustavo C., Piedmonte, Marion, O'Malley, David M., de la Hoya, Miguel, Caldes, Trinidad, Aittomäki, Kristiina, Nevanlinna, Heli, Collée, J. Margriet, Rookus, Matti A., Oosterwijk, Jan C., Tihomirova, Laima, Tung, Nadine, Hamann, Ute, Isaacs, Claudine, Tischkowitz, Marc, Imyanitov, Evgeny N., Caligo, Maria A., Campbell, Ian, Hogervorst, Frans B.L., Olah, Edith, Diez, Orland, Blanco, Ignacio, Brunet, Joan, Lazaro, Conxi, Pujana, Miquel Angel, Jakubowska, Anna, Gronwald, Jacek, Lubinski, Jan, Sukiennicki, Grzegorz, Barkardottir, Rosa B., Plante, Marie, Simard, Jacques, Soucy, Penny, Montagna, Marco, Tognazzo, Silvia, Teixeira, Manuel R., Pankratz, Vernon S., Wang, Xianshu, Lindor, Noralane, Szabo, Csilla I., Kauff, Noah, Vijai, Joseph, Aghajanian, Carol A., Pfeiler, Georg, Berger, Andreas, Singer, Christian F., Tea, Muy-Kheng, Phelan, Catherine M., Greene, Mark H., Mai, Phuong L., Rennert, Gad, Mulligan, Anna Marie, Tchatchou, Sandrine, Andrulis, Irene L., Glendon, Gord, Toland, Amanda Ewart, Jensen, Uffe Birk, Kruse, Torben A., Thomassen, Mads, Bojesen, Anders, Zidan, Jamal, Friedman, Eitan, Laitman, Yael, Soller, Maria, Liljegren, Annelie, Arver, Brita, Einbeigi, Zakaria, Stenmark-Askmalm, Marie, Olopade, Olufunmilayo I., Nussbaum, Robert L., Rebbeck, Timothy R., Nathanson, Katherine L., Domchek, Susan M., Lu, Karen H., Karlan, Beth Y., Walsh, Christine, Lester, Jenny, Hein, Alexander, Ekici, Arif B., Beckmann, Matthias W., Fasching, Peter A., Lambrechts, Diether, Nieuwenhuysen, Els Van, Vergote, Ignace, Lambrechts, Sandrina, Dicks, Ed, Doherty, Jennifer A., Wicklund, Kristine G., Rossing, Mary Anne, Rudolph, Anja, Chang-Claude, Jenny, Wang-Gohrke, Shan, Eilber, Ursula, Moysich, Kirsten B., Odunsi, Kunle, Sucheston-Campbell, Lara, Lele, Shashi, Wilkens, Lynne R., Goodman, Marc T., Thompson, Pamela J., Shvetsov, Yurii B., Runnebaum, Ingo B., Dürst, Matthias, Hillemanns, Peter, Dörk, Thilo, Antonenkova, Natalia, Bogdanova, Natalia, Leminen, Arto, Pelttari, Liisa M., Butzow, Ralf, Modugno, Francesmary, Kelley, Joseph L., Edwards, Robert P., Ness, Roberta B., du Bois, Andreas, Heitz, Florian, Schwaab, Ira, Harter, Philipp, Matsuo, Keitaro, Hosono, Satoyo, Orsulic, Sandra, Jensen, Allan, Kjaer, Susanne Kruger, Hogdall, Estrid, Hasmad, Hanis Nazihah, Noor Azmi, Mat Adenan, Teo, Soo-Hwang, Woo, Yin-Ling, Fridley, Brooke L., Goode, Ellen L., Cunningham, Julie M., Vierkant, Robert A., Bruinsma, Fiona, Giles, Graham G., Liang, Dong, Hildebrandt, Michelle A.T., Wu, Xifeng, Levine, Douglas A., Bisogna, Maria, Berchuck, Andrew, Iversen, Edwin S., Schildkraut, Joellen M., Concannon, Patrick, Weber, Rachel Palmieri, Cramer, Daniel W., Terry, Kathryn L., Poole, Elizabeth M., Tworoger, Shelley S., Bandera, Elisa V., Orlow, Irene, Olson, Sara H., Krakstad, Camilla, Salvesen, Helga B., Tangen, Ingvild L., Bjorge, Line, van Altena, Anne M., Aben, Katja K.H., Kiemeney, Lambertus A., Massuger, Leon F.A.G., Kellar, Melissa, Brooks-Wilson, Angela, Kelemen, Linda E., Cook, Linda S., Le, Nhu D., Cybulski, Cezary, Yang, Hannah, Lissowska, Jolanta, Brinton, Louise A., Wentzensen, Nicolas, Hogdall, Claus, Lundvall, Lene, Nedergaard, Lotte, Baker, Helen, Song, Honglin, Eccles, Diana, McNeish, Ian, Paul, James, Carty, Karen, Siddiqui, Nadeem, Glasspool, Rosalind, Whittemore, Alice S., Rothstein, Joseph H., McGuire, Valerie, Sieh, Weiva, Ji, Bu-Tian, Zheng, Wei, Shu, Xiao-Ou, Gao, Yu-Tang, Rosen, Barry, Risch, Harvey A., McLaughlin, John R., Narod, Steven A., Monteiro, Alvaro N., Chen, Ann, Lin, Hui-Yi, Permuth-Wey, Jenny, Sellers, Thomas A., Tsai, Ya-Yu, Chen, Zhihua, Ziogas, Argyrios, Anton-Culver, Hoda, Gentry-Maharaj, Aleksandra, Menon, Usha, Harrington, Patricia, Lee, Alice W., Wu, Anna H., Pearce, Celeste L., Coetzee, Gerhard A., Pike, Malcolm C., Dansonka-Mieszkowska, Agnieszka, Timorek, Agnieszka, Rzepecka, Iwona K., Kupryjanczyk, Jolanta, Freedman, Matt, Noushmehr, Houtan, Easton, Douglas F., Offit, Kenneth, Couch, Fergus J., Gayther, Simon, Pharoah, Paul P., Antoniou, Antonis C., and Chenevix-Trench, Georgia

Published
2014
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31. Locus-Wide Chromatin Remodeling and Enhanced Androgen Receptor-Mediated Transcription in Recurrent Prostate Tumor Cells.

Author

Li Jia, Shen, Howard C., Wantroba, Marcus, Khalid, Omar, Liang, Gangning, Wang, Qingcai, Gentzschein, Elisabet, Pinski, Jacek K., Stanczyk, Frank Z., Jones, Peter A., and Coetzee, Gerhard A.

Subjects
*PROSTATE cancer, *ANDROGENS, *CELLS, *HISTONES, *MOLECULAR genetics
Abstract

Prostate cancers (PCas) become resistant to hormone withdrawal through increased androgen receptor (AR) signaling. Here we show increased AR-mediated transcription efficiency in PCa cells that have acquired the ability to grow in low concentrations of androgen. Compared to androgen-dependent PCa cells, these cells showed increased activity of transiently transfected reporters and increased mRNA synthesis relative to levels of AR occupancy of the prostate-specific antigen (PSA) gene. The locus also displayed up to 10-fold-higher levels of histone H3-K9/K14 acetylation and H3-K4 methylation across the entire body of the gene. Although similar increased mRNA expression and locus-wide histone acetylation were also observed at another kallikrein locus (KLK2), at a third AR target locus (TMPRSS2) increased gene expression and locus-wide histone acetylation were not seen in the absence of ligand. Androgen-independent PCa cells have thus evolved three distinctive alterations in AR-mediated transcription. First, increased RNA polymerase initiation and processivity contributed to increased gene expression. Second, AR signaling was more sensitive to ligand. Third, locus-wide chromatin remodeling conducive to the increased gene expression in the absence of ligand was apparent and depended on sustained AR activity. Therefore, increased AR ligand sensitivity as well as locus-specific chromatin alterations contribute to basal gene expression of a subpopulation of specific AR target genes in androgen-independent PCa cells. These features contribute to the androgen-independent phenotype of these cells. [ABSTRACT FROM AUTHOR]

Published
2006
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32. Cross-Seeding Assay in the Investigation of the Amyloid Core of Prion Fibrils.

Author

Chu BK, Lin YS, Shen HC, and Chen RP

Subjects
Humans, Amyloid chemistry, Amyloidogenic Proteins, Prions chemistry, Amyloidosis, Prion Diseases
Abstract

Amyloidogenesis, self-propagation of protein or peptide monomers to amyloid fibrils, has been linked to incurable pathogenesis of neurodegenerative diseases such as Alzheimer's disease and prion diseases. Investigations of amyloid structures and how monomers are transformed through seeding are therefore crucial for developing therapeutics toward these diseases. Here we describe a cross-seeding method to explore the amyloid core in prion fibrils that uses preformed amyloid fibrils as a seed to induce the transformation of other protein or peptide monomers to amyloid fibrils., (© 2023. Springer Science+Business Media, LLC, part of Springer Nature.)

Published
2023
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