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1. Membrane-tethered delta-like 1 homolog (DLK1) restricts adipose tissue size by inhibiting preadipocyte proliferation

Author: Mortensen, Sussi B., Jensen, Charlotte H., Schneider, Mikael, Thomassen, Mads, Kruse, Torben A., Laborda, Jorge, Sheikh, Soren P., and Andersen, Ditte C.
Subjects: Adipose tissues -- Research -- Analysis -- Physiological aspects, Fat cells -- Research -- Analysis -- Physiological aspects, Health
Abstract: Adipocyte renewal from preadipocytes has been shown to occur throughout life and to contribute to obesity, yet very tittle is known about the molecular circuits that control preadipocyte expansion. The [...]
Published: 2012
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2. Genomic profiling of a randomized trial of interferon-α vs hydroxyurea in MPN reveals mutation-specific responses

Author: Knudsen, Trine Alma, Skov, Vibe, Stevenson, Kristen, Werner, Lillian, Duke, William, Laurore, Charles, Gibson, Christopher J., Nag, Anwesha, Thorner, Aaron R., Wollison, Bruce, Hansen, Dennis Lund, Ellervik, Christina, El Fassi, Daniel, de Stricker, Karin, Ocias, Lukas Frans, Brabrand, Mette, Bjerrum, Ole Weis, Overgaard, Ulrik Malthe, Frederiksen, Mikael, Kristensen, Thomas Kielsgaard, Kruse, Torben A., Thomassen, Mads, Mourits-Andersen, Torben, Severinsen, Marianne Tang, Stentoft, Jesper, Starklint, Joern, Neuberg, Donna S., Kjaer, Lasse, Larsen, Thomas Stauffer, Hasselbalch, Hans Carl, Lindsley, R. Coleman, and Mullally, Ann
Abstract: Although somatic mutations influence the pathogenesis, phenotype, and outcome of myeloproliferative neoplasms (MPNs), little is known about their impact on molecular response to cytoreductive treatment. We performed targeted next-generation sequencing (NGS) on 202 pretreatment samples obtained from patients with MPN enrolled in the DALIAH trial (A Study of Low Dose Interferon Alpha Versus Hydroxyurea in Treatment of Chronic Myeloid Neoplasms; #NCT01387763), a randomized controlled phase 3 clinical trial, and 135 samples obtained after 24 months of therapy with recombinant interferon-alpha (IFNα) or hydroxyurea. The primary aim was to evaluate the association between complete clinicohematologic response (CHR) at 24 months and molecular response through sequential assessment of 120 genes using NGS. Among JAK2-mutated patients treated with IFNα, those with CHR had a greater reduction in the JAK2 variant allele frequency (median, 0.29 to 0.07; P < .0001) compared with those not achieving CHR (median, 0.27 to 0.14; P < .0001). In contrast, the CALR variant allele frequency did not significantly decline in those achieving CHR or in those not achieving CHR. Treatment-emergent mutations in DNMT3A were observed more commonly in patients treated with IFNα compared with hydroxyurea (P = .04). Furthermore, treatment-emergent DNMT3A mutations were significantly enriched in IFNα–treated patients not attaining CHR (P = .02). A mutation in TET2, DNMT3A, or ASXL1 was significantly associated with prior stroke (age-adjusted odds ratio, 5.29; 95% confidence interval, 1.59-17.54; P = .007), as was a mutation in TET2 alone (age-adjusted odds ratio, 3.03; 95% confidence interval, 1.03-9.01; P = .044). At 24 months, we found mutation-specific response patterns to IFNα: (1) JAK2- and CALR-mutated MPN exhibited distinct molecular responses; and (2) DNMT3A-mutated clones/subclones emerged on treatment.
Published: 2022
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3. Polygenic risk modeling for prediction of epithelial ovarian cancer risk

Author: Dareng, Eileen O., Tyrer, Jonathan P., Barnes, Daniel R., Jones, Michelle R., Yang, Xin, Aben, Katja K. H., Adank, Muriel A., Agata, Simona, Andrulis, Irene L., Anton-Culver, Hoda, Antonenkova, Natalia N., Aravantinos, Gerasimos, Arun, Banu K., Augustinsson, Annelie, Balmaña, Judith, Bandera, Elisa V., Barkardottir, Rosa B., Barrowdale, Daniel, Beckmann, Matthias W., Beeghly-Fadiel, Alicia, Benitez, Javier, Bermisheva, Marina, Bernardini, Marcus Q., Bjorge, Line, Black, Amanda, Bogdanova, Natalia V., Bonanni, Bernardo, Borg, Ake, Brenton, James D., Budzilowska, Agnieszka, Butzow, Ralf, Buys, Saundra S., Cai, Hui, Caligo, Maria A., Campbell, Ian, Cannioto, Rikki, Cassingham, Hayley, Chang-Claude, Jenny, Chanock, Stephen J., Chen, Kexin, Chiew, Yoke-Eng, Chung, Wendy K., Claes, Kathleen B. M., Colonna, Sarah, Cook, Linda S., Couch, Fergus J., Daly, Mary B., Dao, Fanny, Davies, Eleanor, de la Hoya, Miguel, de Putter, Robin, Dennis, Joe, DePersia, Allison, Devilee, Peter, Diez, Orland, Ding, Yuan Chun, Doherty, Jennifer A., Domchek, Susan M., Dörk, Thilo, du Bois, Andreas, Dürst, Matthias, Eccles, Diana M., Eliassen, Heather A., Engel, Christoph, Evans, Gareth D., Fasching, Peter A., Flanagan, James M., Fortner, Renée T., Machackova, Eva, Friedman, Eitan, Ganz, Patricia A., Garber, Judy, Gensini, Francesca, Giles, Graham G., Glendon, Gord, Godwin, Andrew K., Goodman, Marc T., Greene, Mark H., Gronwald, Jacek, Hahnen, Eric, Haiman, Christopher A., Håkansson, Niclas, Hamann, Ute, Hansen, Thomas V. O., Harris, Holly R., Hartman, Mikael, Heitz, Florian, Hildebrandt, Michelle A. T., Høgdall, Estrid, Høgdall, Claus K., Hopper, John L., Huang, Ruea-Yea, Huff, Chad, Hulick, Peter J., Huntsman, David G., Imyanitov, Evgeny N., Isaacs, Claudine, Jakubowska, Anna, James, Paul A., Janavicius, Ramunas, Jensen, Allan, Johannsson, Oskar Th., John, Esther M., Jones, Michael E., Kang, Daehee, Karlan, Beth Y., Karnezis, Anthony, Kelemen, Linda E., Khusnutdinova, Elza, Kiemeney, Lambertus A., Kim, Byoung-Gie, Kjaer, Susanne K., Komenaka, Ian, Kupryjanczyk, Jolanta, Kurian, Allison W., Kwong, Ava, Lambrechts, Diether, Larson, Melissa C., Lazaro, Conxi, Le, Nhu D., Leslie, Goska, Lester, Jenny, Lesueur, Fabienne, Levine, Douglas A., Li, Lian, Li, Jingmei, Loud, Jennifer T., Lu, Karen H., Lubiński, Jan, Mai, Phuong L., Manoukian, Siranoush, Marks, Jeffrey R., Matsuno, Rayna Kim, Matsuo, Keitaro, May, Taymaa, McGuffog, Lesley, McLaughlin, John R., McNeish, Iain A., Mebirouk, Noura, Menon, Usha, Miller, Austin, Milne, Roger L., Minlikeeva, Albina, Modugno, Francesmary, Montagna, Marco, Moysich, Kirsten B., Munro, Elizabeth, Nathanson, Katherine L., Neuhausen, Susan L., Nevanlinna, Heli, Yie, Joanne Ngeow Yuen, Nielsen, Henriette Roed, Nielsen, Finn C., Nikitina-Zake, Liene, Odunsi, Kunle, Offit, Kenneth, Olah, Edith, Olbrecht, Siel, Olopade, Olufunmilayo I., Olson, Sara H., Olsson, Håkan, Osorio, Ana, Papi, Laura, Park, Sue K., Parsons, Michael T., Pathak, Harsha, Pedersen, Inge Sokilde, Peixoto, Ana, Pejovic, Tanja, Perez-Segura, Pedro, Permuth, Jennifer B., Peshkin, Beth, Peterlongo, Paolo, Piskorz, Anna, Prokofyeva, Darya, Radice, Paolo, Rantala, Johanna, Riggan, Marjorie J., Risch, Harvey A., Rodriguez-Antona, Cristina, Ross, Eric, Rossing, Mary Anne, Runnebaum, Ingo, Sandler, Dale P., Santamariña, Marta, Soucy, Penny, Schmutzler, Rita K., Setiawan, V. Wendy, Shan, Kang, Sieh, Weiva, Simard, Jacques, Singer, Christian F., Sokolenko, Anna P., Song, Honglin, Southey, Melissa C., Steed, Helen, Stoppa-Lyonnet, Dominique, Sutphen, Rebecca, Swerdlow, Anthony J., Tan, Yen Yen, Teixeira, Manuel R., Teo, Soo Hwang, Terry, Kathryn L., Terry, Mary Beth, Thomassen, Mads, Thompson, Pamela J., Thomsen, Liv Cecilie Vestrheim, Thull, Darcy L., Tischkowitz, Marc, Titus, Linda, Toland, Amanda E., Torres, Diana, Trabert, Britton, Travis, Ruth, Tung, Nadine, Tworoger, Shelley S., Valen, Ellen, van Altena, Anne M., van der Hout, Annemieke H., Van Nieuwenhuysen, Els, van Rensburg, Elizabeth J., Vega, Ana, Edwards, Digna Velez, Vierkant, Robert A., Wang, Frances, Wappenschmidt, Barbara, Webb, Penelope M., Weinberg, Clarice R., Weitzel, Jeffrey N., Wentzensen, Nicolas, White, Emily, Whittemore, Alice S., Winham, Stacey J., Wolk, Alicja, Woo, Yin-Ling, Wu, Anna H., Yan, Li, Yannoukakos, Drakoulis, Zavaglia, Katia M., Zheng, Wei, Ziogas, Argyrios, Zorn, Kristin K., Kleibl, Zdenek, Easton, Douglas, Lawrenson, Kate, DeFazio, Anna, Sellers, Thomas A., Ramus, Susan J., Pearce, Celeste L., Monteiro, Alvaro N., Cunningham, Julie, Goode, Ellen L., Schildkraut, Joellen M., Berchuck, Andrew, Chenevix-Trench, Georgia, Gayther, Simon A., Antoniou, Antonis C., and Pharoah, Paul D. P.
Abstract: Polygenic risk scores (PRS) for epithelial ovarian cancer (EOC) have the potential to improve risk stratification. Joint estimation of Single Nucleotide Polymorphism (SNP) effects in models could improve predictive performance over standard approaches of PRS construction. Here, we implemented computationally efficient, penalized, logistic regression models (lasso, elastic net, stepwise) to individual level genotype data and a Bayesian framework with continuous shrinkage, “select and shrink for summary statistics” (S4), to summary level data for epithelial non-mucinous ovarian cancer risk prediction. We developed the models in a dataset consisting of 23,564 non-mucinous EOC cases and 40,138 controls participating in the Ovarian Cancer Association Consortium (OCAC) and validated the best models in three populations of different ancestries: prospective data from 198,101 women of European ancestries; 7,669 women of East Asian ancestries; 1,072 women of African ancestries, and in 18,915 BRCA1and 12,337 BRCA2pathogenic variant carriers of European ancestries. In the external validation data, the model with the strongest association for non-mucinous EOC risk derived from the OCAC model development data was the S4 model (27,240 SNPs) with odds ratios (OR) of 1.38 (95% CI: 1.28–1.48, AUC: 0.588) per unit standard deviation, in women of European ancestries; 1.14 (95% CI: 1.08–1.19, AUC: 0.538) in women of East Asian ancestries; 1.38 (95% CI: 1.21–1.58, AUC: 0.593) in women of African ancestries; hazard ratios of 1.36 (95% CI: 1.29–1.43, AUC: 0.592) in BRCA1pathogenic variant carriers and 1.49 (95% CI: 1.35–1.64, AUC: 0.624) in BRCA2pathogenic variant carriers. Incorporation of the S4 PRS in risk prediction models for ovarian cancer may have clinical utility in ovarian cancer prevention programs.
Published: 2022
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4. Risks of breast and ovarian cancer for women harboring pathogenic missense variants in BRCA1and BRCA2compared with those harboring protein truncating variants

Author: Li, Hongyan, Engel, Christoph, de la Hoya, Miguel, Peterlongo, Paolo, Yannoukakos, Drakoulis, Livraghi, Luca, Radice, Paolo, Thomassen, Mads, Hansen, Thomas V.O., Gerdes, Anne-Marie, Nielsen, Henriette R., Caputo, Sandrine M., Zambelli, Alberto, Borg, Ake, Solano, Angela, Thomas, Abigail, Parsons, Michael T., Antoniou, Antonis C., Leslie, Goska, Yang, Xin, Chenevix-Trench, Georgia, Caldes, Trinidad, Kwong, Ava, Pedersen, Inge Søkilde, Lautrup, Charlotte K., John, Esther M., Terry, Mary Beth, Hopper, John L., Southey, Melissa C., Andrulis, Irene L., Tischkowitz, Marc, Janavicius, Ramunas, Boonen, Susanne E., Kroeldrup, Lone, Varesco, Liliana, Hamann, Ute, Vega, Ana, Palmero, Edenir I., Garber, Judy, Montagna, Marco, Van Asperen, Christi J., Foretova, Lenka, Greene, Mark H., Selkirk, Tina, Moller, Pal, Toland, Amanda E., Domchek, Susan M., James, Paul A., Thorne, Heather, Eccles, Diana M., Nielsen, Sarah M., Manoukian, Siranoush, Pasini, Barbara, Caligo, Maria A., Lazaro, Conxi, Kirk, Judy, Wappenschmidt, Barbara, Spurdle, Amanda B., Couch, Fergus J., Schmutzler, Rita, and Goldgar, David E.
Abstract: Germline genetic testing for BRCA1and BRCA2variants has been a part of clinical practice for >2 decades. However, no studies have compared the cancer risks associated with missense pathogenic variants (PVs) with those associated with protein truncating (PTC) variants.
Published: 2022
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5. Quality of Life and Symptom Burden of Patients with MPN during Treatment with Hydroxyurea or Pegylated Interferon-alpha2: Results from a Randomized Controlled Trial

Author: Knudsen, Trine A., Hansen, Dennis Lund, Ocias, Lukas Frans, Bjerrum, Ole Weis, Brabrand, Mette, Christensen, Sarah F., Eickhardt-Dalbøge, Christina Schjellerup S., Ellervik, Christina, Fassi, Daniel El, Frederiksen, Mikael, Kjær, Lasse, Kristensen, Thomas Kielsgaard, Kruse, Torben A., Kranker Larsen, Morten, Mourits-Andersen, Torben, Overgaard, Ulrik Malthe, Severinsen, Marianne Tang, Skov, Vibe, Sørensen, Anders Lindholm, Stentoft, Jesper, Starklint, Jørn, Stricker, Karin de, Thomassen, Mads, Larsen, Thomas S., and Hasselbalch, Hans Carl
Published: 2022
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6. Increased oxidative stress with substantial dysregulation of genes related to oxidative stress and DNA repair after laparoscopic colon cancer surgery

Author: Watt, Sara Kehlet, Hasselbalch, Hans Carl, Skov, Vibe, Kjær, Lasse, Thomassen, Mads, Kruse, Torben A., Burton, Mark, Poulsen, Henrik Enghusen, and Gögenur, Ismail
Abstract: Surgical stress is followed by oxidative stress, where reactive oxygene species may act as regulators of pathways related to cancer cell survival and metastatic ability. Furthermore, reactive oxygene species may cause DNA and RNA damage.
Published: 2020
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7. Polygenic risk scores and breast and epithelial ovarian cancer risks for carriers of BRCA1and BRCA2pathogenic variants

Author: Barnes, Daniel R., Rookus, Matti A., McGuffog, Lesley, Leslie, Goska, Mooij, Thea M., Dennis, Joe, Mavaddat, Nasim, Adlard, Julian, Ahmed, Munaza, Aittomäki, Kristiina, Andrieu, Nadine, Andrulis, Irene L., Arnold, Norbert, Arun, Banu K., Azzollini, Jacopo, Balmaña, Judith, Barkardottir, Rosa B., Barrowdale, Daniel, Benitez, Javier, Berthet, Pascaline, Białkowska, Katarzyna, Blanco, Amie M., Blok, Marinus J., Bonanni, Bernardo, Boonen, Susanne E., Borg, Åke, Bozsik, Aniko, Bradbury, Angela R., Brennan, Paul, Brewer, Carole, Brunet, Joan, Buys, Saundra S., Caldés, Trinidad, Caligo, Maria A., Campbell, Ian, Christensen, Lise Lotte, Chung, Wendy K., Claes, Kathleen B.M., Colas, Chrystelle, Berthet, Pascaline, Colas, Chrystelle, Collonge-Rame, Marie-Agnès, Delnatte, Capucine, Faivre, Laurence, Giraud, Sophie, Lasset, Christine, Mari, Véronique, Mebirouk, Noura, Mouret-Fourme, Emmanuelle, Schuster, Hélène, Stoppa-Lyonnet, Dominique, Adlard, Julian, Ahmed, Munaza, Antoniou, Antonis, Barrowdale, Daniel, Brennan, Paul, Brewer, Carole, Cook, Jackie, Davidson, Rosemarie, Easton, Douglas, Eeles, Ros, Evans, D. Gareth, Frost, Debra, Hanson, Helen, Izatt, Louise, Ong, Kai-ren, Side, Lucy, O’Shaughnessy-Kirwan, Aoife, Tischkowitz, Marc, Walker, Lisa, Collonge-Rame, Marie-Agnès, Cook, Jackie, Daly, Mary B., Davidson, Rosemarie, de la Hoya, Miguel, de Putter, Robin, Delnatte, Capucine, Devilee, Peter, Diez, Orland, Ding, Yuan Chun, Domchek, Susan M., Dorfling, Cecilia M., Dumont, Martine, Eeles, Ros, Ejlertsen, Bent, Engel, Christoph, Evans, D. Gareth, Faivre, Laurence, Foretova, Lenka, Fostira, Florentia, Friedlander, Michael, Friedman, Eitan, Frost, Debra, Ganz, Patricia A., Garber, Judy, Gehrig, Andrea, Gerdes, Anne-Marie, Gesta, Paul, Giraud, Sophie, Glendon, Gord, Godwin, Andrew K., Goldgar, David E., González-Neira, Anna, Greene, Mark H., Gschwantler-Kaulich, Daphne, Hahnen, Eric, Hamann, Ute, Hanson, Helen, Hentschel, Julia, Hogervorst, Frans B.L., Hooning, Maartje J., Horvath, Judit, Hu, Chunling, Hulick, Peter J., Imyanitov, Evgeny N., Chenevix-Trench, Georgia, Phillips, Kelly-Anne, Spurdle, Amanda, Blok, Marinus, Devilee, Peter, Hogervorst, Frans, Hooning, Maartje, Koudijs, Marco, Mensenkamp, Arjen, Meijers-Heijboer, Hanne, Rookus, Matti, Engelen, Klaartje van, Andrieu, Nadine, Noguès, Catherine, Isaacs, Claudine, Izatt, Louise, Izquierdo, Angel, Jakubowska, Anna, James, Paul A., Janavicius, Ramunas, John, Esther M., Joseph, Vijai, Karlan, Beth Y., Kast, Karin, Koudijs, Marco, Kruse, Torben A., Kwong, Ava, Laitman, Yael, Lasset, Christine, Lazaro, Conxi, Lester, Jenny, Lesueur, Fabienne, Liljegren, Annelie, Loud, Jennifer T., Lubiński, Jan, Mai, Phuong L., Manoukian, Siranoush, Mari, Véronique, Mebirouk, Noura, Meijers-Heijboer, Hanne E.J., Meindl, Alfons, Mensenkamp, Arjen R., Miller, Austin, Montagna, Marco, Mouret-Fourme, Emmanuelle, Mukherjee, Semanti, Mulligan, Anna Marie, Nathanson, Katherine L., Neuhausen, Susan L., Nevanlinna, Heli, Niederacher, Dieter, Nielsen, Finn Cilius, Nikitina-Zake, Liene, Noguès, Catherine, Olah, Edith, Olopade, Olufunmilayo I., Ong, Kai-ren, O’Shaughnessy-Kirwan, Aoife, Osorio, Ana, Ott, Claus-Eric, Papi, Laura, Park, Sue K., Parsons, Michael T., Pedersen, Inge Sokilde, Peissel, Bernard, Peixoto, Ana, Peterlongo, Paolo, Pfeiler, Georg, Phillips, Kelly-Anne, Prajzendanc, Karolina, Pujana, Miquel Angel, Radice, Paolo, Ramser, Juliane, Ramus, Susan J., Rantala, Johanna, Rennert, Gad, Risch, Harvey A., Robson, Mark, Rønlund, Karina, Salani, Ritu, Schuster, Hélène, Senter, Leigha, Shah, Payal D., Sharma, Priyanka, Side, Lucy E., Singer, Christian F., Slavin, Thomas P., Soucy, Penny, Southey, Melissa C., Spurdle, Amanda B., Steinemann, Doris, Steinsnyder, Zoe, Stoppa-Lyonnet, Dominique, Sutter, Christian, Tan, Yen Yen, Teixeira, Manuel R., Teo, Soo Hwang, Thull, Darcy L., Tischkowitz, Marc, Tognazzo, Silvia, Toland, Amanda E., Trainer, Alison H., Tung, Nadine, van Engelen, Klaartje, van Rensburg, Elizabeth J., Vega, Ana, Vierstraete, Jeroen, Wagner, Gabriel, Walker, Lisa, Wang-Gohrke, Shan, Wappenschmidt, Barbara, Weitzel, Jeffrey N., Yadav, Siddhartha, Yang, Xin, Yannoukakos, Drakoulis, Zimbalatti, Dario, Offit, Kenneth, Thomassen, Mads, Couch, Fergus J., Schmutzler, Rita K., Simard, Jacques, Easton, Douglas F., Chenevix-Trench, Georgia, and Antoniou, Antonis C.
Abstract: We assessed the associations between population-based polygenic risk scores (PRS) for breast (BC) or epithelial ovarian cancer (EOC) with cancer risks for BRCA1and BRCA2pathogenic variant carriers.
Published: 2020
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8. Characterization of the Cancer Spectrum in Men With Germline BRCA1 and BRCA2 Pathogenic Variants: Results From the Consortium of Investigators of Modifiers of BRCA1/2 (CIMBA)

Author: Silvestri, Valentina, Leslie, Goska, Barnes, Daniel R., Agnarsson, Bjarni A., Aittomäki, Kristiina, Alducci, Elisa, Andrulis, Irene L., Barkardottir, Rosa B., Barroso, Alicia, Barrowdale, Daniel, Benitez, Javier, Bonanni, Bernardo, Borg, Ake, Buys, Saundra S., Caldés, Trinidad, Caligo, Maria A., Capalbo, Carlo, Campbell, Ian, Chung, Wendy K., Claes, Kathleen B.M., Colonna, Sarah V., Cortesi, Laura, Couch, Fergus J., de la Hoya, Miguel, Diez, Orland, Ding, Yuan Chun, Domchek, Susan, Easton, Douglas F., Ejlertsen, Bent, Engel, Christoph, Evans, D. Gareth, Feliubadalò, Lidia, Foretova, Lenka, Fostira, Florentia, Géczi, Lajos, Gerdes, Anne-Marie, Glendon, Gord, Godwin, Andrew K., Goldgar, David E., Hahnen, Eric, Hogervorst, Frans B.L., Hopper, John L., Hulick, Peter J., Isaacs, Claudine, Izquierdo, Angel, James, Paul A., Janavicius, Ramunas, Jensen, Uffe Birk, John, Esther M., Joseph, Vijai, Konstantopoulou, Irene, Kurian, Allison W., Kwong, Ava, Landucci, Elisabetta, Lesueur, Fabienne, Loud, Jennifer T., Machackova, Eva, Mai, Phuong L., Majidzadeh-A, Keivan, Manoukian, Siranoush, Montagna, Marco, Moserle, Lidia, Mulligan, Anna Marie, Nathanson, Katherine L., Nevanlinna, Heli, Ngeow, Joanne, Nikitina-Zake, Liene, Offit, Kenneth, Olah, Edith, Olopade, Olufunmilayo I., Osorio, Ana, Papi, Laura, Park, Sue K., Pedersen, Inge Sokilde, Perez-Segura, Pedro, Petersen, Annabeth H., Pinto, Pedro, Porfirio, Berardino, Pujana, Miquel Angel, Radice, Paolo, Rantala, Johanna, Rashid, Muhammad U., Rosenzweig, Barak, Rossing, Maria, Santamariña, Marta, Schmutzler, Rita K., Senter, Leigha, Simard, Jacques, Singer, Christian F., Solano, Angela R., Southey, Melissa C., Steele, Linda, Steinsnyder, Zoe, Stoppa-Lyonnet, Dominique, Tan, Yen Yen, Teixeira, Manuel R., Teo, Soo H., Terry, Mary Beth, Thomassen, Mads, Toland, Amanda E., Torres-Esquius, Sara, Tung, Nadine, van Asperen, Christi J., Vega, Ana, Viel, Alessandra, Vierstraete, Jeroen, Wappenschmidt, Barbara, Weitzel, Jeffrey N., Wieme, Greet, Yoon, Sook-Yee, Zorn, Kristin K., McGuffog, Lesley, Parsons, Michael T., Hamann, Ute, Greene, Mark H., Kirk, Judy A., Neuhausen, Susan L., Rebbeck, Timothy R., Tischkowitz, Marc, Chenevix-Trench, Georgia, Antoniou, Antonis C., Friedman, Eitan, and Ottini, Laura
Abstract: IMPORTANCE: The limited data on cancer phenotypes in men with germline BRCA1 and BRCA2 pathogenic variants (PVs) have hampered the development of evidence-based recommendations for early cancer detection and risk reduction in this population. OBJECTIVE: To compare the cancer spectrum and frequencies between male BRCA1 and BRCA2 PV carriers. DESIGN, SETTING, AND PARTICIPANTS: Retrospective cohort study of 6902 men, including 3651 BRCA1 and 3251 BRCA2 PV carriers, older than 18 years recruited from cancer genetics clinics from 1966 to 2017 by 53 study groups in 33 countries worldwide collaborating through the Consortium of Investigators of Modifiers of BRCA1/2 (CIMBA). Clinical data and pathologic characteristics were collected. MAIN OUTCOMES AND MEASURES: BRCA1/2 status was the outcome in a logistic regression, and cancer diagnoses were the independent predictors. All odds ratios (ORs) were adjusted for age, country of origin, and calendar year of the first interview. RESULTS: Among the 6902 men in the study (median [range] age, 51.6 [18-100] years), 1634 cancers were diagnosed in 1376 men (19.9%), the majority (922 of 1,376 [67%]) being BRCA2 PV carriers. Being affected by any cancer was associated with a higher probability of being a BRCA2, rather than a BRCA1, PV carrier (OR, 3.23; 95% CI, 2.81-3.70; P < .001), as well as developing 2 (OR, 7.97; 95% CI, 5.47-11.60; P < .001) and 3 (OR, 19.60; 95% CI, 4.64-82.89; P < .001) primary tumors. A higher frequency of breast (OR, 5.47; 95% CI, 4.06-7.37; P < .001) and prostate (OR, 1.39; 95% CI, 1.09-1.78; P = .008) cancers was associated with a higher probability of being a BRCA2 PV carrier. Among cancers other than breast and prostate, pancreatic cancer was associated with a higher probability (OR, 3.00; 95% CI, 1.55-5.81; P = .001) and colorectal cancer with a lower probability (OR, 0.47; 95% CI, 0.29-0.78; P = .003) of being a BRCA2 PV carrier. CONCLUSIONS AND RELEVANCE: Significant differences in the cancer spectrum were observed in male BRCA2, compared with BRCA1, PV carriers. These data may inform future recommendations for surveillance of BRCA1/2-associated cancers and guide future prospective studies for estimating cancer risks in men with BRCA1/2 PVs.
Published: 2020
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9. Genome-wide association study identifies 32 novel breast cancer susceptibility loci from overall and subtype-specific analyses

Author: Zhang, Haoyu, Ahearn, Thomas U., Lecarpentier, Julie, Barnes, Daniel, Beesley, Jonathan, Qi, Guanghao, Jiang, Xia, O’Mara, Tracy A., Zhao, Ni, Bolla, Manjeet K., Dunning, Alison M., Dennis, Joe, Wang, Qin, Ful, Zumuruda Abu, Aittomäki, Kristiina, Andrulis, Irene L., Anton-Culver, Hoda, Arndt, Volker, Aronson, Kristan J., Arun, Banu K., Auer, Paul L., Azzollini, Jacopo, Barrowdale, Daniel, Becher, Heiko, Beckmann, Matthias W., Behrens, Sabine, Benitez, Javier, Bermisheva, Marina, Bialkowska, Katarzyna, Blanco, Ana, Blomqvist, Carl, Bogdanova, Natalia V., Bojesen, Stig E., Bonanni, Bernardo, Bondavalli, Davide, Borg, Ake, Brauch, Hiltrud, Brenner, Hermann, Briceno, Ignacio, Broeks, Annegien, Brucker, Sara Y., Brüning, Thomas, Burwinkel, Barbara, Buys, Saundra S., Byers, Helen, Caldés, Trinidad, Caligo, Maria A., Calvello, Mariarosaria, Campa, Daniele, Castelao, Jose E., Chang-Claude, Jenny, Chanock, Stephen J., Christiaens, Melissa, Christiansen, Hans, Chung, Wendy K., Claes, Kathleen B. M., Clarke, Christine L., Cornelissen, Sten, Couch, Fergus J., Cox, Angela, Cross, Simon S., Czene, Kamila, Daly, Mary B., Devilee, Peter, Diez, Orland, Domchek, Susan M., Dörk, Thilo, Dwek, Miriam, Eccles, Diana M., Ekici, Arif B., Evans, D. Gareth, Fasching, Peter A., Figueroa, Jonine, Foretova, Lenka, Fostira, Florentia, Friedman, Eitan, Frost, Debra, Gago-Dominguez, Manuela, Gapstur, Susan M., Garber, Judy, García-Sáenz, José A., Gaudet, Mia M., Gayther, Simon A., Giles, Graham G., Godwin, Andrew K., Goldberg, Mark S., Goldgar, David E., González-Neira, Anna, Greene, Mark H., Gronwald, Jacek, Guénel, Pascal, Häberle, Lothar, Hahnen, Eric, Haiman, Christopher A., Hake, Christopher R., Hall, Per, Hamann, Ute, Harkness, Elaine F., Heemskerk-Gerritsen, Bernadette A. M., Hillemanns, Peter, Hogervorst, Frans B. L., Holleczek, Bernd, Hollestelle, Antoinette, Hooning, Maartje J., Hoover, Robert N., Hopper, John L., Howell, Anthony, Huebner, Hanna, Hulick, Peter J., Imyanitov, Evgeny N., Isaacs, Claudine, Izatt, Louise, Jager, Agnes, Jakimovska, Milena, Jakubowska, Anna, James, Paul, Janavicius, Ramunas, Janni, Wolfgang, John, Esther M., Jones, Michael E., Jung, Audrey, Kaaks, Rudolf, Kapoor, Pooja Middha, Karlan, Beth Y., Keeman, Renske, Khan, Sofia, Khusnutdinova, Elza, Kitahara, Cari M., Ko, Yon-Dschun, Konstantopoulou, Irene, Koppert, Linetta B., Koutros, Stella, Kristensen, Vessela N., Laenkholm, Anne-Vibeke, Lambrechts, Diether, Larsson, Susanna C., Laurent-Puig, Pierre, Lazaro, Conxi, Lazarova, Emilija, Lejbkowicz, Flavio, Leslie, Goska, Lesueur, Fabienne, Lindblom, Annika, Lissowska, Jolanta, Lo, Wing-Yee, Loud, Jennifer T., Lubinski, Jan, Lukomska, Alicja, MacInnis, Robert J., Mannermaa, Arto, Manoochehri, Mehdi, Manoukian, Siranoush, Margolin, Sara, Martinez, Maria Elena, Matricardi, Laura, McGuffog, Lesley, McLean, Catriona, Mebirouk, Noura, Meindl, Alfons, Menon, Usha, Miller, Austin, Mingazheva, Elvira, Montagna, Marco, Mulligan, Anna Marie, Mulot, Claire, Muranen, Taru A., Nathanson, Katherine L., Neuhausen, Susan L., Nevanlinna, Heli, Neven, Patrick, Newman, William G., Nielsen, Finn C., Nikitina-Zake, Liene, Nodora, Jesse, Offit, Kenneth, Olah, Edith, Olopade, Olufunmilayo I., Olsson, Håkan, Orr, Nick, Papi, Laura, Papp, Janos, Park-Simon, Tjoung-Won, Parsons, Michael T., Peissel, Bernard, Peixoto, Ana, Peshkin, Beth, Peterlongo, Paolo, Peto, Julian, Phillips, Kelly-Anne, Piedmonte, Marion, Plaseska-Karanfilska, Dijana, Prajzendanc, Karolina, Prentice, Ross, Prokofyeva, Darya, Rack, Brigitte, Radice, Paolo, Ramus, Susan J., Rantala, Johanna, Rashid, Muhammad U., Rennert, Gad, Rennert, Hedy S., Risch, Harvey A., Romero, Atocha, Rookus, Matti A., Rübner, Matthias, Rüdiger, Thomas, Saloustros, Emmanouil, Sampson, Sarah, Sandler, Dale P., Sawyer, Elinor J., Scheuner, Maren T., Schmutzler, Rita K., Schneeweiss, Andreas, Schoemaker, Minouk J., Schöttker, Ben, Schürmann, Peter, Senter, Leigha, Sharma, Priyanka, Sherman, Mark E., Shu, Xiao-Ou, Singer, Christian F., Smichkoska, Snezhana, Soucy, Penny, Southey, Melissa C., Spinelli, John J., Stone, Jennifer, Stoppa-Lyonnet, Dominique, Swerdlow, Anthony J., Szabo, Csilla I., Tamimi, Rulla M., Tapper, William J., Taylor, Jack A., Teixeira, Manuel R., Terry, MaryBeth, Thomassen, Mads, Thull, Darcy L., Tischkowitz, Marc, Toland, Amanda E., Tollenaar, Rob A. E. M., Tomlinson, Ian, Torres, Diana, Troester, Melissa A., Truong, Thérèse, Tung, Nadine, Untch, Michael, Vachon, Celine M., van den Ouweland, Ans M. W., van der Kolk, Lizet E., van Veen, Elke M., vanRensburg, Elizabeth J., Vega, Ana, Wappenschmidt, Barbara, Weinberg, Clarice R., Weitzel, Jeffrey N., Wildiers, Hans, Winqvist, Robert, Wolk, Alicja, Yang, Xiaohong R., Yannoukakos, Drakoulis, Zheng, Wei, Zorn, Kristin K., Milne, Roger L., Kraft, Peter, Simard, Jacques, Pharoah, Paul D. P., Michailidou, Kyriaki, Antoniou, Antonis C., Schmidt, Marjanka K., Chenevix-Trench, Georgia, Easton, Douglas F., Chatterjee, Nilanjan, and García-Closas, Montserrat
Abstract: Breast cancer susceptibility variants frequently show heterogeneity in associations by tumor subtype1–3. To identify novel loci, we performed a genome-wide association study including 133,384 breast cancer cases and 113,789 controls, plus 18,908 BRCA1mutation carriers (9,414 with breast cancer) of European ancestry, using both standard and novel methodologies that account for underlying tumor heterogeneity by estrogen receptor, progesterone receptor and human epidermal growth factor receptor 2 status and tumor grade. We identified 32 novel susceptibility loci (P< 5.0 × 10−8), 15 of which showed evidence for associations with at least one tumor feature (false discovery rate < 0.05). Five loci showed associations (P< 0.05) in opposite directions between luminal and non-luminal subtypes. In silico analyses showed that these five loci contained cell-specific enhancers that differed between normal luminal and basal mammary cells. The genetic correlations between five intrinsic-like subtypes ranged from 0.35 to 0.80. The proportion of genome-wide chip heritability explained by all known susceptibility loci was 54.2% for luminal A-like disease and 37.6% for triple-negative disease. The odds ratios of polygenic risk scores, which included 330 variants, for the highest 1% of quantiles compared with middle quantiles were 5.63 and 3.02 for luminal A-like and triple-negative disease, respectively. These findings provide an improved understanding of genetic predisposition to breast cancer subtypes and will inform the development of subtype-specific polygenic risk scores.
Published: 2020
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10. Fine-mapping of 150 breast cancer risk regions identifies 191 likely target genes

Author: Fachal, Laura, Aschard, Hugues, Beesley, Jonathan, Barnes, Daniel R., Allen, Jamie, Kar, Siddhartha, Pooley, Karen A., Dennis, Joe, Michailidou, Kyriaki, Turman, Constance, Soucy, Penny, Lemaçon, Audrey, Lush, Michael, Tyrer, Jonathan P., Ghoussaini, Maya, Moradi Marjaneh, Mahdi, Jiang, Xia, Agata, Simona, Aittomäki, Kristiina, Alonso, M. Rosario, Andrulis, Irene L., Anton-Culver, Hoda, Antonenkova, Natalia N., Arason, Adalgeir, Arndt, Volker, Aronson, Kristan J., Arun, Banu K., Auber, Bernd, Auer, Paul L., Azzollini, Jacopo, Balmaña, Judith, Barkardottir, Rosa B., Barrowdale, Daniel, Beeghly-Fadiel, Alicia, Benitez, Javier, Bermisheva, Marina, Białkowska, Katarzyna, Blanco, Amie M., Blomqvist, Carl, Blot, William, Bogdanova, Natalia V., Bojesen, Stig E., Bolla, Manjeet K., Bonanni, Bernardo, Borg, Ake, Bosse, Kristin, Brauch, Hiltrud, Brenner, Hermann, Briceno, Ignacio, Brock, Ian W., Brooks-Wilson, Angela, Brüning, Thomas, Burwinkel, Barbara, Buys, Saundra S., Cai, Qiuyin, Caldés, Trinidad, Caligo, Maria A., Camp, Nicola J., Campbell, Ian, Canzian, Federico, Carroll, Jason S., Carter, Brian D., Castelao, Jose E., Chiquette, Jocelyne, Christiansen, Hans, Chung, Wendy K., Claes, Kathleen B. M., Clarke, Christine L., Collée, J. Margriet, Cornelissen, Sten, Couch, Fergus J., Cox, Angela, Cross, Simon S., Cybulski, Cezary, Czene, Kamila, Daly, Mary B., de la Hoya, Miguel, Devilee, Peter, Diez, Orland, Ding, Yuan Chun, Dite, Gillian S., Domchek, Susan M., Dörk, Thilo, dos-Santos-Silva, Isabel, Droit, Arnaud, Dubois, Stéphane, Dumont, Martine, Duran, Mercedes, Durcan, Lorraine, Dwek, Miriam, Eccles, Diana M., Engel, Christoph, Eriksson, Mikael, Evans, D. Gareth, Fasching, Peter A., Fletcher, Olivia, Floris, Giuseppe, Flyger, Henrik, Foretova, Lenka, Foulkes, William D., Friedman, Eitan, Fritschi, Lin, Frost, Debra, Gabrielson, Marike, Gago-Dominguez, Manuela, Gambino, Gaetana, Ganz, Patricia A., Gapstur, Susan M., Garber, Judy, García-Sáenz, José A., Gaudet, Mia M., Georgoulias, Vassilios, Giles, Graham G., Glendon, Gord, Godwin, Andrew K., Goldberg, Mark S., Goldgar, David E., González-Neira, Anna, Tibiletti, Maria Grazia, Greene, Mark H., Grip, Mervi, Gronwald, Jacek, Grundy, Anne, Guénel, Pascal, Hahnen, Eric, Haiman, Christopher A., Håkansson, Niclas, Hall, Per, Hamann, Ute, Harrington, Patricia A., Hartikainen, Jaana M., Hartman, Mikael, He, Wei, Healey, Catherine S., Heemskerk-Gerritsen, Bernadette A. M., Heyworth, Jane, Hillemanns, Peter, Hogervorst, Frans B. L., Hollestelle, Antoinette, Hooning, Maartje J., Hopper, John L., Howell, Anthony, Huang, Guanmengqian, Hulick, Peter J., Imyanitov, Evgeny N., Isaacs, Claudine, Iwasaki, Motoki, Jager, Agnes, Jakimovska, Milena, Jakubowska, Anna, James, Paul A., Janavicius, Ramunas, Jankowitz, Rachel C., John, Esther M., Johnson, Nichola, Jones, Michael E., Jukkola-Vuorinen, Arja, Jung, Audrey, Kaaks, Rudolf, Kang, Daehee, Kapoor, Pooja Middha, Karlan, Beth Y., Keeman, Renske, Kerin, Michael J., Khusnutdinova, Elza, Kiiski, Johanna I., Kirk, Judy, Kitahara, Cari M., Ko, Yon-Dschun, Konstantopoulou, Irene, Kosma, Veli-Matti, Koutros, Stella, Kubelka-Sabit, Katerina, Kwong, Ava, Kyriacou, Kyriacos, Laitman, Yael, Lambrechts, Diether, Lee, Eunjung, Leslie, Goska, Lester, Jenny, Lesueur, Fabienne, Lindblom, Annika, Lo, Wing-Yee, Long, Jirong, Lophatananon, Artitaya, Loud, Jennifer T., Lubiński, Jan, MacInnis, Robert J., Maishman, Tom, Makalic, Enes, Mannermaa, Arto, Manoochehri, Mehdi, Manoukian, Siranoush, Margolin, Sara, Martinez, Maria Elena, Matsuo, Keitaro, Maurer, Tabea, Mavroudis, Dimitrios, Mayes, Rebecca, McGuffog, Lesley, McLean, Catriona, Mebirouk, Noura, Meindl, Alfons, Miller, Austin, Miller, Nicola, Montagna, Marco, Moreno, Fernando, Muir, Kenneth, Mulligan, Anna Marie, Muñoz-Garzon, Victor M., Muranen, Taru A., Narod, Steven A., Nassir, Rami, Nathanson, Katherine L., Neuhausen, Susan L., Nevanlinna, Heli, Neven, Patrick, Nielsen, Finn C., Nikitina-Zake, Liene, Norman, Aaron, Offit, Kenneth, Olah, Edith, Olopade, Olufunmilayo I., Olsson, Håkan, Orr, Nick, Osorio, Ana, Pankratz, V. Shane, Papp, Janos, Park, Sue K., Park-Simon, Tjoung-Won, Parsons, Michael T., Paul, James, Pedersen, Inge Sokilde, Peissel, Bernard, Peshkin, Beth, Peterlongo, Paolo, Peto, Julian, Plaseska-Karanfilska, Dijana, Prajzendanc, Karolina, Prentice, Ross, Presneau, Nadege, Prokofyeva, Darya, Pujana, Miquel Angel, Pylkäs, Katri, Radice, Paolo, Ramus, Susan J., Rantala, Johanna, Rau-Murthy, Rohini, Rennert, Gad, Risch, Harvey A., Robson, Mark, Romero, Atocha, Rossing, Maria, Saloustros, Emmanouil, Sánchez-Herrero, Estela, Sandler, Dale P., Santamariña, Marta, Saunders, Christobel, Sawyer, Elinor J., Scheuner, Maren T., Schmidt, Daniel F., Schmutzler, Rita K., Schneeweiss, Andreas, Schoemaker, Minouk J., Schöttker, Ben, Schürmann, Peter, Scott, Christopher, Scott, Rodney J., Senter, Leigha, Seynaeve, Caroline M., Shah, Mitul, Sharma, Priyanka, Shen, Chen-Yang, Shu, Xiao-Ou, Singer, Christian F., Slavin, Thomas P., Smichkoska, Snezhana, Southey, Melissa C., Spinelli, John J., Spurdle, Amanda B., Stone, Jennifer, Stoppa-Lyonnet, Dominique, Sutter, Christian, Swerdlow, Anthony J., Tamimi, Rulla M., Tan, Yen Yen, Tapper, William J., Taylor, Jack A., Teixeira, Manuel R., Tengström, Maria, Teo, Soo Hwang, Terry, Mary Beth, Teulé, Alex, Thomassen, Mads, Thull, Darcy L., Tischkowitz, Marc, Toland, Amanda E., Tollenaar, Rob A. E. M., Tomlinson, Ian, Torres, Diana, Torres-Mejía, Gabriela, Troester, Melissa A., Truong, Thérèse, Tung, Nadine, Tzardi, Maria, Ulmer, Hans-Ulrich, Vachon, Celine M., van Asperen, Christi J., van der Kolk, Lizet E., van Rensburg, Elizabeth J., Vega, Ana, Viel, Alessandra, Vijai, Joseph, Vogel, Maartje J., Wang, Qin, Wappenschmidt, Barbara, Weinberg, Clarice R., Weitzel, Jeffrey N., Wendt, Camilla, Wildiers, Hans, Winqvist, Robert, Wolk, Alicja, Wu, Anna H., Yannoukakos, Drakoulis, Zhang, Yan, Zheng, Wei, Hunter, David, Pharoah, Paul D. P., Chang-Claude, Jenny, García-Closas, Montserrat, Schmidt, Marjanka K., Milne, Roger L., Kristensen, Vessela N., French, Juliet D., Edwards, Stacey L., Antoniou, Antonis C., Chenevix-Trench, Georgia, Simard, Jacques, Easton, Douglas F., Kraft, Peter, and Dunning, Alison M.
Abstract: Genome-wide association studies have identified breast cancer risk variants in over 150 genomic regions, but the mechanisms underlying risk remain largely unknown. These regions were explored by combining association analysis with in silico genomic feature annotations. We defined 205 independent risk-associated signals with the set of credible causal variants in each one. In parallel, we used a Bayesian approach (PAINTOR) that combines genetic association, linkage disequilibrium and enriched genomic features to determine variants with high posterior probabilities of being causal. Potentially causal variants were significantly over-represented in active gene regulatory regions and transcription factor binding sites. We applied our INQUSIT pipeline for prioritizing genes as targets of those potentially causal variants, using gene expression (expression quantitative trait loci), chromatin interaction and functional annotations. Known cancer drivers, transcription factors and genes in the developmental, apoptosis, immune system and DNA integrity checkpoint gene ontology pathways were over-represented among the highest-confidence target genes.
Published: 2020
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11. Final Analysis of the Daliah Trial: A Randomized Phase III Trial of Interferon-α Versus Hydroxyurea in Patients with MPN

Author: Knudsen, Trine Alma, Hansen, Dennis Lund, Ocias, Lukas Frans, Bjerrum, Ole, Brabrand, Mette, Christensen, Sarah Friis, Eickhardt-Dalbøge, Christina Schjellerup, Ellervik, Christina, El Fassi, Daniel, Frederiksen, Mikael, Kjær, Lasse, Kristensen, Thomas Kielsgaard, Kruse, Torben A., Larsen, Morten Kranker, Mourits-Andersen, Torben, Möller, Sören, Overgaard, Ulrik Malthe, Severinsen, Marianne Tang, Skov, Vibe, Sørensen, Anders Lindholm, Stentoft, Jesper, Starklint, Jørn, de Stricker, Karin, Thomassen, Mads, Larsen, Thomas S., and Hasselbalch, Hans C.
Abstract: Background:Hydroxyurea (HU) is the most commonly used first-line cytoreductive treatment option for patients with myeloproliferative neoplasms (MPN) worldwide. However, increasing evidence on the efficacy and safety of pegylated interferon-alpha2 (IFNα) is emerging, and optimal first-line treatment is to be established.
Published: 2023
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12. The Optimal Sequencing Depth of Tumor Biopsies for Identifying Clonal Cell Populations

Author: Tabatabaeifar, Siavosh, Larsen, Martin J., Thomassen, Mads, Larsen, Stine R., Kruse, Torben A., and Sørensen, Jens A.
Abstract: The tumor content of a biopsy and the average depth of coverage are two essential aspects when performing DNA sequencing using next-generation sequencing technologies. The heterogeneous nature of cancer necessitates the identification of distinct clonal cell populations to better understand and treat cancer. Deep sequencing enables researchers to identify these populations, but no consensus on an optimal depth exists for identifying clonal populations. Data from eight deep-sequenced oral squamous cell carcinoma biopsies obtained from three stage IV patients, with various degrees of tumor content, were used to randomly down sample the depth before being subjected to cluster analysis. An increase in coverage resulted in an increase in resolution for clusters of mutations, enabling the identification of distinct clonal cell populations and clonal events. From a depth of 800×, limited gain in resolution can be achieved; and from a depth of 1200×, the resolution stabilizes. Overall, researchers should aim for an average depth of 1000× to 1200× when performing deep sequencing. The tumor content will, however, dictate the resolution and fidelity of the analysis, as an increase in tumor complexity increases the need for higher tumor content.
Published: 2019
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13. CFP suppresses breast cancer cell growth by TES-mediated upregulation of the transcription factor DDIT3

Author: Block, Ines, Müller, Carolin, Sdogati, Daniel, Pedersen, Henriette, List, Markus, Jaskot, Aleksandra M., Syse, Silje Damkjær, Lund Hansen, Pernille, Schmidt, Steffen, Christiansen, Helle, Casella, Cinzia, Bering Olsen, Sidsel, Blomstrøm, Monica M., Riedel, Angela, Thomassen, Mads, Kruse, Torben A., Karlskov Hansen, Søren W., Kioschis, Petra, and Mollenhauer, Jan
Abstract: Breast cancer is a heterogeneous genetic disease driven by the accumulation of individual mutations per tumor. Whole-genome sequencing approaches have identified numerous genes with recurrent mutations in primary tumors. Although mutations in well characterized tumor suppressors and oncogenes are overrepresented in these sets, the majority of the genetically altered genes have so far unknown roles in breast cancer progression. To improve the basic understanding of the complex disease breast cancer and to potentially identify novel drug targets or regulators of known cancer-driving pathways, we analyzed 86 wild-type genes and 94 mutated variants for their effect on cell growth using a serially constructed panel of MCF7 cell lines. We demonstrate in subsequent experiments that the metal cation transporter CNNM4 regulates growth by induction of apoptosis and identified a tumor suppressive role of complement factor properdin (CFP) in vitro and in vivo. CFP appears to induce the intracellular upregulation of the pro-apoptotic transcription factor DDIT3 which is associated with endoplasmic reticulum-stress response.
Published: 2019
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14. Interferon-alpha2 Favorably Impacts Deregulated Atherosclerosis Genes in Polycythemia Vera and Related Neoplasms

Author: Skov, Vibe, Thomassen, Mads, Kjær, Lasse, Larsen, Morten Kranker, Ellervik, Christina, Knudsen, Trine Alma, Kruse, Torben A., and Hasselbalch, Hans Carl
Published: 2022
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15. The BRCA1c. 5096G>A p.Arg1699Gln (R1699Q) intermediate risk variant: breast and ovarian cancer risk estimation and recommendations for clinical management from the ENIGMA consortium

Author: Moghadasi, Setareh, Meeks, Huong D, Vreeswijk, Maaike PG, Janssen, Linda AM, Borg, Åke, Ehrencrona, Hans, Paulsson-Karlsson, Ylva, Wappenschmidt, Barbara, Engel, Christoph, Gehrig, Andrea, Arnold, Norbert, Hansen, Thomas Van Overeem, Thomassen, Mads, Jensen, Uffe Birk, Kruse, Torben A, Ejlertsen, Bent, Gerdes, Anne-Marie, Pedersen, Inge Søkilde, Caputo, Sandrine M, Couch, Fergus, Hallberg, Emily J, van den Ouweland, Ans MW, CollÅée, Margriet J, Teugels, Erik, Adank, Muriel A, van der Luijt, Rob B, Mensenkamp, Arjen R, Oosterwijk, Jan C, Blok, Marinus J, Janin, Nicolas, Claes, Kathleen BM, Tucker, Kathy, Viassolo, Valeria, Toland, Amanda Ewart, Eccles, Diana E, Devilee, Peter, Van Asperen, Christie J, Spurdle, Amanda B, Goldgar, David E, and GarcÅéóía, Encarna GÅéómez
Abstract: BackgroundWe previously showed that the BRCA1variant c.5096G>A p.Arg1699Gln (R1699Q) was associated with an intermediate risk of breast cancer (BC) and ovarian cancer (OC). This study aimed to assess these cancer risks for R1699Q carriers in a larger cohort, including follow-up of previously studied families, to further define cancer risks and to propose adjusted clinical management of female BRCA1*R1699Q carriers.MethodsData were collected from 129 BRCA1*R1699Q families ascertained internationally by ENIGMA (Evidence-based Network for the Interpretation of Germline Mutant Alleles) consortium members. A modified segregation analysis was used to calculate BC and OC risks. Relative risks were calculated under both monogenic model and major gene plus polygenic model assumptions.ResultsIn this cohort the cumulative risk of BC and OC by age 70 years was 20% and 6%, respectively. The relative risk for developing cancer was higher when using a model that included the effects of both the R1699Q variant and a residual polygenic component compared with monogenic model (for BC 3.67 vs 2.83, and for OC 6.41 vs 5.83).ConclusionOur results confirm that BRCA1*R1699Q confers an intermediate risk for BC and OC. Breast surveillance for female carriers based on mammogram annually from age 40 is advised. Bilateral salpingo-oophorectomy should be considered based on family history.
Published: 2018
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16. Identification of ten variants associated with risk of estrogen-receptor-negative breast cancer

Author: Milne, Roger L, Kuchenbaecker, Karoline B, Michailidou, Kyriaki, Beesley, Jonathan, Kar, Siddhartha, Lindström, Sara, Hui, Shirley, Lemaçon, Audrey, Soucy, Penny, Dennis, Joe, Jiang, Xia, Rostamianfar, Asha, Finucane, Hilary, Bolla, Manjeet K, McGuffog, Lesley, Wang, Qin, Aalfs, Cora M, Adams, Marcia, Adlard, Julian, Agata, Simona, Ahmed, Shahana, Ahsan, Habibul, Aittomäki, Kristiina, Al-Ejeh, Fares, Allen, Jamie, Ambrosone, Christine B, Amos, Christopher I, Andrulis, Irene L, Anton-Culver, Hoda, Antonenkova, Natalia N, Arndt, Volker, Arnold, Norbert, Aronson, Kristan J, Auber, Bernd, Auer, Paul L, Ausems, Margreet G E M, Azzollini, Jacopo, Bacot, François, Balmaña, Judith, Barile, Monica, Barjhoux, Laure, Barkardottir, Rosa B, Barrdahl, Myrto, Barnes, Daniel, Barrowdale, Daniel, Baynes, Caroline, Beckmann, Matthias W, Benitez, Javier, Bermisheva, Marina, Bernstein, Leslie, Bignon, Yves-Jean, Blazer, Kathleen R, Blok, Marinus J, Blomqvist, Carl, Blot, William, Bobolis, Kristie, Boeckx, Bram, Bogdanova, Natalia V, Bojesen, Anders, Bojesen, Stig E, Bonanni, Bernardo, Børresen-Dale, Anne-Lise, Bozsik, Aniko, Bradbury, Angela R, Brand, Judith S, Brauch, Hiltrud, Brenner, Hermann, Bressac-de Paillerets, Brigitte, Brewer, Carole, Brinton, Louise, Broberg, Per, Brooks-Wilson, Angela, Brunet, Joan, Brüning, Thomas, Burwinkel, Barbara, Buys, Saundra S, Byun, Jinyoung, Cai, Qiuyin, Caldés, Trinidad, Caligo, Maria A, Campbell, Ian, Canzian, Federico, Caron, Olivier, Carracedo, Angel, Carter, Brian D, Castelao, J Esteban, Castera, Laurent, Caux-Moncoutier, Virginie, Chan, Salina B, Chang-Claude, Jenny, Chanock, Stephen J, Chen, Xiaoqing, Cheng, Ting-Yuan David, Chiquette, Jocelyne, Christiansen, Hans, Claes, Kathleen B M, Clarke, Christine L, Conner, Thomas, Conroy, Don M, Cook, Jackie, Cordina-Duverger, Emilie, Cornelissen, Sten, Coupier, Isabelle, Cox, Angela, Cox, David G, Cross, Simon S, Cuk, Katarina, Cunningham, Julie M, Czene, Kamila, Daly, Mary B, Damiola, Francesca, Darabi, Hatef, Davidson, Rosemarie, De Leeneer, Kim, Devilee, Peter, Dicks, Ed, Diez, Orland, Ding, Yuan Chun, Ditsch, Nina, Doheny, Kimberly F, Domchek, Susan M, Dorfling, Cecilia M, Dörk, Thilo, dos-Santos-Silva, Isabel, Dubois, Stéphane, Dugué, Pierre-Antoine, Dumont, Martine, Dunning, Alison M, Durcan, Lorraine, Dwek, Miriam, Dworniczak, Bernd, Eccles, Diana, Eeles, Ros, Ehrencrona, Hans, Eilber, Ursula, Ejlertsen, Bent, Ekici, Arif B, Eliassen, A Heather, Engel, Christoph, Eriksson, Mikael, Fachal, Laura, Faivre, Laurence, Fasching, Peter A, Faust, Ulrike, Figueroa, Jonine, Flesch-Janys, Dieter, Fletcher, Olivia, Flyger, Henrik, Foulkes, William D, Friedman, Eitan, Fritschi, Lin, Frost, Debra, Gabrielson, Marike, Gaddam, Pragna, Gammon, Marilie D, Ganz, Patricia A, Gapstur, Susan M, Garber, Judy, Garcia-Barberan, Vanesa, García-Sáenz, José A, Gaudet, Mia M, Gauthier-Villars, Marion, Gehrig, Andrea, Georgoulias, Vassilios, Gerdes, Anne-Marie, Giles, Graham G, Glendon, Gord, Godwin, Andrew K, Goldberg, Mark S, Goldgar, David E, González-Neira, Anna, Goodfellow, Paul, Greene, Mark H, Alnæs, Grethe I Grenaker, Grip, Mervi, Gronwald, Jacek, Grundy, Anne, Gschwantler-Kaulich, Daphne, Guénel, Pascal, Guo, Qi, Haeberle, Lothar, Hahnen, Eric, Haiman, Christopher A, Håkansson, Niclas, Hallberg, Emily, Hamann, Ute, Hamel, Nathalie, Hankinson, Susan, Hansen, Thomas V O, Harrington, Patricia, Hart, Steven N, Hartikainen, Jaana M, Healey, Catherine S, Hein, Alexander, Helbig, Sonja, Henderson, Alex, Heyworth, Jane, Hicks, Belynda, Hillemanns, Peter, Hodgson, Shirley, Hogervorst, Frans B, Hollestelle, Antoinette, Hooning, Maartje J, Hoover, Bob, Hopper, John L, Hu, Chunling, Huang, Guanmengqian, Hulick, Peter J, Humphreys, Keith, Hunter, David J, Imyanitov, Evgeny N, Isaacs, Claudine, Iwasaki, Motoki, Izatt, Louise, Jakubowska, Anna, James, Paul, Janavicius, Ramunas, Janni, Wolfgang, Jensen, Uffe Birk, John, Esther M, Johnson, Nichola, Jones, Kristine, Jones, Michael, Jukkola-Vuorinen, Arja, Kaaks, Rudolf, Kabisch, Maria, Kaczmarek, Katarzyna, Kang, Daehee, Kast, Karin, Keeman, Renske, Kerin, Michael J, Kets, Carolien M, Keupers, Machteld, Khan, Sofia, Khusnutdinova, Elza, Kiiski, Johanna I, Kim, Sung-Won, Knight, Julia A, Konstantopoulou, Irene, Kosma, Veli-Matti, Kristensen, Vessela N, Kruse, Torben A, Kwong, Ava, Lænkholm, Anne-Vibeke, Laitman, Yael, Lalloo, Fiona, Lambrechts, Diether, Landsman, Keren, Lasset, Christine, Lazaro, Conxi, Le Marchand, Loic, Lecarpentier, Julie, Lee, Andrew, Lee, Eunjung, Lee, Jong Won, Lee, Min Hyuk, Lejbkowicz, Flavio, Lesueur, Fabienne, Li, Jingmei, Lilyquist, Jenna, Lincoln, Anne, Lindblom, Annika, Lissowska, Jolanta, Lo, Wing-Yee, Loibl, Sibylle, Long, Jirong, Loud, Jennifer T, Lubinski, Jan, Luccarini, Craig, Lush, Michael, MacInnis, Robert J, Maishman, Tom, Makalic, Enes, Kostovska, Ivana Maleva, Malone, Kathleen E, Manoukian, Siranoush, Manson, JoAnn E, Margolin, Sara, Martens, John W M, Martinez, Maria Elena, Matsuo, Keitaro, Mavroudis, Dimitrios, Mazoyer, Sylvie, McLean, Catriona, Meijers-Heijboer, Hanne, Menéndez, Primitiva, Meyer, Jeffery, Miao, Hui, Miller, Austin, Miller, Nicola, Mitchell, Gillian, Montagna, Marco, Muir, Kenneth, Mulligan, Anna Marie, Mulot, Claire, Nadesan, Sue, Nathanson, Katherine L, Neuhausen, Susan L, Nevanlinna, Heli, Nevelsteen, Ines, Niederacher, Dieter, Nielsen, Sune F, Nordestgaard, Børge G, Norman, Aaron, Nussbaum, Robert L, Olah, Edith, Olopade, Olufunmilayo I, Olson, Janet E, Olswold, Curtis, Ong, Kai-ren, Oosterwijk, Jan C, Orr, Nick, Osorio, Ana, Pankratz, V Shane, Papi, Laura, Park-Simon, Tjoung-Won, Paulsson-Karlsson, Ylva, Lloyd, Rachel, Pedersen, Inge Søkilde, Peissel, Bernard, Peixoto, Ana, Perez, Jose I A, Peterlongo, Paolo, Peto, Julian, Pfeiler, Georg, Phelan, Catherine M, Pinchev, Mila, Plaseska-Karanfilska, Dijana, Poppe, Bruce, Porteous, Mary E, Prentice, Ross, Presneau, Nadege, Prokofieva, Darya, Pugh, Elizabeth, Pujana, Miquel Angel, Pylkäs, Katri, Rack, Brigitte, Radice, Paolo, Rahman, Nazneen, Rantala, Johanna, Rappaport-Fuerhauser, Christine, Rennert, Gad, Rennert, Hedy S, Rhenius, Valerie, Rhiem, Kerstin, Richardson, Andrea, Rodriguez, Gustavo C, Romero, Atocha, Romm, Jane, Rookus, Matti A, Rudolph, Anja, Ruediger, Thomas, Saloustros, Emmanouil, Sanders, Joyce, Sandler, Dale P, Sangrajrang, Suleeporn, Sawyer, Elinor J, Schmidt, Daniel F, Schoemaker, Minouk J, Schumacher, Fredrick, Schürmann, Peter, Schwentner, Lukas, Scott, Christopher, Scott, Rodney J, Seal, Sheila, Senter, Leigha, Seynaeve, Caroline, Shah, Mitul, Sharma, Priyanka, Shen, Chen-Yang, Sheng, Xin, Shimelis, Hermela, Shrubsole, Martha J, Shu, Xiao-Ou, Side, Lucy E, Singer, Christian F, Sohn, Christof, Southey, Melissa C, Spinelli, John J, Spurdle, Amanda B, Stegmaier, Christa, Stoppa-Lyonnet, Dominique, Sukiennicki, Grzegorz, Surowy, Harald, Sutter, Christian, Swerdlow, Anthony, Szabo, Csilla I, Tamimi, Rulla M, Tan, Yen Y, Taylor, Jack A, Tejada, Maria-Isabel, Tengström, Maria, Teo, Soo H, Terry, Mary B, Tessier, Daniel C, Teulé, Alex, Thöne, Kathrin, Thull, Darcy L, Tibiletti, Maria Grazia, Tihomirova, Laima, Tischkowitz, Marc, Toland, Amanda E, Tollenaar, Rob A E M, Tomlinson, Ian, Tong, Ling, Torres, Diana, Tranchant, Martine, Truong, Thérèse, Tucker, Kathy, Tung, Nadine, Tyrer, Jonathan, Ulmer, Hans-Ulrich, Vachon, Celine, van Asperen, Christi J, Van Den Berg, David, van den Ouweland, Ans M W, van Rensburg, Elizabeth J, Varesco, Liliana, Varon-Mateeva, Raymonda, Vega, Ana, Viel, Alessandra, Vijai, Joseph, Vincent, Daniel, Vollenweider, Jason, Walker, Lisa, Wang, Zhaoming, Wang-Gohrke, Shan, Wappenschmidt, Barbara, Weinberg, Clarice R, Weitzel, Jeffrey N, Wendt, Camilla, Wesseling, Jelle, Whittemore, Alice S, Wijnen, Juul T, Willett, Walter, Winqvist, Robert, Wolk, Alicja, Wu, Anna H, Xia, Lucy, Yang, Xiaohong R, Yannoukakos, Drakoulis, Zaffaroni, Daniela, Zheng, Wei, Zhu, Bin, Ziogas, Argyrios, Ziv, Elad, Zorn, Kristin K, Gago-Dominguez, Manuela, Mannermaa, Arto, Olsson, Håkan, Teixeira, Manuel R, Stone, Jennifer, Offit, Kenneth, Ottini, Laura, Park, Sue K, Thomassen, Mads, Hall, Per, Meindl, Alfons, Schmutzler, Rita K, Droit, Arnaud, Bader, Gary D, Pharoah, Paul D P, Couch, Fergus J, Easton, Douglas F, Kraft, Peter, Chenevix-Trench, Georgia, García-Closas, Montserrat, Schmidt, Marjanka K, Antoniou, Antonis C, and Simard, Jacques
Abstract: Most common breast cancer susceptibility variants have been identified through genome-wide association studies (GWAS) of predominantly estrogen receptor (ER)-positive disease. We conducted a GWAS using 21,468 ER-negative cases and 100,594 controls combined with 18,908 BRCA1 mutation carriers (9,414 with breast cancer), all of European origin. We identified independent associations at P < 5 × 10−8with ten variants at nine new loci. At P < 0.05, we replicated associations with 10 of 11 variants previously reported in ER-negative disease or BRCA1 mutation carrier GWAS and observed consistent associations with ER-negative disease for 105 susceptibility variants identified by other studies. These 125 variants explain approximately 16% of the familial risk of this breast cancer subtype. There was high genetic correlation (0.72) between risk of ER-negative breast cancer and breast cancer risk for BRCA1 mutation carriers. These findings may lead to improved risk prediction and inform further fine-mapping and functional work to better understand the biological basis of ER-negative breast cancer.
Published: 2017
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17. Correction: Polygenic risk modeling for prediction of epithelial ovarian cancer risk

Author: Dareng, Eileen O., Tyrer, Jonathan P., Barnes, Daniel R., Jones, Michelle R., Yang, Xin, Aben, Katja K. H., Adank, Muriel A., Agata, Simona, Andrulis, Irene L., Anton-Culver, Hoda, Antonenkova, Natalia N., Aravantinos, Gerasimos, Arun, Banu K., Augustinsson, Annelie, Balmaña, Judith, Bandera, Elisa V., Barkardottir, Rosa B., Barrowdale, Daniel, Beckmann, Matthias W., Beeghly-Fadiel, Alicia, Benitez, Javier, Bermisheva, Marina, Bernardini, Marcus Q., Bjorge, Line, Black, Amanda, Bogdanova, Natalia V., Bonanni, Bernardo, Borg, Ake, Brenton, James D., Budzilowska, Agnieszka, Butzow, Ralf, Buys, Saundra S., Cai, Hui, Caligo, Maria A., Campbell, Ian, Cannioto, Rikki, Cassingham, Hayley, Chang-Claude, Jenny, Chanock, Stephen J., Chen, Kexin, Chiew, Yoke-Eng, Chung, Wendy K., Claes, Kathleen B. M., Colonna, Sarah, Cook, Linda S., Couch, Fergus J., Daly, Mary B., Dao, Fanny, Davies, Eleanor, de la Hoya, Miguel, de Putter, Robin, Dennis, Joe, DePersia, Allison, Devilee, Peter, Diez, Orland, Ding, Yuan Chun, Doherty, Jennifer A., Domchek, Susan M., Dörk, Thilo, du Bois, Andreas, Dürst, Matthias, Eccles, Diana M., Eliassen, Heather A., Engel, Christoph, Evans, Gareth D., Fasching, Peter A., Flanagan, James M., Fortner, Renée T., Machackova, Eva, Friedman, Eitan, Ganz, Patricia A., Garber, Judy, Gensini, Francesca, Giles, Graham G., Glendon, Gord, Godwin, Andrew K., Goodman, Marc T., Greene, Mark H., Gronwald, Jacek, Hahnen, Eric, Haiman, Christopher A., Håkansson, Niclas, Hamann, Ute, Hansen, Thomas V. O., Harris, Holly R., Hartman, Mikael, Heitz, Florian, Hildebrandt, Michelle A. T., Høgdall, Estrid, Høgdall, Claus K., Hopper, John L., Huang, Ruea-Yea, Huff, Chad, Hulick, Peter J., Huntsman, David G., Imyanitov, Evgeny N., Isaacs, Claudine, Jakubowska, Anna, James, Paul A., Janavicius, Ramunas, Jensen, Allan, Johannsson, Oskar Th., John, Esther M., Jones, Michael E., Kang, Daehee, Karlan, Beth Y., Karnezis, Anthony, Kelemen, Linda E., Khusnutdinova, Elza, Kiemeney, Lambertus A., Kim, Byoung-Gie, Kjaer, Susanne K., Komenaka, Ian, Kupryjanczyk, Jolanta, Kurian, Allison W., Kwong, Ava, Lambrechts, Diether, Larson, Melissa C., Lazaro, Conxi, Le, Nhu D., Leslie, Goska, Lester, Jenny, Lesueur, Fabienne, Levine, Douglas A., Li, Lian, Li, Jingmei, Loud, Jennifer T., Lu, Karen H., Lubiński, Jan, Mai, Phuong L., Manoukian, Siranoush, Marks, Jeffrey R., Matsuno, Rayna Kim, Matsuo, Keitaro, May, Taymaa, McGuffog, Lesley, McLaughlin, John R., McNeish, Iain A., Mebirouk, Noura, Menon, Usha, Miller, Austin, Milne, Roger L., Minlikeeva, Albina, Modugno, Francesmary, Montagna, Marco, Moysich, Kirsten B., Munro, Elizabeth, Nathanson, Katherine L., Neuhausen, Susan L., Nevanlinna, Heli, Yie, Joanne Ngeow Yuen, Nielsen, Henriette Roed, Nielsen, Finn C., Nikitina-Zake, Liene, Odunsi, Kunle, Offit, Kenneth, Olah, Edith, Olbrecht, Siel, Olopade, Olufunmilayo I., Olson, Sara H., Olsson, Håkan, Osorio, Ana, Papi, Laura, Park, Sue K., Parsons, Michael T., Pathak, Harsha, Pedersen, Inge Sokilde, Peixoto, Ana, Pejovic, Tanja, Perez-Segura, Pedro, Permuth, Jennifer B., Peshkin, Beth, Peterlongo, Paolo, Piskorz, Anna, Prokofyeva, Darya, Radice, Paolo, Rantala, Johanna, Riggan, Marjorie J., Risch, Harvey A., Rodriguez-Antona, Cristina, Ross, Eric, Rossing, Mary Anne, Runnebaum, Ingo, Sandler, Dale P., Santamariña, Marta, Soucy, Penny, Schmutzler, Rita K., Setiawan, V. Wendy, Shan, Kang, Sieh, Weiva, Simard, Jacques, Singer, Christian F., Sokolenko, Anna P., Song, Honglin, Southey, Melissa C., Steed, Helen, Stoppa-Lyonnet, Dominique, Sutphen, Rebecca, Swerdlow, Anthony J., Tan, Yen Yen, Teixeira, Manuel R., Teo, Soo Hwang, Terry, Kathryn L., Terry, Mary Beth, Thomassen, Mads, Thompson, Pamela J., Thomsen, Liv Cecilie Vestrheim, Thull, Darcy L., Tischkowitz, Marc, Titus, Linda, Toland, Amanda E., Torres, Diana, Trabert, Britton, Travis, Ruth, Tung, Nadine, Tworoger, Shelley S., Valen, Ellen, van Altena, Anne M., van der Hout, Annemieke H., Van Nieuwenhuysen, Els, van Rensburg, Elizabeth J., Vega, Ana, Edwards, Digna Velez, Vierkant, Robert A., Wang, Frances, Wappenschmidt, Barbara, Webb, Penelope M., Weinberg, Clarice R., Weitzel, Jeffrey N., Wentzensen, Nicolas, White, Emily, Whittemore, Alice S., Winham, Stacey J., Wolk, Alicja, Woo, Yin-Ling, Wu, Anna H., Yan, Li, Yannoukakos, Drakoulis, Zavaglia, Katia M., Zheng, Wei, Ziogas, Argyrios, Zorn, Kristin K., Kleibl, Zdenek, Easton, Douglas, Lawrenson, Kate, DeFazio, Anna, Sellers, Thomas A., Ramus, Susan J., Pearce, Celeste L., Monteiro, Alvaro N., Cunningham, Julie, Goode, Ellen L., Schildkraut, Joellen M., Berchuck, Andrew, Chenevix-Trench, Georgia, Gayther, Simon A., Antoniou, Antonis C., and Pharoah, Paul D. P.
Published: 2022
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18. Identification of 12 new susceptibility loci for different histotypes of epithelial ovarian cancer

Author: Phelan, Catherine M, Kuchenbaecker, Karoline B, Tyrer, Jonathan P, Kar, Siddhartha P, Lawrenson, Kate, Winham, Stacey J, Dennis, Joe, Pirie, Ailith, Riggan, Marjorie J, Chornokur, Ganna, Earp, Madalene A, Lyra, Paulo C, Lee, Janet M, Coetzee, Simon, Beesley, Jonathan, McGuffog, Lesley, Soucy, Penny, Dicks, Ed, Lee, Andrew, Barrowdale, Daniel, Lecarpentier, Julie, Leslie, Goska, Aalfs, Cora M, Aben, Katja K H, Adams, Marcia, Adlard, Julian, Andrulis, Irene L, Anton-Culver, Hoda, Antonenkova, Natalia, Aravantinos, Gerasimos, Arnold, Norbert, Arun, Banu K, Arver, Brita, Azzollini, Jacopo, Balmaña, Judith, Banerjee, Susana N, Barjhoux, Laure, Barkardottir, Rosa B, Bean, Yukie, Beckmann, Matthias W, Beeghly-Fadiel, Alicia, Benitez, Javier, Bermisheva, Marina, Bernardini, Marcus Q, Birrer, Michael J, Bjorge, Line, Black, Amanda, Blankstein, Kenneth, Blok, Marinus J, Bodelon, Clara, Bogdanova, Natalia, Bojesen, Anders, Bonanni, Bernardo, Borg, Åke, Bradbury, Angela R, Brenton, James D, Brewer, Carole, Brinton, Louise, Broberg, Per, Brooks-Wilson, Angela, Bruinsma, Fiona, Brunet, Joan, Buecher, Bruno, Butzow, Ralf, Buys, Saundra S, Caldes, Trinidad, Caligo, Maria A, Campbell, Ian, Cannioto, Rikki, Carney, Michael E, Cescon, Terence, Chan, Salina B, Chang-Claude, Jenny, Chanock, Stephen, Chen, Xiao Qing, Chiew, Yoke-Eng, Chiquette, Jocelyne, Chung, Wendy K, Claes, Kathleen B M, Conner, Thomas, Cook, Linda S, Cook, Jackie, Cramer, Daniel W, Cunningham, Julie M, D'Aloisio, Aimee A, Daly, Mary B, Damiola, Francesca, Damirovna, Sakaeva Dina, Dansonka-Mieszkowska, Agnieszka, Dao, Fanny, Davidson, Rosemarie, DeFazio, Anna, Delnatte, Capucine, Doheny, Kimberly F, Diez, Orland, Ding, Yuan Chun, Doherty, Jennifer Anne, Domchek, Susan M, Dorfling, Cecilia M, Dörk, Thilo, Dossus, Laure, Duran, Mercedes, Dürst, Matthias, Dworniczak, Bernd, Eccles, Diana, Edwards, Todd, Eeles, Ros, Eilber, Ursula, Ejlertsen, Bent, Ekici, Arif B, Ellis, Steve, Elvira, Mingajeva, Eng, Kevin H, Engel, Christoph, Evans, D Gareth, Fasching, Peter A, Ferguson, Sarah, Ferrer, Sandra Fert, Flanagan, James M, Fogarty, Zachary C, Fortner, Renée T, Fostira, Florentia, Foulkes, William D, Fountzilas, George, Fridley, Brooke L, Friebel, Tara M, Friedman, Eitan, Frost, Debra, Ganz, Patricia A, Garber, Judy, García, María J, Garcia-Barberan, Vanesa, Gehrig, Andrea, Gentry-Maharaj, Aleksandra, Gerdes, Anne-Marie, Giles, Graham G, Glasspool, Rosalind, Glendon, Gord, Godwin, Andrew K, Goldgar, David E, Goranova, Teodora, Gore, Martin, Greene, Mark H, Gronwald, Jacek, Gruber, Stephen, Hahnen, Eric, Haiman, Christopher A, Håkansson, Niclas, Hamann, Ute, Hansen, Thomas V O, Harrington, Patricia A, Harris, Holly R, Hauke, Jan, Hein, Alexander, Henderson, Alex, Hildebrandt, Michelle A T, Hillemanns, Peter, Hodgson, Shirley, Høgdall, Claus K, Høgdall, Estrid, Hogervorst, Frans B L, Holland, Helene, Hooning, Maartje J, Hosking, Karen, Huang, Ruea-Yea, Hulick, Peter J, Hung, Jillian, Hunter, David J, Huntsman, David G, Huzarski, Tomasz, Imyanitov, Evgeny N, Isaacs, Claudine, Iversen, Edwin S, Izatt, Louise, Izquierdo, Angel, Jakubowska, Anna, James, Paul, Janavicius, Ramunas, Jernetz, Mats, Jensen, Allan, Jensen, Uffe Birk, John, Esther M, Johnatty, Sharon, Jones, Michael E, Kannisto, Päivi, Karlan, Beth Y, Karnezis, Anthony, Kast, Karin, Kennedy, Catherine J, Khusnutdinova, Elza, Kiemeney, Lambertus A, Kiiski, Johanna I, Kim, Sung-Won, Kjaer, Susanne K, Köbel, Martin, Kopperud, Reidun K, Kruse, Torben A, Kupryjanczyk, Jolanta, Kwong, Ava, Laitman, Yael, Lambrechts, Diether, Larrañaga, Nerea, Larson, Melissa C, Lazaro, Conxi, Le, Nhu D, Le Marchand, Loic, Lee, Jong Won, Lele, Shashikant B, Leminen, Arto, Leroux, Dominique, Lester, Jenny, Lesueur, Fabienne, Levine, Douglas A, Liang, Dong, Liebrich, Clemens, Lilyquist, Jenna, Lipworth, Loren, Lissowska, Jolanta, Lu, Karen H, Lubinński, Jan, Luccarini, Craig, Lundvall, Lene, Mai, Phuong L, Mendoza-Fandiño, Gustavo, Manoukian, Siranoush, Massuger, Leon F A G, May, Taymaa, Mazoyer, Sylvie, McAlpine, Jessica N, McGuire, Valerie, McLaughlin, John R, McNeish, Iain, Meijers-Heijboer, Hanne, Meindl, Alfons, Menon, Usha, Mensenkamp, Arjen R, Merritt, Melissa A, Milne, Roger L, Mitchell, Gillian, Modugno, Francesmary, Moes-Sosnowska, Joanna, Moffitt, Melissa, Montagna, Marco, Moysich, Kirsten B, Mulligan, Anna Marie, Musinsky, Jacob, Nathanson, Katherine L, Nedergaard, Lotte, Ness, Roberta B, Neuhausen, Susan L, Nevanlinna, Heli, Niederacher, Dieter, Nussbaum, Robert L, Odunsi, Kunle, Olah, Edith, Olopade, Olufunmilayo I, Olsson, Håkan, Olswold, Curtis, O'Malley, David M, Ong, Kai-ren, Onland-Moret, N Charlotte, Orr, Nicholas, Orsulic, Sandra, Osorio, Ana, Palli, Domenico, Papi, Laura, Park-Simon, Tjoung-Won, Paul, James, Pearce, Celeste L, Pedersen, Inge Søkilde, Peeters, Petra H M, Peissel, Bernard, Peixoto, Ana, Pejovic, Tanja, Pelttari, Liisa M, Permuth, Jennifer B, Peterlongo, Paolo, Pezzani, Lidia, Pfeiler, Georg, Phillips, Kelly-Anne, Piedmonte, Marion, Pike, Malcolm C, Piskorz, Anna M, Poblete, Samantha R, Pocza, Timea, Poole, Elizabeth M, Poppe, Bruce, Porteous, Mary E, Prieur, Fabienne, Prokofyeva, Darya, Pugh, Elizabeth, Pujana, Miquel Angel, Pujol, Pascal, Radice, Paolo, Rantala, Johanna, Rappaport-Fuerhauser, Christine, Rennert, Gad, Rhiem, Kerstin, Rice, Patricia, Richardson, Andrea, Robson, Mark, Rodriguez, Gustavo C, Rodríguez-Antona, Cristina, Romm, Jane, Rookus, Matti A, Rossing, Mary Anne, Rothstein, Joseph H, Rudolph, Anja, Runnebaum, Ingo B, Salvesen, Helga B, Sandler, Dale P, Schoemaker, Minouk J, Senter, Leigha, Setiawan, V Wendy, Severi, Gianluca, Sharma, Priyanka, Shelford, Tameka, Siddiqui, Nadeem, Side, Lucy E, Sieh, Weiva, Singer, Christian F, Sobol, Hagay, Song, Honglin, Southey, Melissa C, Spurdle, Amanda B, Stadler, Zsofia, Steinemann, Doris, Stoppa-Lyonnet, Dominique, Sucheston-Campbell, Lara E, Sukiennicki, Grzegorz, Sutphen, Rebecca, Sutter, Christian, Swerdlow, Anthony J, Szabo, Csilla I, Szafron, Lukasz, Tan, Yen Y, Taylor, Jack A, Tea, Muy-Kheng, Teixeira, Manuel R, Teo, Soo-Hwang, Terry, Kathryn L, Thompson, Pamela J, Thomsen, Liv Cecilie Vestrheim, Thull, Darcy L, Tihomirova, Laima, Tinker, Anna V, Tischkowitz, Marc, Tognazzo, Silvia, Toland, Amanda Ewart, Tone, Alicia, Trabert, Britton, Travis, Ruth C, Trichopoulou, Antonia, Tung, Nadine, Tworoger, Shelley S, van Altena, Anne M, Van Den Berg, David, van der Hout, Annemarie H, van der Luijt, Rob B, Van Heetvelde, Mattias, Van Nieuwenhuysen, Els, van Rensburg, Elizabeth J, Vanderstichele, Adriaan, Varon-Mateeva, Raymonda, Vega, Ana, Edwards, Digna Velez, Vergote, Ignace, Vierkant, Robert A, Vijai, Joseph, Vratimos, Athanassios, Walker, Lisa, Walsh, Christine, Wand, Dorothea, Wang-Gohrke, Shan, Wappenschmidt, Barbara, Webb, Penelope M, Weinberg, Clarice R, Weitzel, Jeffrey N, Wentzensen, Nicolas, Whittemore, Alice S, Wijnen, Juul T, Wilkens, Lynne R, Wolk, Alicja, Woo, Michelle, Wu, Xifeng, Wu, Anna H, Yang, Hannah, Yannoukakos, Drakoulis, Ziogas, Argyrios, Zorn, Kristin K, Narod, Steven A, Easton, Douglas F, Amos, Christopher I, Schildkraut, Joellen M, Ramus, Susan J, Ottini, Laura, Goodman, Marc T, Park, Sue K, Kelemen, Linda E, Risch, Harvey A, Thomassen, Mads, Offit, Kenneth, Simard, Jacques, Schmutzler, Rita Katharina, Hazelett, Dennis, Monteiro, Alvaro N, Couch, Fergus J, Berchuck, Andrew, Chenevix-Trench, Georgia, Goode, Ellen L, Sellers, Thomas A, Gayther, Simon A, Antoniou, Antonis C, and Pharoah, Paul D P
Abstract: To identify common alleles associated with different histotypes of epithelial ovarian cancer (EOC), we pooled data from multiple genome-wide genotyping projects totaling 25,509 EOC cases and 40,941 controls. We identified nine new susceptibility loci for different EOC histotypes: six for serous EOC histotypes (3q28, 4q32.3, 8q21.11, 10q24.33, 18q11.2 and 22q12.1), two for mucinous EOC (3q22.3 and 9q31.1) and one for endometrioid EOC (5q12.3). We then performed meta-analysis on the results for high-grade serous ovarian cancer with the results from analysis of 31,448 BRCA1 and BRCA2 mutation carriers, including 3,887 mutation carriers with EOC. This identified three additional susceptibility loci at 2q13, 8q24.1 and 12q24.31. Integrated analyses of genes and regulatory biofeatures at each locus predicted candidate susceptibility genes, including OBFC1, a new candidate susceptibility gene for low-grade and borderline serous EOC.
Published: 2017
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19. Toward cytogenomics: Technical assessment of long-read Nanopore whole-genome sequencing for detecting large chromosomal alterations in mantle cell lymphoma

Author: Hansen, Marcus Høy, Cédile, Oriane, Grube Kjeldsen, Marie Louise, Thomassen, Mads, Preiss, Birgitte, von Neuhoff, Nils, Abildgaard, Niels, and Nyvold, Charlotte Guldborg
Abstract: The current advances and success of next-generation sequencing (NGS) hold the potential for the transition of cancer cytogenetics toward comprehensive cytogenomics. However, the conventional usage of short reads impedes the resolution of chromosomal aberrations with current NGS modalities. Thus, this study evaluated the detection and reproducibility of extensive copy-number alterations and chromosomal translocations using long-read Oxford Nanopore Technologies (ONT) whole-genome sequencing compared to short-read Illumina sequencing. Based on the mantle cell lymphoma cell line Granta-519, almost 99% copy-number reproducibility at the 100 kilobases (Kb) resolution between replicates was demonstrated, with 98% concordance to Illumina. Collectively, the performance of copy-number calling from 1.5–7.5 million long reads was comparable to 1 billion Illumina-based reads (50x coverage). Expectedly, the long-read resolution of canonical translocation t(11;14)(q13;q32) was superior with a sequence similarity of 89% to the already published CCND1/IGHjunction (9x coverage), spanning up to 69 Kb. The cytogenetic profile of Granta-519 was in general agreement with the literature and karyotype, although several differences remained unresolved. In conclusion, contemporary long-read sequencing is primed for future cytogenomics or sequencing-guided cytogenetics. The combined strength of long and short-read sequencing is apparent, where the high-precision junctional mapping complements and split paired-end reads. The potential is emphasized by the flexible single-sample genomic data acquisition of ONT with the high resolution of allelic imbalances using Illumina short-read sequencing.
Published: 2023
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20. Breast cancer risk variants at 6q25 display different phenotype associations and regulate ESR1, RMND1 and CCDC170

Author: Dunning, Alison M, Michailidou, Kyriaki, Kuchenbaecker, Karoline B, Thompson, Deborah, French, Juliet D, Beesley, Jonathan, Healey, Catherine S, Kar, Siddhartha, Pooley, Karen A, Lopez-Knowles, Elena, Dicks, Ed, Barrowdale, Daniel, Sinnott-Armstrong, Nicholas A, Sallari, Richard C, Hillman, Kristine M, Kaufmann, Susanne, Sivakumaran, Haran, Marjaneh, Mahdi Moradi, Lee, Jason S, Hills, Margaret, Jarosz, Monika, Drury, Suzie, Canisius, Sander, Bolla, Manjeet K, Dennis, Joe, Wang, Qin, Hopper, John L, Southey, Melissa C, Broeks, Annegien, Schmidt, Marjanka K, Lophatananon, Artitaya, Muir, Kenneth, Beckmann, Matthias W, Fasching, Peter A, dos-Santos-Silva, Isabel, Peto, Julian, Sawyer, Elinor J, Tomlinson, Ian, Burwinkel, Barbara, Marme, Frederik, Guénel, Pascal, Truong, Thérèse, Bojesen, Stig E, Flyger, Henrik, González-Neira, Anna, Perez, Jose I A, Anton-Culver, Hoda, Eunjung, Lee, Arndt, Volker, Brenner, Hermann, Meindl, Alfons, Schmutzler, Rita K, Brauch, Hiltrud, Hamann, Ute, Aittomäki, Kristiina, Blomqvist, Carl, Ito, Hidemi, Matsuo, Keitaro, Bogdanova, Natasha, Dörk, Thilo, Lindblom, Annika, Margolin, Sara, Kosma, Veli-Matti, Mannermaa, Arto, Tseng, Chiu-chen, Wu, Anna H, Lambrechts, Diether, Wildiers, Hans, Chang-Claude, Jenny, Rudolph, Anja, Peterlongo, Paolo, Radice, Paolo, Olson, Janet E, Giles, Graham G, Milne, Roger L, Haiman, Christopher A, Henderson, Brian E, Goldberg, Mark S, Teo, Soo H, Yip, Cheng Har, Nord, Silje, Borresen-Dale, Anne-Lise, Kristensen, Vessela, Long, Jirong, Zheng, Wei, Pylkäs, Katri, Winqvist, Robert, Andrulis, Irene L, Knight, Julia A, Devilee, Peter, Seynaeve, Caroline, Figueroa, Jonine, Sherman, Mark E, Czene, Kamila, Darabi, Hatef, Hollestelle, Antoinette, van den Ouweland, Ans M W, Humphreys, Keith, Gao, Yu-Tang, Shu, Xiao-Ou, Cox, Angela, Cross, Simon S, Blot, William, Cai, Qiuyin, Ghoussaini, Maya, Perkins, Barbara J, Shah, Mitul, Choi, Ji-Yeob, Kang, Daehee, Lee, Soo Chin, Hartman, Mikael, Kabisch, Maria, Torres, Diana, Jakubowska, Anna, Lubinski, Jan, Brennan, Paul, Sangrajrang, Suleeporn, Ambrosone, Christine B, Toland, Amanda E, Shen, Chen-Yang, Wu, Pei-Ei, Orr, Nick, Swerdlow, Anthony, McGuffog, Lesley, Healey, Sue, Lee, Andrew, Kapuscinski, Miroslav, John, Esther M, Terry, Mary Beth, Daly, Mary B, Goldgar, David E, Buys, Saundra S, Janavicius, Ramunas, Tihomirova, Laima, Tung, Nadine, Dorfling, Cecilia M, van Rensburg, Elizabeth J, Neuhausen, Susan L, Ejlertsen, Bent, Hansen, Thomas V O, Osorio, Ana, Benitez, Javier, Rando, Rachel, Weitzel, Jeffrey N, Bonanni, Bernardo, Peissel, Bernard, Manoukian, Siranoush, Papi, Laura, Ottini, Laura, Konstantopoulou, Irene, Apostolou, Paraskevi, Garber, Judy, Rashid, Muhammad Usman, Frost, Debra, Izatt, Louise, Ellis, Steve, Godwin, Andrew K, Arnold, Norbert, Niederacher, Dieter, Rhiem, Kerstin, Bogdanova-Markov, Nadja, Sagne, Charlotte, Stoppa-Lyonnet, Dominique, Damiola, Francesca, Sinilnikova, Olga M, Mazoyer, Sylvie, Isaacs, Claudine, Claes, Kathleen B M, De Leeneer, Kim, de la Hoya, Miguel, Caldes, Trinidad, Nevanlinna, Heli, Khan, Sofia, Mensenkamp, Arjen R, Hooning, Maartje J, Rookus, Matti A, Kwong, Ava, Olah, Edith, Diez, Orland, Brunet, Joan, Pujana, Miquel Angel, Gronwald, Jacek, Huzarski, Tomasz, Barkardottir, Rosa B, Laframboise, Rachel, Soucy, Penny, Montagna, Marco, Agata, Simona, Teixeira, Manuel R, Park, Sue Kyung, Lindor, Noralane, Couch, Fergus J, Tischkowitz, Marc, Foretova, Lenka, Vijai, Joseph, Offit, Kenneth, Singer, Christian F, Rappaport, Christine, Phelan, Catherine M, Greene, Mark H, Mai, Phuong L, Rennert, Gad, Imyanitov, Evgeny N, Hulick, Peter J, Phillips, Kelly-Anne, Piedmonte, Marion, Mulligan, Anna Marie, Glendon, Gord, Bojesen, Anders, Thomassen, Mads, Caligo, Maria A, Yoon, Sook-Yee, Friedman, Eitan, Laitman, Yael, Borg, Ake, von Wachenfeldt, Anna, Ehrencrona, Hans, Rantala, Johanna, Olopade, Olufunmilayo I, Ganz, Patricia A, Nussbaum, Robert L, Gayther, Simon A, Nathanson, Katherine L, Domchek, Susan M, Arun, Banu K, Mitchell, Gillian, Karlan, Beth Y, Lester, Jenny, Maskarinec, Gertraud, Woolcott, Christy, Scott, Christopher, Stone, Jennifer, Apicella, Carmel, Tamimi, Rulla, Luben, Robert, Khaw, Kay-Tee, Helland, Åslaug, Haakensen, Vilde, Dowsett, Mitch, Pharoah, Paul D P, Simard, Jacques, Hall, Per, García-Closas, Montserrat, Vachon, Celine, Chenevix-Trench, Georgia, Antoniou, Antonis C, Easton, Douglas F, and Edwards, Stacey L
Abstract: We analyzed 3,872 common genetic variants across the ESR1 locus (encoding estrogen receptor α) in 118,816 subjects from three international consortia. We found evidence for at least five independent causal variants, each associated with different phenotype sets, including estrogen receptor (ER+or ER−) and human ERBB2 (HER2+or HER2−) tumor subtypes, mammographic density and tumor grade. The best candidate causal variants for ER−tumors lie in four separate enhancer elements, and their risk alleles reduce expression of ESR1, RMND1 and CCDC170, whereas the risk alleles of the strongest candidates for the remaining independent causal variant disrupt a silencer element and putatively increase ESR1 and RMND1 expression.
Published: 2016
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21. Clinical Relevance of Sensitive and Quantitative STAT3Mutation Analysis Using Next-Generation Sequencing in T-Cell Large Granular Lymphocytic Leukemia

Author: Kristensen, Thomas, Larsen, Martin, Rewes, Annika, Frederiksen, Henrik, Thomassen, Mads, and Møller, Michael Boe
Abstract: Diagnosis of T-cell large granular lymphocytic leukemia (T-LGL) is often challenging because clinical and laboratory characteristics are overlapping with nonneoplastic conditions. Recently, mutation in the STAT3gene has been identified as a recurrent genetic abnormality in T-LGL. STAT3mutation, therefore, represents a promising marker in T-LGL diagnostics. We developed a new quantitative next-generation sequencing assay that allows sensitive analysis of the STAT3gene. The assay was used to study the utility of STAT3mutation analysis as a diagnostic tool in T-LGL. The study included 16 T-LGL patients. A total of 15 mutations, including 2 new mutations (G618Rand K658R), were detected in 12 patients (75%), with mutation levels ranging from 2.5% to 45.6% mutation-positive alleles. Next-generation sequencing detected 50% more mutations than Sanger sequencing. Blood samples from 20 healthy blood donors all tested negative, thus demonstrating the specificity of the assay. The results also indicated that mutation levels in blood and bone marrow are not systematically different, and next-generation sequencing–based STAT3 mutation analysis represents a sensitive method for monitoring residual disease as demonstrated in a patient receiving pentostatin. We demonstrate the clinical relevance of next-generation sequencing–based STAT3mutation analysis, which represents a sensitive and specific diagnostic marker in T-LGL that allows assessment of molecular residual disease, which may improve clinical decision making.
Published: 2014
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22. Novel radioisotope-based nanomedical approaches

Author: Olsen, Birgitte Brinkmann, Thisgaard, Helge, Vogel, Stefan, Thomassen, Mads, Kruse, Torben A., Needham, David, Mollenhauer, Jan, and Flemming Høilund-Carlsen, Poul
Abstract: AbstractRadioisotope therapy of cancer is on the rise applying mainly β-emitting radionuclides. However, due to exposure of healthy tissues, the maximum achievable radiation dose with these is limited. Auger-electron emitters (AEs) represent a promising alternative because of their mode of decay within a short nanometer range. The challenge is that their therapeutic efficacy relies on a close vicinity to DNA. To overcome this and to minimize toxicity, the construction of smart nanomedical devices is required, which ascertain tumor cell targeting with succeeding cellular uptake and nuclear translocation. In this review we describe the potential of AEs with focus on their delivery down to the DNA level and their cellular effects. Reported efforts comprise different tumor-targeting strategies, including the use of antibodies or peptides with nuclear localizing sequences. Recently, attention has shifted to various nanoparticle formats for overcoming delivery problems. To this end, these approaches have mostly been tested in cell lines in vitro applying AEs more suited for imaging than therapy. This defines a demand for nanomedical formulations with documented in vivo activity, using AEs selected for their therapeutic potential to come closer to real clinical settings.
Published: 2013
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23. Breast cancer stem cells: a moving target for cancer nanomedicine

Author: Mollenhauer, Jan, Knoop, Ann, Bak, Martin, Lænkholm, Anne-Vibeke, Thomassen, Mads, Kruse, Torben A., and Høilund-Carlsen, Poul Flemming
Abstract: AbstractThe identification of so-called cancer stem cells (CSCs) has sustainably changed our views on cancer by adding hierarchical principles, where tumor cells emerge from a founder population similar to steady-state regenerative processes in normal tissues. The rare founder population of CSCs is thought to be responsible for the recurrence of treatment-resistant tumors and metastatic spread and thus has been declared as the number one target for the next generation of anti-cancer drugs. Here, we will review the state of the art in research on breast cancer stem cells (BCSCs), for which a huge amount of data has accumulated in the past few years. Initial studies have suggested that the CD44+/CD24- profile and epithelial-to-mesenchymal transition (EMT) are associated with BCSCs, which has resulted in the recent identification of first compounds with BCSC-eliminating properties. In this early phase, however, it remains mostly unclear, to which extent these new compounds may exert toxicity to normal stem cells, since a substantial part targets molecular pathways critical for normal stem cell function. Moreover, these new drugs often require combination with conventional chemotherapeutics potentially posing new challenges to nanomedicine in circumventing toxicity and enabling targeted delivery. Most recent data further suggests that normal breast cancer cells might be able to re-create BCSCs and that additional, yet undiscovered kinds of BCSCs may exist. This points to future escape mechanisms. As a consequence, another broad future field of nanomedicine might be finding new drugs via systematic screening approaches. Collectively, this area provides ample possibilities for both traditional and novel nanomedical approaches.
Published: 2012
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24. The Impact of Somatic Mutations upon the Response to Combination Therapy with Ruxolitinib and Interferon in MPN Patients

Author: Skov, Vibe, Sørensen, Anders Lindholm, Knudsen, Trine Alma, Bjørn, Mads Emil, Ellervik, Christina, Kranker Larsen, Morten, Eickhardt-Dalbøge, Christina Schjellerup Schjellerup, Christensen, Sarah Friis, Thomassen, Mads, Kruse, Torben A, and Hasselbalch, Hans C.
Abstract: Introduction: The Philadelphia-negative myeloproliferative neoplasms (MPN) are associated with driver mutations in JAK2, CALR, and MPLgenes. Non-driver mutations affect disease progression and treatment response. Combination therapy with pegylated interferon-alpha2 (IFN) and ruxolitinib has recently been shown to induce hematologic and molecular responses in patients (pts) with MPN. We studied 25 pts by targeted next generation sequencing (NGS) of 42 genes and investigated the impact of somatic mutations (mut) on treatment response.
Published: 2021
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25. A Missense Mutation in Exon 13 in BRCA2, c.7235G>A, Results in Skipping of Exon 13

Author: Thomassen, Mads, Kruse, Torben A., Jensen, Peter K.A., and Gerdes, Anne-Marie
Abstract: We report here the functional characterisation of a missense mutation c.7235G>A in BRCA2. By reverse transcriptase polymerase chain reaction the mutation is demonstrated to cause skipping of exon 13. We conclude that the mutation is most likely deleterious.
Published: 2006
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26. Loss of heterozygosity at BRCA2 in a ductal carcinoma in situand three invasive breast carcinomas in a family with a germline BRCA2 mutation

Author: Thomassen, Mads, Kruse, Torben, Olsen, Karen, Borg, A., and Gerdes, Anne
Abstract: We have examined a family with a germline BRCA2 mutation in three cases of invasive breast cancer and one case of ductal carcinoma in situ(DCIS). Loss of heterozygosity (LOH) has been demonstrated at the BRCA2 locus in all cases. This result may suggest that the germline mutation in BRCA2 is the initiating step of DCIS and support the theory that DCIS is a precursor of invasive breast carcinoma in hereditary breast cancer.
Published: 2004
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27. Highly Deregulated Fibulins in Patients with Philadelphia-Negative Chronic Myeloproliferative Neoplasms

Author: Skov, Vibe, Thomassen, Mads, Kjær, Lasse, Larsen, Thomas Stauffer, Kruse, Torben A, and Hasselbalch, Hans
Abstract: Hasselbalch: Novartis: Research Funding; AOP Orphan Pharmaceuticals: Other: Data monitoring board.
Published: 2019
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28. Genomic Profiling of a Phase III Clinical Trial of Interferon Versus Hydroxyurea in MPN Patients Reveals Mutation-Specific and Treatment-Specific Patterns of Response

Author: Knudsen, Trine Alma, Skov, Vibe, Werner, Lillian, Duke, William, Gibson, Christopher J., Nag, Anwesha, Thorner, Aaron R., Wollison, Bruce, Hansen, Dennis Lund, Larsen, Thomas Stauffer, Ellervik, Christina, El Fassi, Daniel, Stricker, Karin de, Ocias, Lukas Frans, Brabrand, Mette, Bjerrum, Ole Weis, Overgaard, Ulrik Malthe, Frederiksen, Mikael, Kristensen, Thomas Kielsgaard, Kruse, Torben A, Thomassen, Mads, Mourits-Andersen, Torben, Severinsen, Marianne Tang, Stentoft, Jesper, Starklint, Joern, Møller, Peter, Neuberg, Donna S, Kjær, Lasse, Hasselbalch, Hans, Lindsley, R. Coleman, and Mullally, Ann
Abstract: Background: To investigate the role of genomics in determining response and resistance to front line treatment in MPN, we performed somatic mutational profiling of the DALIAH trial, a randomized controlled phase III trial of interferon versus hydroxyurea in newly diagnosed MPN patients.
Published: 2019
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29. Significantly Upregulated Thrombo-Inflammatory Genes Are Normoregulated or Significantly Downregulated during Treatment with Interferon-Alpha2 in Patients with Philadelphia-Negative Chronic Myeloproliferative Neoplasms

Author: Skov, Vibe, Riley, Caroline, Thomassen, Mads, Kjær, Lasse, Larsen, Thomas Stauffer, Kruse, Torben A, and Hasselbalch, Hans
Abstract: Introduction:The Philadelphia-negative chronic myeloproliferative neoplasms (MPNs) are associated with a high risk of arterial and venous thrombosis, which are attributed to several mechanisms, including elevated blood cell counts per se, in vivo leukocyte and platelet activation with increased adhesion of granulocytes, monocytes and platelets to each other and to a dysfunctional endothelium. In recent years, evidence has accumulated that chronic inflammation is an important pathogenetic mechanism for MPN-disease development and disease progression, inducing increasing genomic instability in hematopoietic cells and thereby emergence of additional mutations of significance for myelofibrotic and leukemic transformation. Recent studies have shown several thrombo-inflammatory genes to be upregulated in patients with MPNs, likely contributing to the increased risk of thrombosis. Several studies have documented that long term treatment with interferon-alpha2 (IFN) is able to normalize elevated cell counts in concert with induction of a remarkable decrease in the JAK2V617Fallele burden and accordingly impacting important thrombosis promoting factors in MPNs. Herein, using whole blood gene expression profiling we for the first time report that treatment with IFN is able to normoregulate or significantly downregulate upregulated thrombo-inflammatory genes in patients with MPNs.
Published: 2019
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30. The Impact of the Mutational Landscape upon the Molecular Responses to Interferon-Alfa2 in Calr-Mutated MPN Patients

Author: Skov, Vibe, Kjær, Lasse, Thomassen, Mads, Koschmieder, Steffen, Czech, Julia, Chatain, Nicolas, Pallisgaard, Niels, Cordua, Sabrina, Kruse, Torben A, and Hasselbalch, Hans Carl
Abstract: Hasselbalch: Novartis: Research Funding.
Published: 2018
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31. Whole Blood Transcriptional Profiling Reveals Highly Deregulated Atherosclerosis Genes in Myeloproliferative Cancer

Author: Skov, Vibe, Thomassen, Mads, Kjær, Lasse, Riley, Caroline, Larsen, Thomas Stauffer, Bjerrum, Ole Weis, Kruse, Torben A, and Hasselbalch, Hans Carl
Abstract: Introduction: The Philadelphia-negative chronic myeloproliferative neoplasms (MPNs) are associated with a huge comorbidity burden, including an increased risk of cardiovascular diseases. Recently, chronic inflammation has been suggested to be the driving force for clonal evolution and disease progression in MPNs but also potentially having an impact upon the development of accelerated (premature) atherosclerosis, which is recorded in several other inflammatory diseases. Using whole blood gene expression profiling we have previously reported massive deregulation of inflammation genes and genes involved in oxidative stress. Herein, we extend our studies to explore the landscape of atherosclerosis genes, which have not been investigated previously in MPNs but may add novel important information in regard to deregulation of these genes of potential importance for the development of premature atherosclerosis and accordingly the heavy cardiovascular disease burden in MPNs.
Published: 2018
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32. The Impact of Interferon on Interferon-Related Genes in Polycythemia Vera and Allied Neoplasms

Author: Skov, Vibe, Riley, Caroline, Thomassen, Mads, Kjær, Lasse, Larsen, Thomas Stauffer, Bjerrum, Ole Weis, Kruse, Torben A, and Hasselbalch, Hans Carl
Abstract: Hasselbalch: Novartis: Research Funding.
Published: 2018
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33. Interferon-alfa2 Treatment of Patients with Polycythemia Vera and Related Neoplasms Impacts Deregulation of Oxidative Stress Genes and Antioxidative Defence Mechanisms. Potential Implications of IFN-Alfa Induced Changes in TP53, NRF2 and CXCR4 for Genomic Instability and CD34+ Mobilisation

Author: Skov, Vibe, Riley, Caroline, Thomassen, Mads, Kjær, Lasse, Larsen, Thomas Stauffer, Bjerrum, Ole Weis, Kruse, Torben A, and Hasselbalch, Hans Carl
Abstract: Hasselbalch: Novartis: Research Funding.
Published: 2018
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34. Interferon-alfa2 Treatment of Patients with Polycythemia Vera and Related Neoplasms Influences Deregulated Inflammation and Immune Genes in Polycythemia Vera and Allied Neoplasms

Author: Skov, Vibe, Riley, Caroline, Thomassen, Mads, Kjær, Lasse, Larsen, Thomas Stauffer, Bjerrum, Ole Weis, Kruse, Torben A, and Hasselbalch, Hans Carl
Abstract: Hasselbalch: Novartis: Research Funding.
Published: 2018
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35. Long-Term Efficacy and Safety of Recombinant Interferon Alpha-2 Vs. Hydroxyurea in Polycythemia Vera: Preliminary Results from the Three-Year Analysis of the Daliah Trial - a Randomized Controlled Phase III Clinical Trial

Author: Knudsen, Trine Alma, Hansen, Dennis Lund, Ocias, Lukas Frans, Bjerrum, Ole Weis, Brabrand, Mette, El Fassi, Daniel, Frederiksen, Mikael, Kjær, Lasse, Kristensen, Thomas Kielsgaard, Kruse, Torben A, Mourits-Andersen, Torben, Møller, Peter, Overgaard, Ulrik Malthe, Severinsen, Marianne Tang, Skov, Vibe, Stentoft, Jesper, Starklint, Jørn, de Stricker, Karin, Thomassen, Mads, Larsen, Thomas Stauffer, and Hasselbalch, Hans Carl
Abstract: Stentoft: Bristol-Myers Squibb: Research Funding; Merck Sharp&Dohme: Research Funding. Hasselbalch:Novartis: Research Funding.
Published: 2018
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36. Extracellular Matrix-Related Genes Are Deregulated in Peripheral Blood from Patients with Myelofibrosis and Related Neoplasms

Author: Skov, Vibe, Thomassen, Mads, Kjær, Lasse, Riley, Caroline, Larsen, Thomas Stauffer, Bjerrum, Ole Weis, Kruse, Torben A, and Hasselbalch, Hans Carl
Abstract: Hasselbalch: Novartis: Research Funding.
Published: 2018
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37. Genetic Evidence for Involvement of Human Endogenous Retrovirus Herv-Fc1 in the Pathogenesis of MPNs

Author: Skov, Vibe, Schmidt, Katrine LM, Pedersen, Kasper Mønsted, Hansen, Bettina, Klausen, Tobias Wirenfeldt, Kruse, Torben A, Thomassen, Mads, Kjær, Lasse, Ellervik, Christina, Holmstrøm, Morten, Nexø, Bjørn, Hasselbalch, Hans Carl, and Laska, Magdalena J
Abstract: Hasselbalch: Novartis: Research Funding.
Published: 2018
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38. The Impact of Interferon-alpha2 on HLA-Genes in Patients with Polycythemia Vera and Related Neoplasms

Author: Skov, Vibe, Riley, Caroline H, Thomassen, Mads, Kjær, Lasse, Larsen, Thomas Stauffer, Jensen, Morten K, Bjerrum, Ole Weis, Kruse, Torben A, and Hasselbalch, Hans Carl
Abstract: Bjerrum: Bristoll Myers Squibb, Novartis and Pfizer: Other: educational activities. Hasselbalch:Novartis: Research Funding.
Published: 2015
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39. Safety and Efficacy of Combination Therapy of Interferon-Alpha2 + JAK1-2 Inhibitor in the Philadelphia-Negative Chronic Myeloproliferative Neoplasms. Preliminary Results from the Danish Combi-Trial - an Open Label, Single Arm, Non-Randomized Multicenter Phase II Study

Author: Mikkelsen, Stine Ulrik, Kjær, Lasse, Skov, Vibe, Bjørn, Mads Emil, Andersen, Christen Lykkegaard, Bjerrum, Ole Weis, Brochmann, Nana, El Fassi, Daniel, Kruse, Torben A, Larsen, Thomas Stauffer, Mourits-Andersen, Torben, Nielsen, Claus Henrik, Pallisgaard, Niels, Thomassen, Mads, and Hasselbalch, Hans Carl
Abstract: Off Label Use: The combination therapy with ruxolitinib (JAK1-2 inhibitor) and interferon-alpha is off-label in MPNs. The concept is dual myelosuppressive action and dual clonal suppression in addition to the anti-inflammatory properties of ruxolitinib.. Bjørn:Novartis Oncology: Research Funding. Bjerrum:Bristoll Myers Squibb, Novartis and Pfizer: Other: educational activities. El Fassi:Novartis Denmark: Honoraria, Other: Have conducted an educational session for Novartis Denmark, regarding MPNs and ruxolitinib, for this a honorarium was received.. Nielsen:Novartis: Research Funding. Pallisgaard:Roche: Other: travel grant; Amgen: Membership on an entity's Board of Directors or advisory committees, Other: travel grant, Speakers Bureau; Novartis: Other: travel grant, Research Funding, Speakers Bureau; Qiagen: Membership on an entity's Board of Directors or advisory committees; Bristol Meyer Squibb: Speakers Bureau. Hasselbalch:Novartis: Research Funding.
Published: 2015
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40. DNA Methylation Profiling of Sorted Cells from Myelofibrosis Patients reveals Aberrant Epigenetic Regulation of Immune Pathways and identifies Early MPN Driver Genes

Author: Hasselbalch, Hans Carl, Nielsen, Helene Myrtue, Asmar, Fazila, Andersen, Christen Lykkegaard, Kristensen, Lasse Sommer, Torben, Kruse A, Thomassen, Mads, Larsen, Thomas Stauffer, Skov, Vibe, Riley, Caroline, Hansen, Lise Lotte, Jensen, Morten K., Bjerrum, Ole Weis, Punj, Vasu, and Grønbæk, Kirsten
Abstract: No relevant conflicts of interest to declare.
Published: 2014
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41. Investigation of Archived Formalin-Fixed Paraffin-Embedded Pancreatic Tissue with Whole-Genome Gene Expression Microarray

Author: V. Michelsen, Nete, Brusgaard, Klaus, Tan, Qihua, Thomassen, Mads, Hussain, Khalid, and T. Christesen, Henrik
Abstract: The use of formalin-fixed, paraffin-embedded (FFPE) tissue overcomes the most prominent issues related to research on relatively rare diseases: limited sample size, availability of control tissue, and time frame. The use of FFPE pancreatic tissue in GEM may be especially challenging due to its very high amounts of ribonucleases compared to other tissues/organs. In choosing pancreatic tissue, we therefore indirectly address the applicability of other FFPE tissues to gene expression microarray (GEM). GEM was performed on archived, routinely fixed, FFPE pancreatic tissue from patients with congenital hyperinsulinism (CHI), insulinoma, and deceased age-appropriate neonates, using whole-genome arrays. Although ribonuclease-rich, we obtained biologically relevant and disease-specific, significant genes; cancer-related genes; genes involved in (a) the regulation of insulin secretion and synthesis, (b) amino acid metabolism, and (c) calcium ion homeostasis. These results should encourage future research and GEM studies on FFPE tissue from the invaluable biobanks available at the departments of pathology worldwide.
Published: 2011
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42. Enhanced Gene Expression of EZH2 In Patients with Primary Myelofibrosis

Author: Skov, Vibe, Larsen, Thomas Stauffer, Thomassen, Mads, Riley, Caroline, Jensen, Morten Krogh, Bjerrum, Ole Weis, Kruse, Torben A, and Hasselbalch, Hans Carl
Abstract: The polycomb repressive complex (PRC) 2 contains 3 core proteins, EZH2 (enhancer of zeste homolog 2), SUZ12, and EED, in which the SET (suppressor of vaegation-enhancer of zeste-trithorax) domain of EZH2 mediates the histone methyltransferase activity. This induces trimethylation of lysine 27 on histone H3, regulates the expression of HOX genes, and promotes proliferation and aggressiveness of neoplastic cells. EZH2, a known repressor of gene transcription, has been reported to be overexpressed in many cancers and correlates with poor prognosis. EZH2 may also be involved in disease progression in patients with the classical Philadelphia-negative chronic myeloproliferative neoplasms (CMPNs) encompassing essential thrombocythemia (ET), polycythemia vera (PV), and primary myelofibrosis (PMF). Since the potential oncogenic role of EZH2 in CMPNs has never been investigated, we have assessed gene expression of EZH2 in a cohort of patients with CMPNs.Using Affymetrix HG-U133 2.0 Plus microarrays, recognizing 54675 probe sets (38500 genes), gene expression profiling has been performed on control subjects (n=21) and patients with ET (n =19), PV (n=41), and PMF (n=9). All patients were diagnosed according to the WHO criteria of a CMPN. Total RNA was purified from whole blood and amplified to biotin-labeled RNA and hybridized to microarray chips.We identified 20439, 25307, 17417, and 25421 probe sets which were differentially expressed between controls and patients with ET, PV, PMF, and CPMNs as a whole, respectively (false discovery rate (FDR) adjusted p values < 0.05). These genes included EZH2, which was highly significantly upregulated in patients with PMF as compared to controls (2.3 fold upregulated; uncorrected p-value=1.09×10-8 and FDR=1.75×10-6, and between PMF and non-PMF patients (fold change=2.0, FDR < 0.0005). No significant differences in EZH2 gene expression were recorded between controls and ET patients, controls and PV patients, or controls and the CMPN group as a whole. Within patients, the EZH2 gene was also differentially expressed with the highest levels being recorded in patients with PMF compared to PV patients (fold change=2.4, FDR < 7.5 ×10-6).Using global gene expression profiling we have found the EZH2 gene to be significantly upregulated in CMPN patients, with the highest expression levels being found in PMF. We hypothesize that an altered expression of EZH2 may be involved in the transformation of ET and PV into myelofibrosis. It remains to be clarified if deregulation of EZH2 occurs consequent to mutations in the EZH2-gene. Enhanced EZH2 expression may also be associated with silencing of differentiation genes during myelofibrotic and leukemic transformation. An increased expression of EZH2 may provide a proliferative advantage of the malignant clone through interaction with the pathways of key elements controlling cell growth arrest and differentiation, (e.g. nuclear factor kappa beta and - the proteasome pathway). Studies are in progress to elucidate if genomic loss of distinct microRNAs (microRNA 101 leads to overexpression of EZH2 in cancer is associated with overexpression of EZH2 in CMPNs. Highly expressed EZH2 may be a new marker of an aggressive clinical phenotype which might imply EZH2 as a novel biomarker for predicting prognosis. If so, EZH2-blockade might be a novel approach to be incorporated in the strategies for developing epigenetic therapies in patients with CMPNs.No relevant conflicts of interest to declare.
Published: 2010
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43. Increased Expression of Proteasome-Related Genes In Patients with Primary Myelofibrosis

Author: Skov, Vibe, Larsen, Thomas Stauffer, Thomassen, Mads, Riley, Caroline, Jensen, Morten Krogh, Bjerrum, Ole Weis, Kruse, Torben A, and Hasselbalch, Hans Carl
Abstract: The proteasome is an ubiquituous enzyme complex that plays a critical role in the degradation of many proteins involved in cell cycle regulation, apoptosis, and angiogenesis. Since these pathways and functions are often deregulated in cancer cells, inhibition of the proteasome is an attractive potential anticancer therapy. Bortezomib (Velcade, formerly PS-341) is an extremely potent and selective proteasome inhibitor that shows strong activity against many solid and hematologic tumor types. Moreover, bortezomib, mainly by inhibition of the NF-kappaB pathway, has a chemosensitizing effect when administered together with other antitumoral drugs. Bortezomib is a well-established treatment in multiple myeloma and studies are focusing in the potential benefit of bortezomib in other haematological malignancies, including malignant lymphomas. Since the NF-kappaB pathway is considered to be implicated in the abnormal release of cytokines in primary myelofibrosis (PMF), the proteasome inhibitor bortezomib might be a potential therapy. In a murine model, bortezomib has been demonstrated to inhibit thrombopoietin (TPO)-induced NF-kappaB activation in megakaryocytes and to reduce myeloproliferation induced by high TPO levels. Accordingly, from in vitro studies it was concluded that bortezomib might be a promising therapy for future treatment of PMF patients. Surprisingly, however, these encouraging results have not been achieved in clinical trials testing bortezomib in patients with myelofibrosis. We have performed gene expression profiling of patients with PMF and in patients with other chronic myeloproliferative neoplasms (CMPNs) in order to describe aberrant genes in the proteasome pathway in PMF.The HG-U133 Plus 2.0 microarray from Affymetrix was used to profile expression of 38500 genes in whole blood from 70 patients with CMPNs, including 9 patients with PMF and 61 patients with other CMPNs. All patients were diagnosed according to the WHO criteria of a CMPN (ET=19, PV=41, PMF=9). The patients were diagnosed and followed in two institutions. Most patients were studied on cytoreductive therapy, which for the large majority included hydroxyurea. Total RNA was purified from whole blood and amplified to biotin-labeled aRNA and hybridized to microarray chips.Differences in gene expression between the two groups were calculated for each gene in the dataset by using Welch two sample t test, and the Benjamini Hochberg method was applied to control for multiple hypothesis testing (false discovery rate (FDR) < 0.05). Data were integrated with biological pathways and networks using Gene Microarray Pathway Profiler (GenMAPP 2.1) and Cytoscape 2.6.3, respectively. Hypothesis driven discovery was used to find significantly differentially expressed genes and pathways associated with PMF.Single gene analysis demonstrated significantly elevated expression of seventeen proteasomal subunit genes in patients with PMF (PSMA1, PSMA2, PSMA6, PSMA7, PSMB4, PSMB5, PSMB6, PSMB7, PSMC2, PSMC3, PSMD10, PSMD14, PSMD4, PSMD8, PSMD9, PSMG1, and PSMG3 (FDR < 0.05). Only one gene, PSMB4, was significantly downregulated (FDR < 0.05). Global pathway analysis showed a significant upregulation of the proteasome degradation pathway (adjusted P < 0.03), and the network analysis revealed a significant subnetwork only composed of upregulated genes (CDC25A, CDC6, CDT1, GMNN, ORC1L, PSMA6, PSMA7, PSMB5, PSMB6, PSMB7, PSMC3, PSMD5, PSMD8, PSMD9, PSMD14) of which 10 were proteasomal genes (Z=2.6).In this study, we have for the first time described the gene signature of the proteasome in peripheral blood cells from patients with myelofibrosis and patients with ET and PV. Using single gene analysis, global pathway and network analysis, we found significant upregulation of the proteasomal transcriptome in patients with PMF as compared to patients with ET and PV as a group. This study has added new important information of the genes involved in the upregulation of the proteasome degradation pathway in these patients.No relevant conflicts of interest to declare.
Published: 2010
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44. High Expression of Carcinoembryonic Antigen-Related Cell Adhesion Molecule(CEACAM) 6 In Primary Myelofibrosis

Author: Hasselbalch, Hans Carl, Skov, Vibe, Larsen, Thomas Stauffer, Thomassen, Mads, Riley, Caroline, Jensen, Morten Krogh, Bjerrum, Ole Weis, and Kruse, Torben A
Abstract: Carcinoembryonic antigen-related cell adhesion molecule (CEACAM) 6, also known as non-specific cross-reacting antigen (NCA) or CD66c is a glycosylphosphoinositol (GPI)-linked cell surface protein and a member of the CEA family of proteins. Structurally, this protein shares close homology with CEACAM1, CEACAM7 and CEACAM8. Functionally, CEACAM6 has been implicated in cell adhesion, cellular invasiveness and metastatic behaviour of tumour cells. Expression of CEACAM6 protein has been found in a variety of normal human tissues, including myeloid cells. A key pathophysiological feature of primary myelofibrosis (PMF) is changes in the bone marrow micromilieu, progressive accumulation of connective tissue, pronounced neovascularisation and altered stromal cell adhesion. Consequently, CD34+ cells escape the bone marrow and seed extramedullarily. Being involved in cell adhesion, cellular invasiveness, angiogenesis, and inflammation – all key processes in the pathophysiology of PMF – we hypothesized that CEACAM6 might play an important role in these processes in patients with myelofibrosis. We have assessed gene expression of several CEA genes in patients with PMF and related neoplasms in order to elucidate the significance of CEACAM6 and other members of the CEA family of proteins in these disorders.Gene expression microarray studies have been performed on whole blood from control subjects (n=21) and patients with ET (n =19), PV (n=41), and PMF (n=9). Gene expression profiles were generated using Affymetrix HG-U133 2.0 Plus microarrays recognizing 54.675 probe sets (38.500 genes). Total RNA was purified from whole-blood and amplified to biotin-labeled aRNA and hybridized to microarray chips.20.439, 25.307, 17.417, and 25.421 probe sets were identified to be differentially expressed between controls and patients with ET, PV, PMF, and CPMNs as a whole, respectively (false discovery rate (FDR) adjusted p values < 0.05). Several CEACAM-genes were significantly deregulated. In PMF patients, the CEACAM genes 1, 6 and 8 were significantly upregulated with the highest upregulation of CEACAM6 and CEACAM8 (fold change (FC) 12.5 and 14.0, respectively and FDR adjusted p values 7.71 × 10-7 and 1.48 × 10-5, respectively). Only the CEACAM21 gene was significantly downregulated (FC -1.3 and FDR adjusted p-value 4.14 × 10-7) whereas the other CEACAM-genes tested (3, 4, 5, 7, 19) displayed no significant changes as compared to controls. In ET patients, the CEACAM genes 3, 6, and 7 were significantly upregulated (FC 1.2, 1.8, and 1.1, respectively) and FDR adjusted p values < 0.03). The CEACAM21 gene was significantly downregulated (FC -1.3 and FDR adjusted p-value 0.0004). In PV patients, the CEACAM genes 1, 3, 6 and 7 were significantly upregulated (FC 1.7, 1.2, 1.7, and 1.1, respectively) and FDR adjusted p values 0.0002, 0.0009, 0.0002, and 0.03, respectively. The CEACAM21 gene was significantly downregulated (FC -1.3 and FDR adjusted p-value 4.14×10-5) All other CEACAM-genes showed no significant changes in either ET or PV as compared to controls.When comparing controls with non-PMF-patients, a significant upregulation of the CEACAM genes 1, 3, 6, and 7 were recorded in non-PMF patients (FC 1.5, 1.2, 1.7, and 1.1, respectively; FDR adjusted p values 0.001, 0.0002, 0.002, and 0.02, respectively). The CEACAM19 and CEACAM21 genes were significantly downregulated (FC - 1.1 and -1.4, respectively; adjusted p-values 0.008 and 3.46 × 10-8).Using global gene expression profiling, we have found a pronounced deregulation of CEACAM genes, involving highly significant upregulation of the CEACAM genes 6 and 8 in PMF (FCs 12.0 and 14.0, respectively). Upregulation of CEACAM6 was seen in both ET, PV and PMF by far the highest levels being recorded in PMF-patients. Of note, significant upregulation of CEACAM8 (FC 14) was only seen in patients with myelofibrosis. The elevated expression of CEACAMs genes in ET, PV, and PMF may solely reflect neutrophil activation being most exaggerated in patients with PMF in whom the highest CEACAM6 and 8 expression patterns were recorded. Alternatively, the highly elevated gene expression of CEACAM6 and 8 in PMF are molecular markers of clonal expansion and myelofibrotic transformation, implying enhanced proteolytic activity and egress of CD34+ cells into the circulation.No relevant conflicts of interest to declare.
Published: 2010
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45. Increased Gene Expression of Histone Deacetylases In Patients with Philadelphia-Negative Chronic Myeloproliferative Neoplasms

Author: Skov, Vibe, Larsen, Thomas Stauffer, Thomassen, Mads, Riley, Caroline, Jensen, Morten Krogh, Bjerrum, Ole Weis, Kruse, Torben A, and Hasselbalch, Hans Carl
Abstract: Several new treatment strategies within the Philadelphia-negative chronic myeloproliferative neoplasms CMPNs are beeing explored, among these, agents belonging to the class of HDAC-inhibitors, including givinostat (ITF2357) and vorinostat (suberoylanilide hydroxamic acid (SAHA)). These agents are inhibitors of class I and II HDAC enzymes, promoting cell-cycle arrest and apoptosis of cancer cells. Recently, enhanced histone deacetylase (HDAC) enzyme activity has been found in CD34+ cells from patients with primary myelofibrosis (PMF), enzyme activity levels highly exceeding those recorded in essential thrombocythemia (ET) and polycythemia vera (PV). The raised levels correlated to the degree of splenomegaly, suggesting that HDAC might be recruited as ET or PV progresses into myelofibrosis or PMF progresses into a more advanced stage. In order to further describe HDACs in CMPNs, we have assessed gene expression of several HDACs in a larger cohort of patients with ET, PV and PMF.Gene expression microarray studies have been performed on control subjects (n=21) and patients with ET (n =19), PV (n=41), and PMF (n=9). Most patients were studied on cytoreductive therapy, which for the large majority included hydroxyurea. Gene expression profiles were generated using Affymetrix HG-U133 2.0 Plus microarrays recognizing 54675 probe sets (38.500 genes). Total RNA was purified from whole blood and amplified to biotin-labeled aRNA and hybridized to microarray chips.We identified 20439, 25307, 17417, and 25421 probe sets which were differentially expressed between controls and patients with ET, PV, PMF, and CPMNs as a whole, respectively (false discovery rate (FDR) adjusted p values < 0.05). Several HDAC-genes were significantly deregulated. In ET patients upregulated genes included HDAC5, HDAC9 and downregulated genes HDAC1, HDAC4, HDAC7. In PV-patients HDAC4, HDAC5, HDAC6, HDAC9, and HDAC11 genes were upregulated, and HDAC1, HDAC7, HDAC9, and HDAC11 genes were downregulated. In PMF -patients HDAC4, HDAC6, HDAC9, and HDAC11 genes were upregulated, and HDAC1 and HDAC7 were downregulated. Compared to controls the CMPN-patients as a group exhibited upregulation of HDAC4, HDAC5, HDAC6, HDAC9, and HDAC11 genes. The HDAC genes 9 and 11 were significantly upregulated in both ET, PV, PMF, and CMPNs as a whole, the highest values being recorded in patients with ET, PMF, and CMPNs as compared to controls. In regard to HDAC9 gene expression, the fold changes (FC) were 1.3, 1.2, 1.3, and 1.3 for ET, PV, PMF, and CMPNs, respectively; for HDAC11 the highest values were recorded in patients with ET with the following FCs 1.2, 1.1, 1.1, 1.1 for ET, PV, PMF, and CMPNs, respectively; FDR adjusted p values < 0.05). Within patients, the HDAC6-gene was also differentially expressed with the highest levels being recorded in patients with PMF (FC 1.2, FDR adjusted p values < 0.01). When comparing non-PMF-patients with PMF-patients, a significant upregulation of the HDAC2-gene was found in PMF patients (FC 1.5, FDR adjusted p-value=0.007), whereas the HDAC7-gene was significantly downregulated (FC -1.3, FDR adjusted p-value=0,001.Using global gene expression profiling of whole-blood from patients with CMPNs, we have found a pronounced deregulation of HDAC-genes, involving significant upregulation of the HDAC-genes 9 and 11 with the highest expression levels being found in patients with ET, in PMF (HDAC9) and in CMPNs both HDAC9 and HDAC11. Furthermore, we have identified that the HDAC-6 gene is progressively expressed in patients with ET, PV, and PMF reflecting a steady accumulation of abnormally expressed HDAC-6 during disease evolution. Our results lend further support to HDACs as important epigenetic targets in the future treatment of patients with CMPNs. Since the highest expression levels of HDAC-genes was recorded in ET (HDACs 9 and 11), in PMF (HDAC9) and in the whole CMPN-group both HDACs 9 and 11, their downregulation by HDAC-inhibitors might be associated with decreased disease activity including reduction of splenomegaly in MF. Preliminary data indicate that enlarged spleens are diminished in subsets of patients during treatment with HDAC-inhibitors. Studies are in progress on the impact of vorinostat on global gene expression profiling, including HDAC- gene expression subclasses in patients with CMPNs.No relevant conflicts of interest to declare.
Published: 2010
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46. Gene Expression Profiling with Principal Component Analysis Depicts the Biological Continuum From Essential Thrombocythemia Over Polycythemia Vera to Myelofibrosis

Author: Skov, Vibe, Larsen, Thomas Stauffer, Thomassen, Mads, Riley, Caroline, Jensen, Morten Krogh, Bjerrum, Ole Weis, Kruse, Torben A, and Hasselbalch, Hans Carl
Abstract: The classical Philadelphia-negative chronic myeloproliferative neoplasms (CMPNs) encompass polycythemia vera (PV), essential thrombocythemia (ET), and primary myelofibrosis (PMF). After several years, a proportion of patients with PV may develop increasing splenomegaly and bone marrow fibrosis to terminate in postpolycythemic myelofibrosis, which then has a very poor prognosis with median survival of only a few years. A high proportion of the ET-population has been shown to have prefibrotic PMF or a “PV-like” phenotype, which after a variable time may terminate in myelofibrosis with myeloid metaplasia (MMM). Although the concept of prefibrotic myelofibrosis as a separate disease entity to be distinguished from ET by distinct histopathological features has been questioned, it seems logical that a continuum exists from “early” myelofibrosis with no or minimal bone marrow fibrosis to the advanced stage of myelofibrosis with myeloid metaplasia. Accordingly, a new concept of these diseases as a biological continuum from ET over PV to PMF has emerged. Indeed, this biological continuum reflects the various clinical stages as also described for chronic myelogenous leukaemia (CML) – a chronic stable phase (ET-PV), an accelerated phase (transitional phase), and a terminal myelofibrosis or blast phase of the disease (PMF-BP).It is evident that the JAK2 V617F mutational load is an important determinant of phenotype, but other genetic and epigenetic events contribute to the phenotypic presentation. Several gene expression studies have identified genes which might be of pathogenetic relevance for the development of CMPNs. However, no study has applied an unsupervised method as Principal Component Analysis (PCA) to discover unknown trends in the data. We have carried out gene expression profiling with PCA to ascertain if this analysis might unravel distinct grouping of disease entities supporting the biological continuum from early ET over PV to the advanced myelofibrosis phase.Using HG-U133 Plus 2.0 microarray from Affymetrix, recognizing 54675 probe sets (38500 genes), gene expression microarray studies have been performed on control subjects (n=21) and patients with ET (n =19), PV (n=41), and PMF (n=9). An unsupervised statistical method, PCA, which is an exploratory tool used to uncover unknown trends in the data based on gene expression profiles, was applied to the data.The results from the PCA confirm the hypothesis of a biological continuum from control subjects over ET to PV and finally PMF (figure 1). The figure also reveals that patients with PV in a transitional stage (PVtrans) with pancytosis, huge splenomegaly, and bone marrow fibrosis have a gene profile between PV and PMF. Furthermore, single gene analysis revealed that several genes are highly dysregulated in patients with ET, PV, and PMF compared to control subjects even after correcting for multiple testing.Using global gene expression profiling with PCA in patients with different CMPNs (ET, PV, PMF), we have yielded support to the concept of a biological continuum from early ET to the advanced myelofibrosis stage. Studies are in progress to identify single genes or clusters of genes accounting for the biological continuum and accordingly the progression from ET over PV to myelofibrosis.No relevant conflicts of interest to declare.
Published: 2010
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