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2. Pervasive chromosomal instability and karyotype order in tumour evolution

Author

Watkins, Thomas BK, Lim, Emilia L, Petkovic, Marina, Elizalde, Sergi, Birkbak, Nicolai J, Wilson, Gareth A, Moore, David A, Grönroos, Eva, Rowan, Andrew, Dewhurst, Sally M, Demeulemeester, Jonas, Dentro, Stefan C, Horswell, Stuart, Au, Lewis, Haase, Kerstin, Escudero, Mickael, Rosenthal, Rachel, Bakir, Maise Al, Xu, Hang, Litchfield, Kevin, Lu, Wei Ting, Mourikis, Thanos P, Dietzen, Michelle, Spain, Lavinia, Cresswell, George D, Biswas, Dhruva, Lamy, Philippe, Nordentoft, Iver, Harbst, Katja, Castro-Giner, Francesc, Yates, Lucy R, Caramia, Franco, Jaulin, Fanny, Vicier, Cécile, Tomlinson, Ian PM, Brastianos, Priscilla K, Cho, Raymond J, Bastian, Boris C, Dyrskjøt, Lars, Jönsson, Göran B, Savas, Peter, Loi, Sherene, Campbell, Peter J, Andre, Fabrice, Luscombe, Nicholas M, Steeghs, Neeltje, Tjan-Heijnen, Vivianne CG, Szallasi, Zoltan, Turajlic, Samra, Jamal-Hanjani, Mariam, Van Loo, Peter, Bakhoum, Samuel F, Schwarz, Roland F, McGranahan, Nicholas, and Swanton, Charles

Subjects
Biological Sciences, Biomedical and Clinical Sciences, Genetics, Oncology and Carcinogenesis, Cancer, Human Genome, Chromosomal Instability, Chromosomes, Human, Pair 11, Chromosomes, Human, Pair 8, Clone Cells, Cyclin E, DNA Copy Number Variations, Evolution, Molecular, Female, Humans, Karyotype, Loss of Heterozygosity, Male, Mutagenesis, Neoplasm Metastasis, Neoplasms, Oncogene Proteins, General Science & Technology
Abstract

Chromosomal instability in cancer consists of dynamic changes to the number and structure of chromosomes1,2. The resulting diversity in somatic copy number alterations (SCNAs) may provide the variation necessary for tumour evolution1,3,4. Here we use multi-sample phasing and SCNA analysis of 1,421 samples from 394 tumours across 22 tumour types to show that continuous chromosomal instability results in pervasive SCNA heterogeneity. Parallel evolutionary events, which cause disruption in the same genes (such as BCL9, MCL1, ARNT (also known as HIF1B), TERT and MYC) within separate subclones, were present in 37% of tumours. Most recurrent losses probably occurred before whole-genome doubling, that was found as a clonal event in 49% of tumours. However, loss of heterozygosity at the human leukocyte antigen (HLA) locus and loss of chromosome 8p to a single haploid copy recurred at substantial subclonal frequencies, even in tumours with whole-genome doubling, indicating ongoing karyotype remodelling. Focal amplifications that affected chromosomes 1q21 (which encompasses BCL9, MCL1 and ARNT), 5p15.33 (TERT), 11q13.3 (CCND1), 19q12 (CCNE1) and 8q24.1 (MYC) were frequently subclonal yet appeared to be clonal within single samples. Analysis of an independent series of 1,024 metastatic samples revealed that 13 focal SCNAs were enriched in metastatic samples, including gains in chromosome 8q24.1 (encompassing MYC) in clear cell renal cell carcinoma and chromosome 11q13.3 (encompassing CCND1) in HER2+ breast cancer. Chromosomal instability may enable the continuous selection of SCNAs, which are established as ordered events that often occur in parallel, throughout tumour evolution.

Published
2020

3. Transcriptomic signatures of tumors undergoing T cell attack

Author

Gokuldass, Aishwarya, Schina, Aimilia, Lauss, Martin, Harbst, Katja, Chamberlain, Christopher Aled, Draghi, Arianna, Westergaard, Marie Christine Wulff, Nielsen, Morten, Papp, Krisztian, Sztupinszki, Zsofia, Csabai, Istvan, Svane, Inge Marie, Szallasi, Zoltan, Jönsson, Göran, and Donia, Marco

Published
2022
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4. BioMEL: a translational research biobank of melanocytic lesions and melanoma

Author

Helkkula, Teo, primary, Christensen, Gustav, additional, Ingvar, Christian, additional, Isaksson, Karolin, additional, Harbst, Katja, additional, Persson, Bertil, additional, Ingvar, Åsa, additional, Hafström, Anna, additional, Carneiro, Ana, additional, Gaspar, Viktoria, additional, Jönsson, Göran, additional, and Nielsen, Kari, additional

Published
2024
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5. 918 Functional heterogeneity of CD4+tumor-infiltrating lymphocytes

Author

Draghi, Arianna, primary, Chamberlain, Christopher A, additional, Khan, Shawez, additional, Harbst, Katja, additional, Presti, Mario, additional, Lauss, Martin, additional, Crowther, Michael D, additional, Jensen, Agnete WP, additional, Rasmussen, Anne-Christine K, additional, Albieri, Benedetta, additional, Lorentzen, Torben, additional, Andersen, Mads H, additional, Jönsson, Göran, additional, Svane, Inge, additional, and Donia, Marco, additional

Published
2023
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6. Distinct mechanisms of resistance to fulvestrant treatment dictate level of ER independence and selective response to CDK inhibitors in metastatic breast cancer

Author

Kaminska, Kamila, Akrap, Nina, Staaf, Johan, Alves, Carla L., Ehinger, Anna, Ebbesson, Anna, Hedenfalk, Ingrid, Beumers, Lukas, Veerla, Srinivas, Harbst, Katja, Ehmsen, Sidse, Borgquist, Signe, Borg, Åke, Pérez-Fidalgo, Alejandro, Ditzel, Henrik J., Bosch, Ana, and Honeth, Gabriella

Published
2021
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7. Tertiary lymphoid structures improve immunotherapy and survival in melanoma

Author

Cabrita, Rita, Lauss, Martin, Sanna, Adriana, Donia, Marco, Skaarup Larsen, Mathilde, Mitra, Shamik, Johansson, Iva, Phung, Bengt, Harbst, Katja, Vallon-Christersson, Johan, van Schoiack, Alison, Lövgren, Kristina, Warren, Sarah, Jirström, Karin, Olsson, Håkan, Pietras, Kristian, Ingvar, Christian, Isaksson, Karolin, Schadendorf, Dirk, Schmidt, Henrik, Bastholt, Lars, Carneiro, Ana, Wargo, Jennifer A., Svane, Inge Marie, and Jönsson, Göran

Published
2020
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8. Association of type and location of BRCA1 and BRCA2 mutations with risk of breast and ovarian cancer.

Author

Rebbeck, Timothy R, Mitra, Nandita, Wan, Fei, Sinilnikova, Olga M, Healey, Sue, McGuffog, Lesley, Mazoyer, Sylvie, Chenevix-Trench, Georgia, Easton, Douglas F, Antoniou, Antonis C, Nathanson, Katherine L, CIMBA Consortium, Laitman, Yael, Kushnir, Anya, Paluch-Shimon, Shani, Berger, Raanan, Zidan, Jamal, Friedman, Eitan, Ehrencrona, Hans, Stenmark-Askmalm, Marie, Einbeigi, Zakaria, Loman, Niklas, Harbst, Katja, Rantala, Johanna, Melin, Beatrice, Huo, Dezheng, Olopade, Olufunmilayo I, Seldon, Joyce, Ganz, Patricia A, Nussbaum, Robert L, Chan, Salina B, Odunsi, Kunle, Gayther, Simon A, Domchek, Susan M, Arun, Banu K, Lu, Karen H, Mitchell, Gillian, Karlan, Beth Y, Walsh, Christine, Lester, Jenny, Godwin, Andrew K, Pathak, Harsh, Ross, Eric, Daly, Mary B, Whittemore, Alice S, John, Esther M, Miron, Alexander, Terry, Mary Beth, Chung, Wendy K, Goldgar, David E, Buys, Saundra S, Janavicius, Ramunas, Tihomirova, Laima, Tung, Nadine, Dorfling, Cecilia M, van Rensburg, Elizabeth J, Steele, Linda, Neuhausen, Susan L, Ding, Yuan Chun, Ejlertsen, Bent, Gerdes, Anne-Marie, Hansen, Thomas VO, Ramón y Cajal, Teresa, Osorio, Ana, Benitez, Javier, Godino, Javier, Tejada, Maria-Isabel, Duran, Mercedes, Weitzel, Jeffrey N, Bobolis, Kristie A, Sand, Sharon R, Fontaine, Annette, Savarese, Antonella, Pasini, Barbara, Peissel, Bernard, Bonanni, Bernardo, Zaffaroni, Daniela, Vignolo-Lutati, Francesca, Scuvera, Giulietta, Giannini, Giuseppe, Bernard, Loris, Genuardi, Maurizio, Radice, Paolo, Dolcetti, Riccardo, Manoukian, Siranoush, Pensotti, Valeria, Gismondi, Viviana, Yannoukakos, Drakoulis, Fostira, Florentia, Garber, Judy, Torres, Diana, Rashid, Muhammad Usman, Hamann, Ute, Peock, Susan, Frost, Debra, Platte, Radka, Evans, D Gareth, Eeles, Rosalind, Davidson, Rosemarie, and Eccles, Diana

Subjects
CIMBA Consortium, Humans, Breast Neoplasms, Ovarian Neoplasms, Genetic Predisposition to Disease, Nucleotides, Risk Factors, Age of Onset, Heterozygote, Mutation, Genes, BRCA1, Genes, BRCA2, Adult, Middle Aged, Female, Cancer, Prevention, Rare Diseases, Breast Cancer, Clinical Research, Ovarian Cancer, General & Internal Medicine, Medical and Health Sciences
Abstract

ImportanceLimited information about the relationship between specific mutations in BRCA1 or BRCA2 (BRCA1/2) and cancer risk exists.ObjectiveTo identify mutation-specific cancer risks for carriers of BRCA1/2.Design, setting, and participantsObservational study of women who were ascertained between 1937 and 2011 (median, 1999) and found to carry disease-associated BRCA1 or BRCA2 mutations. The international sample comprised 19,581 carriers of BRCA1 mutations and 11,900 carriers of BRCA2 mutations from 55 centers in 33 countries on 6 continents. We estimated hazard ratios for breast and ovarian cancer based on mutation type, function, and nucleotide position. We also estimated RHR, the ratio of breast vs ovarian cancer hazard ratios. A value of RHR greater than 1 indicated elevated breast cancer risk; a value of RHR less than 1 indicated elevated ovarian cancer risk.ExposuresMutations of BRCA1 or BRCA2.Main outcomes and measuresBreast and ovarian cancer risks.ResultsAmong BRCA1 mutation carriers, 9052 women (46%) were diagnosed with breast cancer, 2317 (12%) with ovarian cancer, 1041 (5%) with breast and ovarian cancer, and 7171 (37%) without cancer. Among BRCA2 mutation carriers, 6180 women (52%) were diagnosed with breast cancer, 682 (6%) with ovarian cancer, 272 (2%) with breast and ovarian cancer, and 4766 (40%) without cancer. In BRCA1, we identified 3 breast cancer cluster regions (BCCRs) located at c.179 to c.505 (BCCR1; RHR = 1.46; 95% CI, 1.22-1.74; P = 2 × 10(-6)), c.4328 to c.4945 (BCCR2; RHR = 1.34; 95% CI, 1.01-1.78; P = .04), and c. 5261 to c.5563 (BCCR2', RHR = 1.38; 95% CI, 1.22-1.55; P = 6 × 10(-9)). We also identified an ovarian cancer cluster region (OCCR) from c.1380 to c.4062 (approximately exon 11) with RHR = 0.62 (95% CI, 0.56-0.70; P = 9 × 10(-17)). In BRCA2, we observed multiple BCCRs spanning c.1 to c.596 (BCCR1; RHR = 1.71; 95% CI, 1.06-2.78; P = .03), c.772 to c.1806 (BCCR1'; RHR = 1.63; 95% CI, 1.10-2.40; P = .01), and c.7394 to c.8904 (BCCR2; RHR = 2.31; 95% CI, 1.69-3.16; P = .00002). We also identified 3 OCCRs: the first (OCCR1) spanned c.3249 to c.5681 that was adjacent to c.5946delT (6174delT; RHR = 0.51; 95% CI, 0.44-0.60; P = 6 × 10(-17)). The second OCCR spanned c.6645 to c.7471 (OCCR2; RHR = 0.57; 95% CI, 0.41-0.80; P = .001). Mutations conferring nonsense-mediated decay were associated with differential breast or ovarian cancer risks and an earlier age of breast cancer diagnosis for both BRCA1 and BRCA2 mutation carriers.Conclusions and relevanceBreast and ovarian cancer risks varied by type and location of BRCA1/2 mutations. With appropriate validation, these data may have implications for risk assessment and cancer prevention decision making for carriers of BRCA1 and BRCA2 mutations.

Published
2015

10. Molecular patterns of resistance to immune checkpoint blockade in melanoma

Author

Jonsson, Goran, primary, Lauss, Martin, additional, Phung, Bengt, additional, Borch, Troels, additional, Harbst, Katja, additional, Kaminska, Kamila, additional, Ebbesson, Anna, additional, Hedenfalk, Ingrid, additional, Yuan, Joan, additional, Nielsen, Kari, additional, Ingvar, Christian, additional, Carneiro, Ana, additional, Isaksson, Karolin, additional, Pietras, Kristian, additional, Svane, Inge Marie, additional, and Donia, Marco, additional

Published
2023
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11. Common variants at 12p11, 12q24, 9p21, 9q31.2 and in ZNF365 are associated with breast cancer risk for BRCA1 and/or BRCA2 mutation carriers

Author

Antoniou, Antonis C, Kuchenbaecker, Karoline B, Soucy, Penny, Beesley, Jonathan, Chen, Xiaoqing, McGuffog, Lesley, Lee, Andrew, Barrowdale, Daniel, Healey, Sue, Sinilnikova, Olga M, Caligo, Maria A, Loman, Niklas, Harbst, Katja, Lindblom, Annika, Arver, Brita, Rosenquist, Richard, Karlsson, Per, Nathanson, Kate, Domchek, Susan, Rebbeck, Tim, Jakubowska, Anna, Lubinski, Jan, Jaworska, Katarzyna, Durda, Katarzyna, Złowowcka-Perłowska, Elżbieta, Osorio, Ana, Durán, Mercedes, Andrés, Raquel, Benítez, Javier, Hamann, Ute, Hogervorst, Frans B, van Os, Theo A, Verhoef, Senno, Meijers-Heijboer, Hanne EJ, Wijnen, Juul, Gómez Garcia, Encarna B, Ligtenberg, Marjolijn J, Kriege, Mieke, Collée, J Margriet, Ausems, Margreet GEM, Oosterwijk, Jan C, Peock, Susan, Frost, Debra, Ellis, Steve D, Platte, Radka, Fineberg, Elena, Evans, D Gareth, Lalloo, Fiona, Jacobs, Chris, Eeles, Ros, Adlard, Julian, Davidson, Rosemarie, Cole, Trevor, Cook, Jackie, Paterson, Joan, Douglas, Fiona, Brewer, Carole, Hodgson, Shirley, Morrison, Patrick J, Walker, Lisa, Rogers, Mark T, Donaldson, Alan, Dorkins, Huw, Godwin, Andrew K, Bove, Betsy, Stoppa-Lyonnet, Dominique, Houdayer, Claude, Buecher, Bruno, de Pauw, Antoine, Mazoyer, Sylvie, Calender, Alain, Léoné, Mélanie, Bressac- de Paillerets, Brigitte, Caron, Olivier, Sobol, Hagay, Frenay, Marc, Prieur, Fabienne, Ferrer, Sandra, Mortemousque, Isabelle, Buys, Saundra, Daly, Mary, Miron, Alexander, Terry, Mary, Hopper, John L, John, Esther M, Southey, Melissa, Goldgar, David, Singer, Christian F, Fink-Retter, Anneliese, Tea, Muy-Kheng, Kaulich, Daphne, Hansen, Thomas VO, Nielsen, Finn C, Barkardottir, Rosa B, Gaudet, Mia, Kirchhoff, Tomas, Joseph, Vijai, Dutra-Clarke, Ana, Offit, Kenneth, and Piedmonte, Marion

Abstract

AbstractIntroductionSeveral common alleles have been shown to be associated with breast and/or ovarian cancer risk for BRCA1 and BRCA2 mutation carriers. Recent genome-wide association studies of breast cancer have identified eight additional breast cancer susceptibility loci: rs1011970 (9p21, CDKN2A/B), rs10995190 (ZNF365), rs704010 (ZMIZ1), rs2380205 (10p15), rs614367 (11q13), rs1292011 (12q24), rs10771399 (12p11 near PTHLH) and rs865686 (9q31.2). MethodsTo evaluate whether these single nucleotide polymorphisms (SNPs) are associated with breast cancer risk for BRCA1 and BRCA2 carriers, we genotyped these SNPs in 12599 BRCA1 and 7132 BRCA2 mutation carriers and analysed the associations with breast cancer risk within a retrospective likelihood framework. ResultsOnly SNP rs10771399 near PTHLH was associated with breast cancer risk for BRCA1 mutation carriers (per-allele Hazard Ratio (HR)= 0.87, 95%CI:0.81-0.94, P-trend=3x10^-4). The association was restricted to mutations proven or predicted to lead to absence of protein expression (HR=0.82, 95%CI:0.74-0.90, P-trend=3.1x10^-5, P-difference=0.03). Four SNPs were associated with the risk of breast cancer for BRCA2 mutation carriers: rs10995190, P-trend=0.015; rs1011970, P-trend=0.048; rs865686, 2df-P=0.007; rs1292011 2df-P=0.03. rs10771399 (PTHLH) was predominantly associated with estrogen receptor (ER)-negative breast cancer for BRCA1 mutation carriers (HR=0.81, 95%CI: 0.74-0.90, P-trend=4x10^-5) and there was marginal evidence of association with ER-negative breast cancer for BRCA2 mutation carriers (HR=0.78, 95%CI:0.62-1.00, P-trend=0.049). ConclusionsThe present findings, in combination with previously identified modifiers of risk, will ultimately lead to more accurate risk prediction and an improved understanding of the disease etiology in BRCA1 and BRCA2 mutation carriers.

Published
2012

13. 159930_1_supp_0_n72rg6.xls from Multiregion Whole-Exome Sequencing Uncovers the Genetic Evolution and Mutational Heterogeneity of Early-Stage Metastatic Melanoma

Author

Harbst, Katja, primary, Lauss, Martin, primary, Cirenajwis, Helena, primary, Isaksson, Karolin, primary, Rosengren, Frida, primary, Törngren, Therese, primary, Kvist, Anders, primary, Johansson, Maria C., primary, Vallon-Christersson, Johan, primary, Baldetorp, Bo, primary, Borg, Åke, primary, Olsson, Håkan, primary, Ingvar, Christian, primary, Carneiro, Ana, primary, and Jönsson, Göran, primary

Published
2023
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14. Data from Acquired Immune Resistance Follows Complete Tumor Regression without Loss of Target Antigens or IFNγ Signaling

Author

Donia, Marco, primary, Harbst, Katja, primary, van Buuren, Marit, primary, Kvistborg, Pia, primary, Lindberg, Mattias F., primary, Andersen, Rikke, primary, Idorn, Manja, primary, Munir Ahmad, Shamaila, primary, Ellebæk, Eva, primary, Mueller, Anja, primary, Fagone, Paolo, primary, Nicoletti, Ferdinando, primary, Libra, Massimo, primary, Lauss, Martin, primary, Hadrup, Sine Reker, primary, Schmidt, Henrik, primary, Andersen, Mads Hald, primary, thor Straten, Per, primary, Nilsson, Jonas A., primary, Schumacher, Ton N., primary, Seliger, Barbara, primary, Jönsson, Göran, primary, and Svane, Inge Marie, primary

Published
2023
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15. Supplementary Methods, Figures 3-5 from Molecular Profiling Reveals Low- and High-Grade Forms of Primary Melanoma

Author

Harbst, Katja, primary, Staaf, Johan, primary, Lauss, Martin, primary, Karlsson, Anna, primary, Måsbäck, Anna, primary, Johansson, Iva, primary, Bendahl, Pär-Ola, primary, Vallon-Christersson, Johan, primary, Törngren, Therese, primary, Ekedahl, Henrik, primary, Geisler, Jürgen, primary, Höglund, Mattias, primary, Ringnér, Markus, primary, Lundgren, Lotta, primary, Jirström, Karin, primary, Olsson, Håkan, primary, Ingvar, Christian, primary, Borg, Åke, primary, Tsao, Hensin, primary, and Jönsson, Göran, primary

Published
2023
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16. Supplementary Figure S1-S5 from Acquired Immune Resistance Follows Complete Tumor Regression without Loss of Target Antigens or IFNγ Signaling

Author

Donia, Marco, primary, Harbst, Katja, primary, van Buuren, Marit, primary, Kvistborg, Pia, primary, Lindberg, Mattias F., primary, Andersen, Rikke, primary, Idorn, Manja, primary, Munir Ahmad, Shamaila, primary, Ellebæk, Eva, primary, Mueller, Anja, primary, Fagone, Paolo, primary, Nicoletti, Ferdinando, primary, Libra, Massimo, primary, Lauss, Martin, primary, Hadrup, Sine Reker, primary, Schmidt, Henrik, primary, Andersen, Mads Hald, primary, thor Straten, Per, primary, Nilsson, Jonas A., primary, Schumacher, Ton N., primary, Seliger, Barbara, primary, Jönsson, Göran, primary, and Svane, Inge Marie, primary

Published
2023
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17. Supplementary Table 4 from Molecular Profiling Reveals Low- and High-Grade Forms of Primary Melanoma

Author

Harbst, Katja, primary, Staaf, Johan, primary, Lauss, Martin, primary, Karlsson, Anna, primary, Måsbäck, Anna, primary, Johansson, Iva, primary, Bendahl, Pär-Ola, primary, Vallon-Christersson, Johan, primary, Törngren, Therese, primary, Ekedahl, Henrik, primary, Geisler, Jürgen, primary, Höglund, Mattias, primary, Ringnér, Markus, primary, Lundgren, Lotta, primary, Jirström, Karin, primary, Olsson, Håkan, primary, Ingvar, Christian, primary, Borg, Åke, primary, Tsao, Hensin, primary, and Jönsson, Göran, primary

Published
2023
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18. Data from Multiregion Whole-Exome Sequencing Uncovers the Genetic Evolution and Mutational Heterogeneity of Early-Stage Metastatic Melanoma

Author

Harbst, Katja, primary, Lauss, Martin, primary, Cirenajwis, Helena, primary, Isaksson, Karolin, primary, Rosengren, Frida, primary, Törngren, Therese, primary, Kvist, Anders, primary, Johansson, Maria C., primary, Vallon-Christersson, Johan, primary, Baldetorp, Bo, primary, Borg, Åke, primary, Olsson, Håkan, primary, Ingvar, Christian, primary, Carneiro, Ana, primary, and Jönsson, Göran, primary

Published
2023
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19. Supplementary Table 3 from Molecular Profiling Reveals Low- and High-Grade Forms of Primary Melanoma

Author

Harbst, Katja, primary, Staaf, Johan, primary, Lauss, Martin, primary, Karlsson, Anna, primary, Måsbäck, Anna, primary, Johansson, Iva, primary, Bendahl, Pär-Ola, primary, Vallon-Christersson, Johan, primary, Törngren, Therese, primary, Ekedahl, Henrik, primary, Geisler, Jürgen, primary, Höglund, Mattias, primary, Ringnér, Markus, primary, Lundgren, Lotta, primary, Jirström, Karin, primary, Olsson, Håkan, primary, Ingvar, Christian, primary, Borg, Åke, primary, Tsao, Hensin, primary, and Jönsson, Göran, primary

Published
2023
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20. Supplementary Figure 2 from Molecular Profiling Reveals Low- and High-Grade Forms of Primary Melanoma

Author

Harbst, Katja, primary, Staaf, Johan, primary, Lauss, Martin, primary, Karlsson, Anna, primary, Måsbäck, Anna, primary, Johansson, Iva, primary, Bendahl, Pär-Ola, primary, Vallon-Christersson, Johan, primary, Törngren, Therese, primary, Ekedahl, Henrik, primary, Geisler, Jürgen, primary, Höglund, Mattias, primary, Ringnér, Markus, primary, Lundgren, Lotta, primary, Jirström, Karin, primary, Olsson, Håkan, primary, Ingvar, Christian, primary, Borg, Åke, primary, Tsao, Hensin, primary, and Jönsson, Göran, primary

Published
2023
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21. Supplementary Methods and References from Multiregion Whole-Exome Sequencing Uncovers the Genetic Evolution and Mutational Heterogeneity of Early-Stage Metastatic Melanoma

Author

Harbst, Katja, primary, Lauss, Martin, primary, Cirenajwis, Helena, primary, Isaksson, Karolin, primary, Rosengren, Frida, primary, Törngren, Therese, primary, Kvist, Anders, primary, Johansson, Maria C., primary, Vallon-Christersson, Johan, primary, Baldetorp, Bo, primary, Borg, Åke, primary, Olsson, Håkan, primary, Ingvar, Christian, primary, Carneiro, Ana, primary, and Jönsson, Göran, primary

Published
2023
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22. Supplementary Table 2 from Molecular Profiling Reveals Low- and High-Grade Forms of Primary Melanoma

Author

Harbst, Katja, primary, Staaf, Johan, primary, Lauss, Martin, primary, Karlsson, Anna, primary, Måsbäck, Anna, primary, Johansson, Iva, primary, Bendahl, Pär-Ola, primary, Vallon-Christersson, Johan, primary, Törngren, Therese, primary, Ekedahl, Henrik, primary, Geisler, Jürgen, primary, Höglund, Mattias, primary, Ringnér, Markus, primary, Lundgren, Lotta, primary, Jirström, Karin, primary, Olsson, Håkan, primary, Ingvar, Christian, primary, Borg, Åke, primary, Tsao, Hensin, primary, and Jönsson, Göran, primary

Published
2023
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23. Supplementary Figure 1 from Molecular Profiling Reveals Low- and High-Grade Forms of Primary Melanoma

Author

Harbst, Katja, primary, Staaf, Johan, primary, Lauss, Martin, primary, Karlsson, Anna, primary, Måsbäck, Anna, primary, Johansson, Iva, primary, Bendahl, Pär-Ola, primary, Vallon-Christersson, Johan, primary, Törngren, Therese, primary, Ekedahl, Henrik, primary, Geisler, Jürgen, primary, Höglund, Mattias, primary, Ringnér, Markus, primary, Lundgren, Lotta, primary, Jirström, Karin, primary, Olsson, Håkan, primary, Ingvar, Christian, primary, Borg, Åke, primary, Tsao, Hensin, primary, and Jönsson, Göran, primary

Published
2023
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24. Supplementary Table 1 from Molecular Profiling Reveals Low- and High-Grade Forms of Primary Melanoma

Author

Harbst, Katja, primary, Staaf, Johan, primary, Lauss, Martin, primary, Karlsson, Anna, primary, Måsbäck, Anna, primary, Johansson, Iva, primary, Bendahl, Pär-Ola, primary, Vallon-Christersson, Johan, primary, Törngren, Therese, primary, Ekedahl, Henrik, primary, Geisler, Jürgen, primary, Höglund, Mattias, primary, Ringnér, Markus, primary, Lundgren, Lotta, primary, Jirström, Karin, primary, Olsson, Håkan, primary, Ingvar, Christian, primary, Borg, Åke, primary, Tsao, Hensin, primary, and Jönsson, Göran, primary

Published
2023
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25. Supplementary Figure Legends 53 from Molecular Profiling Reveals Low- and High-Grade Forms of Primary Melanoma

Author

Harbst, Katja, primary, Staaf, Johan, primary, Lauss, Martin, primary, Karlsson, Anna, primary, Måsbäck, Anna, primary, Johansson, Iva, primary, Bendahl, Pär-Ola, primary, Vallon-Christersson, Johan, primary, Törngren, Therese, primary, Ekedahl, Henrik, primary, Geisler, Jürgen, primary, Höglund, Mattias, primary, Ringnér, Markus, primary, Lundgren, Lotta, primary, Jirström, Karin, primary, Olsson, Håkan, primary, Ingvar, Christian, primary, Borg, Åke, primary, Tsao, Hensin, primary, and Jönsson, Göran, primary

Published
2023
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26. Supplementary Figures S1-S15 from Multiregion Whole-Exome Sequencing Uncovers the Genetic Evolution and Mutational Heterogeneity of Early-Stage Metastatic Melanoma

Author

Harbst, Katja, primary, Lauss, Martin, primary, Cirenajwis, Helena, primary, Isaksson, Karolin, primary, Rosengren, Frida, primary, Törngren, Therese, primary, Kvist, Anders, primary, Johansson, Maria C., primary, Vallon-Christersson, Johan, primary, Baldetorp, Bo, primary, Borg, Åke, primary, Olsson, Håkan, primary, Ingvar, Christian, primary, Carneiro, Ana, primary, and Jönsson, Göran, primary

Published
2023
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27. Supplementary Methods from Acquired Immune Resistance Follows Complete Tumor Regression without Loss of Target Antigens or IFNγ Signaling

Author

Donia, Marco, primary, Harbst, Katja, primary, van Buuren, Marit, primary, Kvistborg, Pia, primary, Lindberg, Mattias F., primary, Andersen, Rikke, primary, Idorn, Manja, primary, Munir Ahmad, Shamaila, primary, Ellebæk, Eva, primary, Mueller, Anja, primary, Fagone, Paolo, primary, Nicoletti, Ferdinando, primary, Libra, Massimo, primary, Lauss, Martin, primary, Hadrup, Sine Reker, primary, Schmidt, Henrik, primary, Andersen, Mads Hald, primary, thor Straten, Per, primary, Nilsson, Jonas A., primary, Schumacher, Ton N., primary, Seliger, Barbara, primary, Jönsson, Göran, primary, and Svane, Inge Marie, primary

Published
2023
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28. 1021 A pan-cancer signature identifies tumor-reacting CD8+TILs and reveals their functional heterogeneity

Author

Chamberlain, Christopher, primary, Draghi, Arianna, additional, Khan, Shawez, additional, Harbst, Katja, additional, Presti, Mario, additional, Schina, Aimilia, additional, Præst Jensen, Agnete Witness, additional, Rasmussen, Anne-Christine Kiel, additional, Lorentzen, Torben, additional, Schou, Jakob Vasehus, additional, Jönsson, Göran, additional, Svane, Inge, additional, and Donia, Marco, additional

Published
2022
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29. DNA promoter hypermethylation of melanocyte lineage genes determines melanoma phenotype

Author

Sanna, Adriana, primary, Phung, Bengt, additional, Mitra, Shamik, additional, Lauss, Martin, additional, Choi, Jiyeon, additional, Zhang, Tongwu, additional, Njauw, Ching-Ni, additional, Cordero, Eugenia, additional, Harbst, Katja, additional, Rosengren, Frida, additional, Cabrita, Rita, additional, Johansson, Iva, additional, Isaksson, Karolin, additional, Ingvar, Christian, additional, Carneiro, Ana, additional, Brown, Kevin, additional, Tsao, Hensin, additional, Andersson, My, additional, Pietras, Kristian, additional, and Jönsson, Göran, additional

Published
2022
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30. Author Correction: Tertiary lymphoid structures improve immunotherapy and survival in melanoma

Author

Cabrita, Rita, Lauss, Martin, Sanna, Adriana, Donia, Marco, Skaarup Larsen, Mathilde, Mitra, Shamik, Johansson, Iva, Phung, Bengt, Harbst, Katja, Vallon-Christersson, Johan, van Schoiack, Alison, Lövgren, Kristina, Warren, Sarah, Jirström, Karin, Olsson, Håkan, Pietras, Kristian, Ingvar, Christian, Isaksson, Karolin, Schadendorf, Dirk, Schmidt, Henrik, Bastholt, Lars, Carneiro, Ana, Wargo, Jennifer A., Svane, Inge Marie, and Jönsson, Göran

Published
2020
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33. Tumor genetic heterogeneity analysis of chronic sun‐damaged melanoma

Author

Sanna, Adriana, Harbst, Katja, Johansson, Iva, Christensen, Gustav, Lauss, Martin, Mitra, Shamik, Rosengren, Frida, Häkkinen, Jari, Vallon‐Christersson, Johan, Olsson, Håkan, Ingvar, Åsa, Isaksson, Karolin, Ingvar, Christian, Nielsen, Kari, and Jönsson, Göran

Subjects
in situ, melanoma, chronic sun damage, Original Article, Original Articles, heterogeneity, invasive, neoplasms
Abstract

Chronic sun‐damaged (CSD) melanoma represents 10%–20% of cutaneous melanomas and is characterized by infrequent BRAF V600E mutations and high mutational load. However, the order of genetic events or the extent of intra‐tumor heterogeneity (ITH) in CSDhigh melanoma is still unknown. Ultra‐deep targeted sequencing of 40 cancer‐associated genes was performed in 72 in situ or invasive CMM, including 23 CSDhigh cases. In addition, we performed whole exome and RNA sequencing on multiple regions of primary tumor and multiple in‐transit metastases from one CSDhigh melanoma patient. We found no significant difference in mutation frequency in melanoma‐related genes or in mutational load between in situ and invasive CSDhigh lesions, while this difference was observed in CSDlow lesions. In addition, increased frequency of BRAF V600K, NF1, and TP53 mutations (p 95% shared mutations. Our results provide evidence that CSDhigh and CSDlow melanomas are distinct molecular entities that progress via different genetic routes.

Published
2019

34. Rapid Identification of the Tumor-Specific Reactive TIL Repertoire via Combined Detection of CD137, TNF, and IFNγ, Following Recognition of Autologous Tumor-Antigens

Author

Draghi, Arianna, primary, Chamberlain, Christopher Aled, additional, Khan, Shawez, additional, Papp, Krisztian, additional, Lauss, Martin, additional, Soraggi, Samuele, additional, Radic, Haja Dominike, additional, Presti, Mario, additional, Harbst, Katja, additional, Gokuldass, Aishwarya, additional, Kverneland, Anders, additional, Nielsen, Morten, additional, Westergaard, Marie Christine Wulff, additional, Andersen, Mads Hald, additional, Csabai, Istvan, additional, Jönsson, Göran, additional, Szallasi, Zoltan, additional, Svane, Inge Marie, additional, and Donia, Marco, additional

Published
2021
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35. Transcriptomic signatures of tumors undergoing T cell attack

Author

Gokuldass, Aishwarya, primary, Schina, Aimilia, additional, Lauss, Martin, additional, Harbst, Katja, additional, Chamberlain, Christopher Aled, additional, Draghi, Arianna, additional, Westergaard, Marie Christine Wulff, additional, Nielsen, Morten, additional, Papp, Krisztian, additional, Sztupinszki, Zsofia, additional, Csabai, Istvan, additional, Svane, Inge Marie, additional, Szallasi, Zoltan, additional, Jönsson, Göran, additional, and Donia, Marco, additional

Published
2021
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36. Clinical efficacy of T-cell therapy after short-term BRAF-inhibitor priming in patients with checkpoint inhibitor-resistant metastatic melanoma

Author

Borch, Troels Holz, primary, Harbst, Katja, additional, Rana, Aynal Haque, additional, Andersen, Rikke, additional, Martinenaite, Evelina, additional, Kongsted, Per, additional, Pedersen, Magnus, additional, Nielsen, Morten, additional, Kjeldsen, Julie Westerlin, additional, Kverneland, Anders Handrup, additional, Lauss, Martin, additional, Hölmich, Lisbet Rosenkrantz, additional, Hendel, Helle, additional, Met, Özcan, additional, Jönsson, Göran, additional, Donia, Marco, additional, and Marie Svane, Inge, additional

Published
2021
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37. Additional file 4 of Distinct mechanisms of resistance to fulvestrant treatment dictate level of ER independence and selective response to CDK inhibitors in metastatic breast cancer

Author

Kaminska, Kamila, Akrap, Nina, Staaf, Johan, Alves, Carla L., Ehinger, Anna, Ebbesson, Anna, Hedenfalk, Ingrid, Beumers, Lukas, Veerla, Srinivas, Harbst, Katja, Ehmsen, Sidse, Borgquist, Signe, Borg, Åke, Pérez-Fidalgo, Alejandro, Ditzel, Henrik J., Bosch, Ana, and Honeth, Gabriella

Abstract

Additional file 4. Figure showing quantification of western blotting band intensities. Quantification of western blotting band intensities presented in Fig. 1c, 2a-c and 5a as well as Additional Files 3F, 5A-C and 9B. Combined data from at least three biological replicates. Bands were normalized to total lane protein and set relative to untreated parental cells, except for CDK6 in (J, L and M) that where set relative to fulvestrant-resistant cells. Statistical differences were determined with one-way ANOVA and Dunnett’s post-hoc test, * represents p-value ≤0.05, ** ≤0.01 and *** ≤0.001 compared to respective untreated parental control.

Published
2021
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38. Additional file 5 of Distinct mechanisms of resistance to fulvestrant treatment dictate level of ER independence and selective response to CDK inhibitors in metastatic breast cancer

Author

Kaminska, Kamila, Akrap, Nina, Staaf, Johan, Alves, Carla L., Ehinger, Anna, Ebbesson, Anna, Hedenfalk, Ingrid, Beumers, Lukas, Veerla, Srinivas, Harbst, Katja, Ehmsen, Sidse, Borgquist, Signe, Borg, Åke, Pérez-Fidalgo, Alejandro, Ditzel, Henrik J., Bosch, Ana, and Honeth, Gabriella

Abstract

Additional file 5. Figure showing fulvestrant-withdrawal data for the ZR-75-1, T47D and EFM-19 models. Fulvestrant dose-response curves (5 nM to 10 μM) and western blotting for ERα expression in fulvestrant-resistant (-FR) ZR-75-1 (A), T47D (B) and EFM-19 (C) cells cultured either continuously with fulvestrant (+F, red solid lines) or after removal of fulvestrant (-F, red dotted lines) from the growth media for the indicated times (Week 1-Week 9). Parental (-P) cells cultured without fulvestrant were used as control (black solid lines). Graphs represent combined data (average ± SEM) from three biological replicates with at least three technical replicates each. Samples for western blotting were collected at each time-point and ERα protein expression was assessed. β-actin was used as loading control. Representative data from three biological replicates is presented under each graph. Quantification of band intensities is presented in Additional file 4E-G. Stars indicate differences between fulvestrant-resistant cells grown with (red, solid lines) or without (red, dotted lines) fulvestrant. Stars are indicated at every other data point due to restricted space.

Published
2021
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39. Additional file 2 of Distinct mechanisms of resistance to fulvestrant treatment dictate level of ER independence and selective response to CDK inhibitors in metastatic breast cancer

Author

Kaminska, Kamila, Akrap, Nina, Staaf, Johan, Alves, Carla L., Ehinger, Anna, Ebbesson, Anna, Hedenfalk, Ingrid, Beumers, Lukas, Veerla, Srinivas, Harbst, Katja, Ehmsen, Sidse, Borgquist, Signe, Borg, Åke, Pérez-Fidalgo, Alejandro, Ditzel, Henrik J., Bosch, Ana, and Honeth, Gabriella

Abstract

Additional file 2. Table showing patient characteristics for patient samples pre and post fulvestrant treatment.

Published
2021
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40. Additional file 10 of Distinct mechanisms of resistance to fulvestrant treatment dictate level of ER independence and selective response to CDK inhibitors in metastatic breast cancer

Author

Kaminska, Kamila, Akrap, Nina, Staaf, Johan, Alves, Carla L., Ehinger, Anna, Ebbesson, Anna, Hedenfalk, Ingrid, Beumers, Lukas, Veerla, Srinivas, Harbst, Katja, Ehmsen, Sidse, Borgquist, Signe, Borg, Åke, Pérez-Fidalgo, Alejandro, Ditzel, Henrik J., Bosch, Ana, and Honeth, Gabriella

Abstract

Additional file 10. Figure showing survival analyses of cyclin E1 and E2 in fulvestrant-treated metastatic breast cancer patients. Kaplan-Meier plot for overall survival (OS) in cyclin E2 low versus high expression in ER+ metastatic breast cancer patients treated with fulvestrant in the advanced setting (A) and for progression-free (PFS) (B) and overall (C) survival in cyclin E1 low versus high expression in the same patient material. P-value represents log-rank test for OS and PFS, respectively, between patients with high and low levels of cyclin E1 or E2 expression.

Published
2021
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41. Additional file 7 of Distinct mechanisms of resistance to fulvestrant treatment dictate level of ER independence and selective response to CDK inhibitors in metastatic breast cancer

Author

Kaminska, Kamila, Akrap, Nina, Staaf, Johan, Alves, Carla L., Ehinger, Anna, Ebbesson, Anna, Hedenfalk, Ingrid, Beumers, Lukas, Veerla, Srinivas, Harbst, Katja, Ehmsen, Sidse, Borgquist, Signe, Borg, Åke, Pérez-Fidalgo, Alejandro, Ditzel, Henrik J., Bosch, Ana, and Honeth, Gabriella

Abstract

Additional file 7. Figure showing BAF and LogR files for copy number data. B allele frequency (BAF) and LogR genome-wide plots for SNP profiled cell line data presented in Fig. 4a. Chromosomes are ordered along the x-axis from 1 (left) to Y (right). Green lines represent segments derived from ASCAT 2 segmentation of the data.

Published
2021
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42. Additional file 3 of Distinct mechanisms of resistance to fulvestrant treatment dictate level of ER independence and selective response to CDK inhibitors in metastatic breast cancer

Author

Kaminska, Kamila, Akrap, Nina, Staaf, Johan, Alves, Carla L., Ehinger, Anna, Ebbesson, Anna, Hedenfalk, Ingrid, Beumers, Lukas, Veerla, Srinivas, Harbst, Katja, Ehmsen, Sidse, Borgquist, Signe, Borg, Åke, Pérez-Fidalgo, Alejandro, Ditzel, Henrik J., Bosch, Ana, and Honeth, Gabriella

Abstract

Additional file 3. Figure showing that fulvestrant-resistant cells proliferate in the presence of fulvestrant and downregulate ER signaling. A) Time in weeks for each parental cell line to develop resistance to fulvestrant, from initial 100 pM dose until able to proliferate in presence of 100 nM fulvestrant. B) Proliferation curves for parental (-P, black lines) and fulvestrant-resistant (-FR, red lines) cells in the absence (ctrl, solid lines) or presence (+F, dotted lines) of 100 nM fulvestrant assessed using SRB assays (CAMA-1, MCF7, HCC1428, ZR-75-1) or xCELLigence system (T47D, EFM-19). Graphs represent combined data (average ± SEM) from two (xCELLigence) or three (SRB) biological experiments with at least three technical replicates each. Statistical differences were determined with two-way ANOVA and Tukey’s post-hoc test. * represents p-value ≤0.01, ** ≤0.001 and *** ≤0.0001 between fulvestrant-treated parental (black dotted lines) and fulvestrant-resistant (red dotted lines) cells. C) Fulvestrant IC50 values in parental and fulvestrant-resistant cells. Calculated from graphs presented in Fig. 1a. P-values were calculated using Extra sum-of-squares F test. D) Quantitative RT-PCR analysis of RNA expression for the ER downstream target genes insulin like growth factor binding protein 4 (IGFBP4), growth regulation by estrogen in breast cancer 1 (GREB1) and progesterone receptor (PGR) in parental and fulvestrant-resistant cells after 24-h treatment with 100 nM fulvestrant (+F) or no treatment (ctrl). Bar graphs represent average expression (± SEM) from two biological experiments with three technical replicates each, normalized against ACTB expression and set relative to untreated parental cells. Statistical differences were determined with one-way ANOVA and Dunnett’s post-hoc test, *** represents p-value ≤0.001 compared to respective untreated parental control. E) ERE reporter activity in parental and fulvestrant-resistant ZR-75-1, T47D and EFM-19 cells after treatment for 24 h with (+F) or without (-F) supplementation of 100 nM fulvestrant. Graphs represent combined data (average ± SEM) from two biological experiments with two technical replicates each. Statistical differences were determined with one-way ANOVA and Tukey’s post-hoc test, *** represents p-value ≤0.0001 between untreated parental and fulvestrant-resistant cells. F) Western blotting for ERα expression in parental and fulvestrant-resistant ZR-75-1, T47D and EFM-19 cells after treatment for 24 h with 100 nM fulvestrant (+F) or DMSO (-F). Representative data from three biological replicates. β-actin was used as loading control. Quantification of band intensities is presented in Additional file 4A.

Published
2021
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43. Additional file 8 of Distinct mechanisms of resistance to fulvestrant treatment dictate level of ER independence and selective response to CDK inhibitors in metastatic breast cancer

Author

Kaminska, Kamila, Akrap, Nina, Staaf, Johan, Alves, Carla L., Ehinger, Anna, Ebbesson, Anna, Hedenfalk, Ingrid, Beumers, Lukas, Veerla, Srinivas, Harbst, Katja, Ehmsen, Sidse, Borgquist, Signe, Borg, Åke, Pérez-Fidalgo, Alejandro, Ditzel, Henrik J., Bosch, Ana, and Honeth, Gabriella

Abstract

Additional file 8. Table showing common processes enriched in fulvestrant-resistant cells identified by DAVID bioinformatics tool. DAVID functional categories and gene ontology (GO) functions as well as KEGG and Biocarta pathways for genes downregulated upon fulvestrant treatment in parental cells and then upregulated again upon development of resistance. The first table show data for CAMA-1, MCF7 and T47D and the second table show data HCC1428.

Published
2021
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44. Additional file 6 of Distinct mechanisms of resistance to fulvestrant treatment dictate level of ER independence and selective response to CDK inhibitors in metastatic breast cancer

Author

Kaminska, Kamila, Akrap, Nina, Staaf, Johan, Alves, Carla L., Ehinger, Anna, Ebbesson, Anna, Hedenfalk, Ingrid, Beumers, Lukas, Veerla, Srinivas, Harbst, Katja, Ehmsen, Sidse, Borgquist, Signe, Borg, Åke, Pérez-Fidalgo, Alejandro, Ditzel, Henrik J., Bosch, Ana, and Honeth, Gabriella

Abstract

Additional file 6. Figure showing estradiol and tamoxifen response in the ZR-75-1, T47D and EFM-19 models. Relative proliferation of parental and fulvestrant-resistant cells in estrogen depleted (A) or normal (B) growth media with or without supplementation with 1 nM estradiol (E2) (A) or 100 nM 4-hydroxytamoxifen (4-OHT) (B) for 6 days. Each graph represents combined data (average ± SEM) from two biological experiments with three technical replicates each. Statistical differences were determined using one-way ANOVA with Tukey’s post-hoc test. *** represents p-value ≤0.0001, ** ≤0.001, ns represents no statistical differences. Stars and ‘ns’ in (A) indicate statistical differences compared to -E2 for each cell model unless indicated otherwise. Stars and ‘ns’ in (B) indicate statistical differences compared to -4-OHT for each cell model unless indicated otherwise.

Published
2021
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45. Additional file 9 of Distinct mechanisms of resistance to fulvestrant treatment dictate level of ER independence and selective response to CDK inhibitors in metastatic breast cancer

Author

Kaminska, Kamila, Akrap, Nina, Staaf, Johan, Alves, Carla L., Ehinger, Anna, Ebbesson, Anna, Hedenfalk, Ingrid, Beumers, Lukas, Veerla, Srinivas, Harbst, Katja, Ehmsen, Sidse, Borgquist, Signe, Borg, Åke, Pérez-Fidalgo, Alejandro, Ditzel, Henrik J., Bosch, Ana, and Honeth, Gabriella

Abstract

Additional file 9. Figure showing cell cycle regulation and response to CDK inhibitors. A) Cell cycle profiles for parental (-P) and fulvestrant-resistant (-FR) CAMA-1 and MCF7 cells showing the proportion of cells in G0/G1, S, and G2/M phase, respectively, after treatment with 100 nM fulvestrant for 72 h (+F) or untreated (ctrl). Combined data from two biological replicates. Statistical differences between the proportion of cells in G0/G1-phase were calculated using student’s t-test. * represents p-value ≤0.05, ns represents no statistical differences. B) Western blotting for expression of cell cycle regulating proteins in parental and fulvestrant-resistant T47D and EFM-19 cells after treatment for 24 h with 100 nM fulvestrant (+F) or DMSO control (-F). Representative data from three biological replicates. β-actin was used as loading control. Quantification of band intensities is presented in Additional file 4 L-M. C) Palbociclib IC50 values in parental and fulvestrant-resistant cells. Calculated from graphs presented in (D) and in Fig. 5b. D) Dose-response curves for parental and fulvestrant-resistant T47D and EFM-19 cells in response to 6-days treatment with increasing concentrations of the CDK4/6 inhibitor palbociclib (1 nM to 10 μM). Graphs represent combined data (average ± SEM) from three biological experiments with three technical replicates each. IC50 values are shown in (C). E) CDKi3 IC50 values in parental and fulvestrant-resistant cells. Calculated from graphs presented in (F) and in Fig. 5c. F) Dose-response curves for parental and fulvestrant-resistant T47D and EFM-19 cells in response to 6-days treatment with increasing concentrations of the CDK1/2 inhibitor CDKi3 (100 pM to 50 μM). Graphs represent combined data (average ± SEM) from three biological experiments with three technical replicates each. IC50 values are shown in (E). G) Time in weeks needed for each parental and fulvestrant-resistant cell line to develop resistance to palbociclib, counted from initial exposure to 100 pM dose until the cells were able to proliferate in presence of 1 μM palbociclib. H) Dose-response curves for parental (-P, solid black lines), fulvestrant-resistant (-FR, solid red lines), palbociclib-resistant (-PalbRes, black dotted lines) and double fulvestrant- and palbociclib-resistant (-FR-PalbRes, red dotted lines) CAMA-1 and MCF7 cells in response to 6-days treatment with palbociclib (1 pM to 10 μM). Graphs represent combined data (average ± SEM) from two biological experiments with three technical replicates each. IC50 values are shown (I). I) Palbociclib IC50 values for graphs in (H). J) Fulvestrant IC50 values for graphs presented in Fig. 5d. P-values in (C, E, I and J) were calculated using Extra sum-of-squares F test.

Published
2021
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46. Molecular and genetic diversity in the metastatic process of melanoma

Author

Harbst, Katja, Lauss, Martin, Cirenajwis, Helena, Winter, Christof, Howlin, Jillian, Törngren, Therese, Kvist, Anders, Nodin, Björn, Olsson, Eleonor, Häkkinen, Jari, Jirström, Karin, Staaf, Johan, Lundgren, Lotta, Olsson, Håkan, Ingvar, Christian, Gruvberger-Saal, Sofia K, Saal, Lao H, and Jönsson, Göran

Published
2014
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47. Additional file 8 of Exploring the link between MORF4L1 and risk of breast cancer

Author

Martrat, Griselda, Maxwell, Christopher A, Tominaga, Emiko, Porta-De-La-Riva, Montserrat, Bonifaci, Núria, Gómez-Baldó, Laia, Bogliolo, Massimo, Conxi Lázaro, Blanco, Ignacio, Brunet, Joan, Aguilar, Helena, Fernández-Rodríguez, Juana, Seal, Sheila, Renwick, Anthony, Nazneen Rahman, Kühl, Julia, Neveling, Kornelia, Schindler, Detlev, Ramírez, María J, Castellà, María, Hernández, Gonzalo, Easton, Douglas F, Peock, Susan, Cook, Margaret, Oliver, Clare T, Frost, Debra, Platte, Radka, D Gareth Evans, Lalloo, Fiona, Eeles, Rosalind, Izatt, Louise, Chu, Carol, Davidson, Rosemarie, Kai-Ren Ong, Cook, Jackie, Douglas, Fiona, Hodgson, Shirley, Brewer, Carole, Morrison, Patrick J, Porteous, Mary, Peterlongo, Paolo, Manoukian, Siranoush, Peissel, Bernard, Zaffaroni, Daniela, Roversi, Gaia, Barile, Monica, Viel, Alessandra, Pasini, Barbara, Ottini, Laura, Putignano, Anna Laura, Savarese, Antonella, Bernard, Loris, Radice, Paolo, Healey, Sue, Spurdle, Amanda, Xiaoqing Chen, Beesley, Jonathan, Rookus, Matti A, Senno Verhoef, Tilanus-Linthorst, Madeleine A, Vreeswijk, Maaike P, Asperen, Christi J, Bodmer, Danielle, Ausems, Margreet GEM, Os, Theo A Van, Blok, Marinus J, Meijers-Heijboer, Hanne EJ, Hogervorst, Frans BL, Goldgar, David E, Buys, Saundra, John, Esther M, Miron, Alexander, Southey, Melissa, Daly, Mary B, Harbst, Katja, Borg, Åke, Rantala, Johanna, Barbany-Bustinza, Gisela, Ehrencrona, Hans, Stenmark-Askmalm, Marie, Kaufman, Bella, Laitman, Yael, Milgrom, Roni, Friedman, Eitan, Domchek, Susan M, Nathanson, Katherine L, Rebbeck, Timothy R, Johannsson, Oskar Thor, Couch, Fergus J, Xianshu Wang, Fredericksen, Zachary, Cuadras, Daniel, Moreno, Víctor, Pientka, Friederike K, Depping, Reinhard, Caldés, Trinidad, Osorio, Ana, Benítez, Javier, Bueren, Juan, Heikkinen, Tuomas, Nevanlinna, Heli, Hamann, Ute, Torres, Diana, Caligo, Maria Adelaide, Godwin, Andrew K, Imyanitov, Evgeny N, Ramunas Janavicius, Sinilnikova, Olga M, Stoppa-Lyonnet, Dominique, Mazoyer, Sylvie, Verny-Pierre, Carole, Castera, Laurent, Pauw, Antoine De, Yves-Jean Bignon, Uhrhammer, Nancy, Jean-Philippe Peyrat, Vennin, Philippe, Ferrer, Sandra Fert, Marie-Agnès Collonge-Rame, Mortemousque, Isabelle, McGuffog, Lesley, Chenevix-Trench, Georgia, Pereira-Smith, Olivia M, Antoniou, Antonis C, Cerón, Julián, Tominaga, Kaoru, Surrallés, Jordi, and Pujana, Miguel Angel

Abstract

Additional file 8: Co-AP assays involving MRG15 and MRGX. Supplementary Figure 4 containing results of co-AP assays involving MRG15 and MRGX. (PDF 1 MB)

Published
2020
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48. Additional file 7 of Exploring the link between MORF4L1 and risk of breast cancer

Author

Martrat, Griselda, Maxwell, Christopher A, Tominaga, Emiko, Porta-De-La-Riva, Montserrat, Bonifaci, Núria, Gómez-Baldó, Laia, Bogliolo, Massimo, Conxi Lázaro, Blanco, Ignacio, Brunet, Joan, Aguilar, Helena, Fernández-Rodríguez, Juana, Seal, Sheila, Renwick, Anthony, Nazneen Rahman, Kühl, Julia, Neveling, Kornelia, Schindler, Detlev, Ramírez, María J, Castellà, María, Hernández, Gonzalo, Easton, Douglas F, Peock, Susan, Cook, Margaret, Oliver, Clare T, Frost, Debra, Platte, Radka, D Gareth Evans, Lalloo, Fiona, Eeles, Rosalind, Izatt, Louise, Chu, Carol, Davidson, Rosemarie, Kai-Ren Ong, Cook, Jackie, Douglas, Fiona, Hodgson, Shirley, Brewer, Carole, Morrison, Patrick J, Porteous, Mary, Peterlongo, Paolo, Manoukian, Siranoush, Peissel, Bernard, Zaffaroni, Daniela, Roversi, Gaia, Barile, Monica, Viel, Alessandra, Pasini, Barbara, Ottini, Laura, Putignano, Anna Laura, Savarese, Antonella, Bernard, Loris, Radice, Paolo, Healey, Sue, Spurdle, Amanda, Xiaoqing Chen, Beesley, Jonathan, Rookus, Matti A, Senno Verhoef, Tilanus-Linthorst, Madeleine A, Vreeswijk, Maaike P, Asperen, Christi J, Bodmer, Danielle, Ausems, Margreet GEM, Os, Theo A Van, Blok, Marinus J, Meijers-Heijboer, Hanne EJ, Hogervorst, Frans BL, Goldgar, David E, Buys, Saundra, John, Esther M, Miron, Alexander, Southey, Melissa, Daly, Mary B, Harbst, Katja, Borg, Åke, Rantala, Johanna, Barbany-Bustinza, Gisela, Ehrencrona, Hans, Stenmark-Askmalm, Marie, Kaufman, Bella, Laitman, Yael, Milgrom, Roni, Friedman, Eitan, Domchek, Susan M, Nathanson, Katherine L, Rebbeck, Timothy R, Johannsson, Oskar Thor, Couch, Fergus J, Xianshu Wang, Fredericksen, Zachary, Cuadras, Daniel, Moreno, Víctor, Pientka, Friederike K, Depping, Reinhard, Caldés, Trinidad, Osorio, Ana, Benítez, Javier, Bueren, Juan, Heikkinen, Tuomas, Nevanlinna, Heli, Hamann, Ute, Torres, Diana, Caligo, Maria Adelaide, Godwin, Andrew K, Imyanitov, Evgeny N, Ramunas Janavicius, Sinilnikova, Olga M, Stoppa-Lyonnet, Dominique, Mazoyer, Sylvie, Verny-Pierre, Carole, Castera, Laurent, Pauw, Antoine De, Yves-Jean Bignon, Uhrhammer, Nancy, Jean-Philippe Peyrat, Vennin, Philippe, Ferrer, Sandra Fert, Marie-Agnès Collonge-Rame, Mortemousque, Isabelle, McGuffog, Lesley, Chenevix-Trench, Georgia, Pereira-Smith, Olivia M, Antoniou, Antonis C, Cerón, Julián, Tominaga, Kaoru, Surrallés, Jordi, and Pujana, Miguel Angel

Subjects
ComputingMethodologies_PATTERNRECOGNITION, ComputerSystemsOrganization_COMPUTER-COMMUNICATIONNETWORKS, ComputingMethodologies_DOCUMENTANDTEXTPROCESSING, Hardware_INTEGRATEDCIRCUITS, Hardware_REGISTER-TRANSFER-LEVELIMPLEMENTATION
Abstract

Additional file 7: Co-AP and co-IP assays. Supplementary Figure 3 containing results of the co-AP and co-IP assays. (PDF 3 MB)

Published
2020
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49. Additional file 16 of Exploring the link between MORF4L1 and risk of breast cancer

Author

Martrat, Griselda, Maxwell, Christopher A, Tominaga, Emiko, Porta-De-La-Riva, Montserrat, Bonifaci, Núria, Gómez-Baldó, Laia, Bogliolo, Massimo, Conxi Lázaro, Blanco, Ignacio, Brunet, Joan, Aguilar, Helena, Fernández-Rodríguez, Juana, Seal, Sheila, Renwick, Anthony, Nazneen Rahman, Kühl, Julia, Neveling, Kornelia, Schindler, Detlev, Ramírez, María J, Castellà, María, Hernández, Gonzalo, Easton, Douglas F, Peock, Susan, Cook, Margaret, Oliver, Clare T, Frost, Debra, Platte, Radka, D Gareth Evans, Lalloo, Fiona, Eeles, Rosalind, Izatt, Louise, Chu, Carol, Davidson, Rosemarie, Kai-Ren Ong, Cook, Jackie, Douglas, Fiona, Hodgson, Shirley, Brewer, Carole, Morrison, Patrick J, Porteous, Mary, Peterlongo, Paolo, Manoukian, Siranoush, Peissel, Bernard, Zaffaroni, Daniela, Roversi, Gaia, Barile, Monica, Viel, Alessandra, Pasini, Barbara, Ottini, Laura, Putignano, Anna Laura, Savarese, Antonella, Bernard, Loris, Radice, Paolo, Healey, Sue, Spurdle, Amanda, Xiaoqing Chen, Beesley, Jonathan, Rookus, Matti A, Senno Verhoef, Tilanus-Linthorst, Madeleine A, Vreeswijk, Maaike P, Asperen, Christi J, Bodmer, Danielle, Ausems, Margreet GEM, Os, Theo A Van, Blok, Marinus J, Meijers-Heijboer, Hanne EJ, Hogervorst, Frans BL, Goldgar, David E, Buys, Saundra, John, Esther M, Miron, Alexander, Southey, Melissa, Daly, Mary B, Harbst, Katja, Borg, Åke, Rantala, Johanna, Barbany-Bustinza, Gisela, Ehrencrona, Hans, Stenmark-Askmalm, Marie, Kaufman, Bella, Laitman, Yael, Milgrom, Roni, Friedman, Eitan, Domchek, Susan M, Nathanson, Katherine L, Rebbeck, Timothy R, Johannsson, Oskar Thor, Couch, Fergus J, Xianshu Wang, Fredericksen, Zachary, Cuadras, Daniel, Moreno, Víctor, Pientka, Friederike K, Depping, Reinhard, Caldés, Trinidad, Osorio, Ana, Benítez, Javier, Bueren, Juan, Heikkinen, Tuomas, Nevanlinna, Heli, Hamann, Ute, Torres, Diana, Caligo, Maria Adelaide, Godwin, Andrew K, Imyanitov, Evgeny N, Ramunas Janavicius, Sinilnikova, Olga M, Stoppa-Lyonnet, Dominique, Mazoyer, Sylvie, Verny-Pierre, Carole, Castera, Laurent, Pauw, Antoine De, Yves-Jean Bignon, Uhrhammer, Nancy, Jean-Philippe Peyrat, Vennin, Philippe, Ferrer, Sandra Fert, Marie-Agnès Collonge-Rame, Mortemousque, Isabelle, McGuffog, Lesley, Chenevix-Trench, Georgia, Pereira-Smith, Olivia M, Antoniou, Antonis C, Cerón, Julián, Tominaga, Kaoru, Surrallés, Jordi, and Pujana, Miguel Angel

Subjects
Data_FILES
Abstract

Authors’ original file for figure 2

Published
2020
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50. Additional file 5 of Exploring the link between MORF4L1 and risk of breast cancer

Author

Martrat, Griselda, Maxwell, Christopher A, Tominaga, Emiko, Porta-De-La-Riva, Montserrat, Bonifaci, Núria, Gómez-Baldó, Laia, Bogliolo, Massimo, Conxi Lázaro, Blanco, Ignacio, Brunet, Joan, Aguilar, Helena, Fernández-Rodríguez, Juana, Seal, Sheila, Renwick, Anthony, Nazneen Rahman, Kühl, Julia, Neveling, Kornelia, Schindler, Detlev, Ramírez, María J, Castellà, María, Hernández, Gonzalo, Easton, Douglas F, Peock, Susan, Cook, Margaret, Oliver, Clare T, Frost, Debra, Platte, Radka, D Gareth Evans, Lalloo, Fiona, Eeles, Rosalind, Izatt, Louise, Chu, Carol, Davidson, Rosemarie, Kai-Ren Ong, Cook, Jackie, Douglas, Fiona, Hodgson, Shirley, Brewer, Carole, Morrison, Patrick J, Porteous, Mary, Peterlongo, Paolo, Manoukian, Siranoush, Peissel, Bernard, Zaffaroni, Daniela, Roversi, Gaia, Barile, Monica, Viel, Alessandra, Pasini, Barbara, Ottini, Laura, Putignano, Anna Laura, Savarese, Antonella, Bernard, Loris, Radice, Paolo, Healey, Sue, Spurdle, Amanda, Xiaoqing Chen, Beesley, Jonathan, Rookus, Matti A, Senno Verhoef, Tilanus-Linthorst, Madeleine A, Vreeswijk, Maaike P, Asperen, Christi J, Bodmer, Danielle, Ausems, Margreet GEM, Os, Theo A Van, Blok, Marinus J, Meijers-Heijboer, Hanne EJ, Hogervorst, Frans BL, Goldgar, David E, Buys, Saundra, John, Esther M, Miron, Alexander, Southey, Melissa, Daly, Mary B, Harbst, Katja, Borg, Åke, Rantala, Johanna, Barbany-Bustinza, Gisela, Ehrencrona, Hans, Stenmark-Askmalm, Marie, Kaufman, Bella, Laitman, Yael, Milgrom, Roni, Friedman, Eitan, Domchek, Susan M, Nathanson, Katherine L, Rebbeck, Timothy R, Johannsson, Oskar Thor, Couch, Fergus J, Xianshu Wang, Fredericksen, Zachary, Cuadras, Daniel, Moreno, Víctor, Pientka, Friederike K, Depping, Reinhard, Caldés, Trinidad, Osorio, Ana, Benítez, Javier, Bueren, Juan, Heikkinen, Tuomas, Nevanlinna, Heli, Hamann, Ute, Torres, Diana, Caligo, Maria Adelaide, Godwin, Andrew K, Imyanitov, Evgeny N, Ramunas Janavicius, Sinilnikova, Olga M, Stoppa-Lyonnet, Dominique, Mazoyer, Sylvie, Verny-Pierre, Carole, Castera, Laurent, Pauw, Antoine De, Yves-Jean Bignon, Uhrhammer, Nancy, Jean-Philippe Peyrat, Vennin, Philippe, Ferrer, Sandra Fert, Marie-Agnès Collonge-Rame, Mortemousque, Isabelle, McGuffog, Lesley, Chenevix-Trench, Georgia, Pereira-Smith, Olivia M, Antoniou, Antonis C, Cerón, Julián, Tominaga, Kaoru, Surrallés, Jordi, and Pujana, Miguel Angel

Subjects
fungi
Abstract

Additional file 5: Gene co-expression. Supplementary Figure 1 containing results of the gene co-expression analysis. (PDF 638 KB)

Published
2020
Full Text
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