206 results on '"Garred, Øystein"'
Search Results
2. RAB5A expression is a predictive biomarker for trastuzumab emtansine in breast cancer
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Engebraaten, Olav, Yau, Christina, Berg, Kristian, Borgen, Elin, Garred, Øystein, Berstad, Maria EB, Fremstedal, Ane SV, DeMichele, Angela, Veer, Laura van ’t, Esserman, Laura, and Weyergang, Anette
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Biomedical and Clinical Sciences ,Oncology and Carcinogenesis ,Clinical Research ,Clinical Trials and Supportive Activities ,Cancer ,Breast Cancer ,4.1 Discovery and preclinical testing of markers and technologies ,Detection ,screening and diagnosis ,Ado-Trastuzumab Emtansine ,Antibodies ,Monoclonal ,Humanized ,Biomarkers ,Tumor ,Breast Neoplasms ,Female ,Humans ,Trastuzumab ,rab5 GTP-Binding Proteins - Abstract
HER2 is a predictive biomarker for HER2-targeted therapeutics. For antibody-drug conjugates (ADCs; e.g., trastuzumab emtansine (T-DM1)), HER2 is utilized as a transport gate for cytotoxic agents into the cell. ADC biomarkers may therefore be more complex, also reflecting the intracellular drug transport. Here we report on a positive correlation between the early endosome marker RAB5A and T-DM1 sensitivity in five HER2-positive cell lines. Correlation between RAB5A expression and T-DM1 sensitivity is confirmed in breast cancer patients treated with trastuzumab emtansine/pertuzumab in the I-SPY2 trial (NCT01042379), but not in the trastuzumab/paclitaxel control arm. The clinical correlation is further verified in patients from the KAMILLA trial (NCT01702571). In conclusion, our results suggest RAB5A as a predictive biomarker for T-DM1 response and outline proteins involved in endocytic trafficking as predictive biomarkers for ADCs.
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- 2021
3. Atezolizumab plus anthracycline-based chemotherapy in metastatic triple-negative breast cancer: the randomized, double-blind phase 2b ALICE trial
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Røssevold, Andreas Hagen, Andresen, Nikolai Kragøe, Bjerre, Christina Annette, Gilje, Bjørnar, Jakobsen, Erik Hugger, Raj, Sunil Xavier, Falk, Ragnhild Sørum, Russnes, Hege Giercksky, Jahr, Thea, Mathiesen, Randi Ruud, Lømo, Jon, Garred, Øystein, Chauhan, Sudhir Kumar, Lereim, Ragnhild Reehorst, Dunn, Claire, Naume, Bjørn, and Kyte, Jon Amund
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- 2022
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4. Germline HOXB13 mutations p.G84E and p.R217C do not confer an increased breast cancer risk
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Bathen, Tone F, Borgen, Elin, Fritzman, Britt, Garred, Øystein, Geitvik, Gry Aarum, Hofvind, Solveig, Langerød, Anita, Lingjærde, Ole Christian, Mælandsmo, Gunhild Mari, Russnes, Hege G, Skjerven, Helle Kristine, and Sørlie, Therese
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Genetics ,Prevention ,Breast Cancer ,Aging ,Clinical Research ,Cancer ,Aetiology ,Detection ,screening and diagnosis ,2.1 Biological and endogenous factors ,4.1 Discovery and preclinical testing of markers and technologies ,Breast Neoplasms ,Female ,Genetic Predisposition to Disease ,Genotyping Techniques ,Germ-Line Mutation ,Homeodomain Proteins ,Humans ,Middle Aged ,Risk Factors ,NBCS Collaborators ,ABCTB Investigators - Abstract
In breast cancer, high levels of homeobox protein Hox-B13 (HOXB13) have been associated with disease progression of ER-positive breast cancer patients and resistance to tamoxifen treatment. Since HOXB13 p.G84E is a prostate cancer risk allele, we evaluated the association between HOXB13 germline mutations and breast cancer risk in a previous study consisting of 3,270 familial non-BRCA1/2 breast cancer cases and 2,327 controls from the Netherlands. Although both recurrent HOXB13 mutations p.G84E and p.R217C were not associated with breast cancer risk, the risk estimation for p.R217C was not very precise. To provide more conclusive evidence regarding the role of HOXB13 in breast cancer susceptibility, we here evaluated the association between HOXB13 mutations and increased breast cancer risk within 81 studies of the international Breast Cancer Association Consortium containing 68,521 invasive breast cancer patients and 54,865 controls. Both HOXB13 p.G84E and p.R217C did not associate with the development of breast cancer in European women, neither in the overall analysis (OR = 1.035, 95% CI = 0.859-1.246, P = 0.718 and OR = 0.798, 95% CI = 0.482-1.322, P = 0.381 respectively), nor in specific high-risk subgroups or breast cancer subtypes. Thus, although involved in breast cancer progression, HOXB13 is not a material breast cancer susceptibility gene.
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- 2020
5. Characterizations of uveal melanoma patients with three additional primary malignancies.
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Eide, Nils Andreas, Faber, Rowan Thomas, Garred, Øystein, Sørum Falk, Ragnhild, and Robsahm, Trude Eid
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PANCREATIC cancer ,SYMPTOMS ,LUNG cancer ,BREAST cancer ,CARCINOMA ,UVEA cancer - Abstract
Purpose: In a population‐based cohort of 960 uveal melanoma (UM) patients, we describe patients with three additional malignancies, including one unique patient with four synchronous primary malignancies. Method: A descriptive presentation of the clinical course and outcome for UM patients with three additional primary malignancies. Results: After more than 20 years of follow‐up of the UM cohort, 11 patients (1.1%) were diagnosed with three additional primary malignancies before, simultaneously or after UM. Among these, one patient had four synchronous primary malignancies, detected during workup for a symptomatic UM. All diagnoses were treated during the following 4 months, firstly the breast cancer, thereafter, the lung and pancreatic cancers and finally the UM. The patient died 3 years later of abdominal carcinomatosis due to the pancreatic cancer. The family history and gene testing did not disclose any genetic predisposition for cancer. A comparison of the four synchronous tumours, morphologically and immunohistochemically, showed no similarities and the expression of antibodies was different. Conclusion: Patients with UM may be diagnosed with non‐ocular additional primary cancers. Thus, a comprehensive workup is obligatory and a further follow‐up of the UM patients seems necessary. The UM is not always the main problem. [ABSTRACT FROM AUTHOR]
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- 2024
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6. Comprehensive multi-omics analysis of breast cancer reveals distinct long-term prognostic subtypes.
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Sharma, Abhibhav, Debik, Julia, Naume, Bjørn, Ohnstad, Hege Oma, Oslo Breast Cancer Consortium (OSBREAC), Sahlber, Kristine Kleivi, Borgen, Elin, Børresen-Dale, Anne-Lise, Engebråten, Olav, Fritzman, Britt, Garred, Øystein, Geisler, Jürgen, Geitvik, Gry Aarum, Hofvind, Solveig, Kristensen, Vessela N, Kåresen, Rolf, Langerød, Anita, Lingjærde, Ole Christian, Mælandsmo, Gunhild Mari, and Russnes, Hege G
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- 2024
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7. Ipilimumab and nivolumab combined with anthracycline-based chemotherapy in metastatic hormone receptor-positive breast cancer: a randomized phase 2b trial
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Andresen, Nikolai Kragøe, primary, Røssevold, Andreas Hagen, additional, Quaghebeur, Claire, additional, Gilje, Bjørnar, additional, Boge, Beate, additional, Gombos, Andrea, additional, Falk, Ragnhild Sørum, additional, Mathiesen, Randi R., additional, Julsrud, Lars, additional, Garred, Øystein, additional, Russnes, Hege G., additional, Lereim, Ragnhild Reehorst, additional, Chauhan, Sudhir Kumar, additional, Lingjærde, Ole Christian, additional, Dunn, Claire, additional, Naume, Bjørn, additional, and Kyte, Jon Amund, additional
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- 2024
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8. Baseline microvessel density predicts response to neoadjuvant bevacizumab treatment of locally advanced breast cancer
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Krüger, Kristi, Silwal-Pandit, Laxmi, Wik, Elisabeth, Straume, Oddbjørn, Stefansson, Ingunn M., Borgen, Elin, Garred, Øystein, Naume, Bjørn, Engebraaten, Olav, and Akslen, Lars A.
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- 2021
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9. Protein Signature Predicts Response to Neoadjuvant Treatment With Chemotherapy and Bevacizumab in HER2-Negative Breast Cancers
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Haugen, Mads H., Lingjærde, Ole Christian, Hedenfalk, Ingrid, Garred, Øystein, Borgen, Elin, Loman, Niklas, Hatschek, Thomas, Børresen-Dale, Anne-Lise, Naume, Bjørn, Mills, Gordon B., Mælandsmo, Gunhild M., and Engebraaten, Olav
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- 2021
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10. Abstract 2170: Pre-treatment protein landscape in HER2-negative breast cancer treated with carboplatin in a neoadjuvant chemotherapy setting
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Dahle, Maria Aanesland, primary, Egeland, Eivind Valen, additional, Prasmickaite, Lina, additional, Lingjærde, Ole Christian, additional, Russnes, Hege, additional, Garred, Øystein, additional, Smebye, Marianne L., additional, Skjerven, Helle, additional, Schlichting, Ellen, additional, Naume, Bjørn, additional, Mælandsmo, Gunhild, additional, Engebraaten, Olav, additional, and Haugen, Mads H., additional
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- 2023
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11. Data from Toward Personalized Computer Simulation of Breast Cancer Treatment: A Multiscale Pharmacokinetic and Pharmacodynamic Model Informed by Multitype Patient Data
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Lai, Xiaoran, primary, Geier, Oliver M., primary, Fleischer, Thomas, primary, Garred, Øystein, primary, Borgen, Elin, primary, Funke, Simon W., primary, Kumar, Surendra, primary, Rognes, Marie E., primary, Seierstad, Therese, primary, Børresen-Dale, Anne-Lise, primary, Kristensen, Vessela N., primary, Engebraaten, Olav, primary, Köhn-Luque, Alvaro, primary, and Frigessi, Arnoldo, primary
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- 2023
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12. Supplementary Text from Toward Personalized Computer Simulation of Breast Cancer Treatment: A Multiscale Pharmacokinetic and Pharmacodynamic Model Informed by Multitype Patient Data
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Lai, Xiaoran, primary, Geier, Oliver M., primary, Fleischer, Thomas, primary, Garred, Øystein, primary, Borgen, Elin, primary, Funke, Simon W., primary, Kumar, Surendra, primary, Rognes, Marie E., primary, Seierstad, Therese, primary, Børresen-Dale, Anne-Lise, primary, Kristensen, Vessela N., primary, Engebraaten, Olav, primary, Köhn-Luque, Alvaro, primary, and Frigessi, Arnoldo, primary
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- 2023
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13. Supplementary Tables from The Longitudinal Transcriptional Response to Neoadjuvant Chemotherapy with and without Bevacizumab in Breast Cancer
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Silwal-Pandit, Laxmi, primary, Nord, Silje, primary, von der Lippe Gythfeldt, Hedda, primary, Møller, Elen K., primary, Fleischer, Thomas, primary, Rødland, Einar, primary, Krohn, Marit, primary, Borgen, Elin, primary, Garred, Øystein, primary, Olsen, Tone, primary, Vu, Phuong, primary, Skjerven, Helle, primary, Fangberget, Anne, primary, Holmen, Marit M., primary, Schlitchting, Ellen, primary, Wille, Elisabeth, primary, Nordberg Stokke, Mette, primary, Moen Vollan, Hans Kristian, primary, Kristensen, Vessela, primary, Langerød, Anita, primary, Lundgren, Steinar, primary, Wist, Erik, primary, Naume, Bjørn, primary, Lingjærde, Ole Christian, primary, Børresen-Dale, Anne-Lise, primary, and Engebraaten, Olav, primary
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- 2023
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14. Abstract PD11-11: PD11-11 Results from ALICE – Atezolizumab Combined with Immunogenic Chemotherapy in Patients with Metastatic Triple Negative Breast Cancer, a Randomized Phase IIb Trial
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Kyte, Jon Amund, primary, Røssevold, Andreas H., additional, Andresen, Nikolai K., additional, Bjerre, Christina Annette, additional, Gilje, Bjørnar, additional, Jakobsen, Erik Hugger, additional, Raj, Sunil Xavier, additional, Falk, Ragnhild Sørum, additional, Borgen, Elin, additional, Jahr, Thea, additional, Garred, Øystein, additional, Lømo, Jon, additional, Mathiesen, Randi Margit, additional, and Naume, Bjørn, additional
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- 2023
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15. Thapsigargin-Induced Transport of Cholera Toxin to the Endoplasmic Reticulum
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Sandvig, Kirsten, Garred, Oystein, and Van Deurs, Bo
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- 1996
16. Breast cancer quantitative proteome and proteogenomic landscape
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Johansson, Henrik J., Socciarelli, Fabio, Vacanti, Nathaniel M., Haugen, Mads H., Zhu, Yafeng, Siavelis, Ioannis, Fernandez-Woodbridge, Alejandro, Aure, Miriam R., Sennblad, Bengt, Vesterlund, Mattias, Branca, Rui M., Orre, Lukas M., Huss, Mikael, Fredlund, Erik, Beraki, Elsa, Garred, Øystein, Boekel, Jorrit, Sauer, Torill, Zhao, Wei, Nord, Silje, Höglander, Elen K., Jans, Daniel C., Brismar, Hjalmar, Haukaas, Tonje H., Bathen, Tone F., Schlichting, Ellen, Naume, Bjørn, Consortia Oslo Breast Cancer Research Consortium (OSBREAC), Luders, Torben, Borgen, Elin, Kristensen, Vessela N., Russnes, Hege G., Lingjærde, Ole Christian, Mills, Gordon B., Sahlberg, Kristine K., Børresen-Dale, Anne-Lise, and Lehtiö, Janne
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- 2019
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17. Time series analysis of neoadjuvant chemotherapy and bevacizumab-treated breast carcinomas reveals a systemic shift in genomic aberrations
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Höglander, Elen Kristine, Nord, Silje, Wedge, David C., Lingjærde, Ole Christian, Silwal-Pandit, Laxmi, Gythfeldt, Hedda vdL, Vollan, Hans Kristian Moen, Fleischer, Thomas, Krohn, Marit, Schlitchting, Ellen, Borgen, Elin, Garred, Øystein, Holmen, Marit M., Wist, Erik, Naume, Bjørn, Van Loo, Peter, Børresen-Dale, Anne-Lise, Engebraaten, Olav, and Kristensen, Vessela
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- 2018
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18. A deep learning system accurately classifies primary and metastatic cancers using passenger mutation patterns
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Jiao, Wei, Atwal, Gurnit, Polak, Paz, Karlic, Rosa, Cuppen, Edwin, Al-Shahrour, Fatima, Bailey, Peter J, Biankin, Andrew V, Boutros, Paul C, Campbell, Peter J, Chang, David K, Cooke, Susanna L, Deshpande, Vikram, Faltas, Bishoy M, Faquin, William C, Garraway, Levi, Getz, Gad, Grimmond, Sean M, Haider, Syed, Hoadley, Katherine A, Kaiser, Vera B, Kato, Mamoru, Kübler, Kirsten, Lazar, Alexander J, Li, Constance H, Louis, David N, Margolin, Adam, Martin, Sancha, Nahal-Bose, Hardeep K, Nielsen, G Petur, Nik-Zainal, Serena, Omberg, Larsson, P’ng, Christine, Perry, Marc D, Rheinbay, Esther, Rubin, Mark A, Semple, Colin A, Sgroi, Dennis C, Shibata, Tatsuhiro, Siebert, Reiner, Smith, Jaclyn, Stein, Lincoln D, Stobbe, Miranda D, Sun, Ren X, Thai, Kevin, Wright, Derek W, Wu, Chin-Lee, Yuan, Ke, Zhang, Junjun, Danyi, Alexandra, de Ridder, Jeroen, van Herpen, Carla, Lolkema, Martijn P, Steeghs, Neeltje, Morris, Quaid D, Aaltonen, Lauri A, Abascal, Federico, Abeshouse, Adam, Aburatani, Hiroyuki, Adams, David J, Agrawal, Nishant, Ahn, Keun Soo, Ahn, Sung-Min, Aikata, Hiroshi, Akbani, Rehan, Akdemir, Kadir C, Al-Ahmadie, Hikmat, Al-Sedairy, Sultan T, Alawi, Malik, Albert, Monique, Aldape, Kenneth, Alexandrov, Ludmil B, Ally, Adrian, Alsop, Kathryn, Alvarez, Eva G, Amary, Fernanda, Amin, Samirkumar B, Aminou, Brice, Ammerpohl, Ole, Anderson, Matthew J, Ang, Yeng, Antonello, Davide, Anur, Pavana, Aparicio, Samuel, Appelbaum, Elizabeth L, Arai, Yasuhito, Aretz, Axel, Arihiro, Koji, Ariizumi, Shun-ichi, Armenia, Joshua, Arnould, Laurent, Asa, Sylvia, Assenov, Yassen, Aukema, Sietse, Auman, J Todd, Aure, Miriam RR, Awadalla, Philip, Aymerich, Marta, Bader, Gary D, Baez-Ortega, Adrian, Bailey, Matthew H, Balasundaram, Miruna, Balu, Saianand, Bandopadhayay, Pratiti, Banks, Rosamonde E, Barbi, Stefano, Barbour, Andrew P, Barenboim, Jonathan, Barnholtz-Sloan, Jill, Barr, Hugh, Barrera, Elisabet, Bartlett, John, Bartolome, Javier, Bassi, Claudio, Bathe, Oliver F, Baumhoer, Daniel, Bavi, Prashant, Baylin, Stephen B, Bazant, Wojciech, Beardsmore, Duncan, Beck, Timothy A, Behjati, Sam, Behren, Andreas, Niu, Beifang, Bell, Cindy, Beltran, Sergi, Benz, Christopher, Berchuck, Andrew, Bergmann, Anke K, Bergstrom, Erik N, Berman, Benjamin P, Berney, Daniel M, Bernhart, Stephan H, Beroukhim, Rameen, Berrios, Mario, Bersani, Samantha, Bertl, Johanna, Betancourt, Miguel, Bhandari, Vinayak, Bhosle, Shriram G, Bieg, Matthias, Bigner, Darell, Binder, Hans, Birney, Ewan, Birrer, Michael, Biswas, Nidhan K, Bjerkehagen, Bodil, Bodenheimer, Tom, Boice, Lori, Bonizzato, Giada, De Bono, Johann S, Boot, Arnoud, Bootwalla, Moiz S, Borg, Ake, Borkhardt, Arndt, Boroevich, Keith A, Borozan, Ivan, Borst, Christoph, Bosenberg, Marcus, Bosio, Mattia, Boultwood, Jacqueline, Bourque, Guillaume, Bova, G Steven, Bowen, David T, Bowlby, Reanne, Bowtell, David DL, Boyault, Sandrine, Boyce, Rich, Boyd, Jeffrey, Brazma, Alvis, Brennan, Paul, Brewer, Daniel S, Brinkman, Arie B, Bristow, Robert G, Broaddus, Russell R, Brock, Jane E, Brock, Malcolm, Broeks, Annegien, Brooks, Angela N, Brooks, Denise, Brors, Benedikt, Brunak, Søren, Bruxner, Timothy JC, Bruzos, Alicia L, Buchanan, Alex, Buchhalter, Ivo, Buchholz, Christiane, Bullman, Susan, Burke, Hazel, Burkhardt, Birgit, Burns, Kathleen H, Busanovich, John, Bustamante, Carlos D, Butler, Adam P, Butte, Atul J, Byrne, Niall J, Børresen-Dale, Anne-Lise, Caesar-Johnson, Samantha J, Cafferkey, Andy, Cahill, Declan, Calabrese, Claudia, Caldas, Carlos, Calvo, Fabien, Camacho, Niedzica, Campo, Elias, Cantù, Cinzia, Cao, Shaolong, Carey, Thomas E, Carlevaro-Fita, Joana, Carlsen, Rebecca, Cataldo, Ivana, Cazzola, Mario, Cebon, Jonathan, Cerfolio, Robert, Chadwick, Dianne E, Chakravarty, Dimple, Chalmers, Don, Chan, Calvin Wing Yiu, Chan, Kin, Chan-Seng-Yue, Michelle, Chandan, Vishal S, Chanock, Stephen J, Chantrill, Lorraine A, Chateigner, Aurélien, Chatterjee, Nilanjan, Chayama, Kazuaki, Chen, Hsiao-Wei, Chen, Jieming, Chen, Ken, Chen, Yiwen, Chen, Zhaohong, Cherniack, Andrew D, Chien, Jeremy, Chiew, Yoke-Eng, Chin, Suet-Feung, Cho, Juok, Cho, Sunghoon, Choi, Jung Kyoon, Choi, Wan, Chomienne, Christine, Chong, Zechen, Choo, Su Pin, Chou, Angela, Christ, Angelika N, Christie, Elizabeth L, Chuah, Eric, Cibulskis, Carrie, Cibulskis, Kristian, Cingarlini, Sara, Clapham, Peter, Claviez, Alexander, Cleary, Sean, Cloonan, Nicole, Cmero, Marek, Collins, Colin C, Connor, Ashton A, Cooper, Colin S, Cope, Leslie, Corbo, Vincenzo, Cordes, Matthew G, Cordner, Stephen M, Cortés-Ciriano, Isidro, Covington, Kyle, Cowin, Prue A, Craft, Brian, Craft, David, Creighton, Chad J, Cun, Yupeng, Curley, Erin, Cutcutache, Ioana, Czajka, Karolina, Czerniak, Bogdan, Dagg, Rebecca A, Danilova, Ludmila, Davi, Maria Vittoria, Davidson, Natalie R, Davies, Helen, Davis, Ian J, Davis-Dusenbery, Brandi N, Dawson, Kevin J, De La Vega, Francisco M, De Paoli-Iseppi, Ricardo, Defreitas, Timothy, Dei Tos, Angelo P, Delaneau, Olivier, Demchok, John A, Demeulemeester, Jonas, Demidov, German M, Demircioğlu, Deniz, Dennis, Nening M, Denroche, Robert E, Dentro, Stefan C, Desai, Nikita, Deshwar, Amit G, Desmedt, Christine, Deu-Pons, Jordi, Dhalla, Noreen, Dhani, Neesha C, Dhingra, Priyanka, Dhir, Rajiv, DiBiase, Anthony, Diamanti, Klev, Ding, Li, Ding, Shuai, Dinh, Huy Q, Dirix, Luc, Doddapaneni, HarshaVardhan, Donmez, Nilgun, Dow, Michelle T, Drapkin, Ronny, Drechsel, Oliver, Drews, Ruben M, Serge, Serge, Dudderidge, Tim, Dueso-Barroso, Ana, Dunford, Andrew J, Dunn, Michael, Dursi, Lewis Jonathan, Duthie, Fraser R, Dutton-Regester, Ken, Eagles, Jenna, Easton, Douglas F, Edmonds, Stuart, Edwards, Paul A, Edwards, Sandra E, Eeles, Rosalind A, Ehinger, Anna, Eils, Juergen, Eils, Roland, El-Naggar, Adel, Eldridge, Matthew, Ellrott, Kyle, Erkek, Serap, Escaramis, Georgia, Espiritu, Shadrielle MG, Estivill, Xavier, Etemadmoghadam, Dariush, Eyfjord, Jorunn E, Fan, Daiming, Fan, Yu, Farcas, Claudiu, Fassan, Matteo, Fatima, Aquila, Favero, Francesco, Fayzullaev, Nodirjon, Felau, Ina, Fereday, Sian, Ferguson, Martin L, Ferretti, Vincent, Feuerbach, Lars, Field, Matthew A, Fink, J Lynn, Finocchiaro, Gaetano, Fisher, Cyril, Fittall, Matthew W, Fitzgerald, Anna, Fitzgerald, Rebecca C, Flanagan, Adrienne M, Fleshner, Neil E, Flicek, Paul, Foekens, John A, Fong, Kwun M, Fonseca, Nuno A, Foster, Christopher S, Fox, Natalie S, Fraser, Michael, Frazer, Scott, Frenkel-Morgenstern, Milana, Friedman, William, Frigola, Joan, Fronick, Catrina C, Fujimoto, Akihiro, Fujita, Masashi, Fukayama, Masashi, Fulton, Lucinda A, Fulton, Robert S, Furuta, Mayuko, Futreal, P Andrew, Füllgrabe, Anja, Gabriel, Stacey B, Gallinger, Steven, Gambacorti-Passerini, Carlo, Gao, Jianjiong, Gao, Shengjie, Garred, Øystein, Garrison, Erik, Garsed, Dale W, Gehlenborg, Nils, Gelpi, Josep LL, George, Joshy, Gerhard, Daniela S, Gerhauser, Clarissa, Gershenwald, Jeffrey E, Gerstein, Mark, Gerstung, Moritz, Ghori, Mohammed, Ghossein, Ronald, Giama, Nasra H, Gibbs, Richard A, Gibson, Bob, Gill, Anthony J, Gill, Pelvender, Giri, Dilip D, Glodzik, Dominik, Gnanapragasam, Vincent J, Goebler, Maria Elisabeth, Goldman, Mary J, Gomez, Carmen, Gonzalez, Santiago, Gonzalez-Perez, Abel, Gordenin, Dmitry A, Gossage, James, Gotoh, Kunihito, Govindan, Ramaswamy, Grabau, Dorthe, Graham, Janet S, Grant, Robert C, Green, Anthony R, Green, Eric, Greger, Liliana, Grehan, Nicola, Grimaldi, Sonia, Grossman, Robert L, Grundhoff, Adam, Gundem, Gunes, Guo, Qianyun, Gupta, Manaswi, Gupta, Shailja, Gut, Ivo G, Gut, Marta, Göke, Jonathan, Ha, Gavin, Haake, Andrea, Haan, David, Haas, Siegfried, Haase, Kerstin, Haber, James E, Habermann, Nina, Hach, Faraz, Hama, Natsuko, Hamdy, Freddie C, Hamilton, Anne, Hamilton, Mark P, Han, Leng, Hanna, George B, Hansmann, Martin, Haradhvala, Nicholas J, Harismendy, Olivier, Harliwong, Ivon, Harmanci, Arif O, Harrington, Eoghan, Hasegawa, Takanori, Haussler, David, Hawkins, Steve, Hayami, Shinya, Hayashi, Shuto, Hayes, D Neil, Hayes, Stephen J, Hayward, Nicholas K, Hazell, Steven, He, Yao, Heath, Allison P, Heath, Simon C, Hedley, David, Hegde, Apurva M, Heiman, David I, Heinold, Michael C, Heins, Zachary, Heisler, Lawrence E, Hellstrom-Lindberg, Eva, Helmy, Mohamed, Heo, Seong Gu, Hepperla, Austin J, Heredia-Genestar, José María, Herrmann, Carl, Hersey, Peter, Hess, Julian M, Hilmarsdottir, Holmfridur, Hinton, Jonathan, Hirano, Satoshi, Hiraoka, Nobuyoshi, Hobolth, Asger, Hodzic, Ermin, Hoell, Jessica I, Hoffmann, Steve, Hofmann, Oliver, Holbrook, Andrea, Holik, Aliaksei Z, Hollingsworth, Michael A, Holmes, Oliver, Holt, Robert A, Hong, Chen, Hong, Eun Pyo, Hong, Jongwhi H, Hooijer, Gerrit K, Hornshøj, Henrik, Hosoda, Fumie, Hou, Yong, Hovestadt, Volker, Howat, William, Hoyle, Alan P, Hruban, Ralph H, Hu, Jianhong, Hu, Taobo, Hua, Xing, Huang, Kuan-lin, Huang, Mei, Huang, Mi Ni, Huang, Vincent, Huang, Yi, Huber, Wolfgang, Hudson, Thomas J, Hummel, Michael, Hung, Jillian A, Huntsman, David, Hupp, Ted R, Huse, Jason, Huska, Matthew R, Hutter, Barbara, Hutter, Carolyn M, Hübschmann, Daniel, Iacobuzio-Donahue, Christine A, Imbusch, Charles David, Imielinski, Marcin, Imoto, Seiya, Isaacs, William B, Isaev, Keren, Ishikawa, Shumpei, Iskar, Murat, Islam, SM Ashiqul, Ittmann, Michael, Ivkovic, Sinisa, Izarzugaza, Jose MG, Jacquemier, Jocelyne, Jakrot, Valerie, Jamieson, Nigel B, Jang, Gun Ho, Jang, Se Jin, Jayaseelan, Joy C, Jayasinghe, Reyka, Jefferys, Stuart R, Jegalian, Karine, Jennings, Jennifer L, Jeon, Seung-Hyup, Jerman, Lara, Ji, Yuan, Johansson, Peter A, Johns, Amber L, Johns, Jeremy, Johnson, Rory, Johnson, Todd A, Jolly, Clemency, Joly, Yann, Jonasson, Jon G, Jones, Corbin D, Jones, David R, Jones, David TW, Jones, Nic, Jones, Steven JM, Jonkers, Jos, Ju, Young Seok, Juhl, Hartmut, Jung, Jongsun, Juul, Malene, Juul, Randi Istrup, Juul, Sissel, Jäger, Natalie, Kabbe, Rolf, Kahles, Andre, Kahraman, Abdullah, Kakavand, Hojabr, Kalimuthu, Sangeetha, von Kalle, Christof, Kang, Koo Jeong, 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Deurzen, Carolien HM, van de Vijver, Marc J, Veer, L van’t, and von Mering, Christian
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Human Biology & Physiology ,Ecology,Evolution & Ethology ,Tumour Biology ,Genetics & Genomics ,Structural Biology & Biophysics ,Computational & Systems Biology - Abstract
In cancer, the primary tumour’s organ of origin and histopathology are the strongest determinants of its clinical behaviour, but in 3% of cases a patient presents with a metastatic tumour and no obvious primary. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, we train a deep learning classifier to predict cancer type based on patterns of somatic passenger mutations detected in whole genome sequencing (WGS) of 2606 tumours representing 24 common cancer types produced by the PCAWG Consortium. Our classifier achieves an accuracy of 91% on held-out tumor samples and 88% and 83% respectively on independent primary and metastatic samples, roughly double the accuracy of trained pathologists when presented with a metastatic tumour without knowledge of the primary. Surprisingly, adding information on driver mutations reduced accuracy. Our results have clinical applicability, underscore how patterns of somatic passenger mutations encode the state of the cell of origin, and can inform future strategies to detect the source of circulating tumour DNA.
- Published
- 2023
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19. Combined burden and functional impact tests for cancer driver discovery using DriverPower
- Author
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Human Biology & Physiology ,Ecology,Evolution & Ethology ,Tumour Biology ,Genetics & Genomics ,Structural Biology & Biophysics ,Computational & Systems Biology - Abstract
The discovery of driver mutations is one of the key motivations for cancer genome sequencing. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2658 cancers across 38 tumour types, we describe DriverPower, a software package that uses mutational burden and functional impact evidence to identify driver mutations in coding and non-coding sites within cancer whole genomes. Using a total of 1373 genomic features derived from public sources, DriverPower’s background mutation model explains up to 93% of the regional variance in the mutation rate across multiple tumour types. By incorporating functional impact scores, we are able to further increase the accuracy of driver discovery. Testing across a collection of 2583 cancer genomes from the PCAWG project, DriverPower identifies 217 coding and 95 non-coding driver candidates. Comparing to six published methods used by the PCAWG Drivers and Functional Interpretation Working Group, DriverPower has the highest F1 score for both coding and non-coding driver discovery. This demonstrates that DriverPower is an effective framework for computational driver discovery.
- Published
- 2023
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20. Integrative pathway enrichment analysis of multivariate omics data
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Paczkowska, Marta, Barenboim, Jonathan, Sintupisut, Nardnisa, Fox, Natalie S, Zhu, Helen, Abd-Rabbo, Diala, Mee, Miles W, Boutros, Paul C, Abascal, Federico, Amin, Samirkumar B, Bader, Gary D, Beroukhim, Rameen, Bertl, Johanna, Boroevich, Keith A, Brunak, Søren, Campbell, Peter J, Carlevaro-Fita, Joana, Chakravarty, Dimple, Chan, Calvin Wing Yiu, Chen, Ken, Choi, Jung Kyoon, Deu-Pons, Jordi, Dhingra, Priyanka, Diamanti, Klev, Feuerbach, Lars, Fink, J Lynn, Fonseca, Nuno A, Frigola, Joan, Gambacorti-Passerini, Carlo, Garsed, Dale W, Gerstein, Mark, Getz, Gad, Gonzalez-Perez, Abel, Guo, Qianyun, Gut, Ivo G, Haan, David, Hamilton, Mark P, Haradhvala, Nicholas J, Harmanci, Arif O, Helmy, Mohamed, Herrmann, Carl, Hess, Julian M, Hobolth, Asger, Hodzic, Ermin, Hong, Chen, Hornshøj, Henrik, Isaev, Keren, Izarzugaza, Jose MG, Johnson, Rory, Johnson, Todd A, Juul, Malene, Juul, Randi Istrup, Kahles, Andre, Kahraman, Abdullah, Kellis, Manolis, Khurana, Ekta, Kim, Jaegil, Kim, Jong K, Kim, Youngwook, Komorowski, Jan, Korbel, Jan O, Kumar, Sushant, Lanzós, Andrés, Lawrence, Michael S, Lee, Donghoon, Lehmann, Kjong-Van, Li, Shantao, Li, Xiaotong, Lin, Ziao, Liu, Eric Minwei, Lochovsky, Lucas, Lou, Shaoke, Madsen, Tobias, Marchal, Kathleen, Martincorena, Iñigo, Martinez-Fundichely, Alexander, Maruvka, Yosef E, McGillivray, Patrick D, Meyerson, William, Muiños, Ferran, Mularoni, Loris, Nakagawa, Hidewaki, Nielsen, Morten Muhlig, Park, Keunchil, Park, Kiejung, Pedersen, Jakob Skou, Pich, Oriol, Pons, Tirso, Pulido-Tamayo, Sergio, Raphael, Benjamin J, Reyes-Salazar, Iker, Reyna, Matthew A, Rheinbay, Esther, Rubin, Mark A, Rubio-Perez, Carlota, Sabarinathan, Radhakrishnan, Sahinalp, S Cenk, Saksena, Gordon, Salichos, Leonidas, Sander, Chris, Schumacher, Steven E, Shackleton, Mark, Shapira, Ofer, Shen, Ciyue, Shrestha, Raunak, Shuai, Shimin, Sidiropoulos, Nikos, Sieverling, Lina, Sinnott-Armstrong, Nasa, Stein, Lincoln D, Stuart, Joshua M, Tamborero, David, Tiao, Grace, Tsunoda, Tatsuhiko, Umer, Husen M, Uusküla-Reimand, Liis, Valencia, Alfonso, Vazquez, Miguel, Verbeke, Lieven PC, Wadelius, Claes, Wadi, Lina, Wang, Jiayin, Warrell, Jonathan, Waszak, Sebastian M, Weischenfeldt, Joachim, Wheeler, David A, Wu, Guanming, Yu, Jun, Zhang, Jing, Zhang, Xuanping, Zhang, Yan, Zhao, Zhongming, Zou, Lihua, von Mering, Christian, Reimand, Jüri, Aaltonen, Lauri A, Abeshouse, Adam, Aburatani, Hiroyuki, Adams, David J, Agrawal, Nishant, Ahn, Keun Soo, Ahn, Sung-Min, Aikata, Hiroshi, Akbani, Rehan, Akdemir, Kadir C, Al-Ahmadie, Hikmat, Al-Sedairy, Sultan T, Al-Shahrour, Fatima, Alawi, Malik, Albert, Monique, Aldape, Kenneth, Alexandrov, Ludmil B, Ally, Adrian, Alsop, Kathryn, Alvarez, Eva G, Amary, Fernanda, Aminou, Brice, Ammerpohl, Ole, Anderson, Matthew J, Ang, Yeng, Antonello, Davide, Anur, Pavana, Aparicio, Samuel, Appelbaum, Elizabeth L, Arai, Yasuhito, Aretz, Axel, Arihiro, Koji, Ariizumi, Shun-ichi, Armenia, Joshua, Arnould, Laurent, Asa, Sylvia, Assenov, Yassen, Atwal, Gurnit, Aukema, Sietse, Auman, J Todd, Aure, Miriam RR, Awadalla, Philip, Aymerich, Marta, Baez-Ortega, Adrian, Bailey, Matthew H, Bailey, Peter J, Balasundaram, Miruna, Balu, Saianand, Bandopadhayay, Pratiti, Banks, Rosamonde E, Barbi, Stefano, Barbour, Andrew P, Barnholtz-Sloan, Jill, Barr, Hugh, Barrera, Elisabet, Bartlett, John, Bartolome, Javier, Bassi, Claudio, Bathe, Oliver F, Baumhoer, Daniel, Bavi, Prashant, Baylin, Stephen B, Bazant, Wojciech, Beardsmore, Duncan, Beck, Timothy A, Behjati, Sam, Behren, Andreas, Niu, Beifang, Bell, Cindy, Beltran, Sergi, Benz, Christopher, Berchuck, Andrew, Bergmann, Anke K, Bergstrom, Erik N, Berman, Benjamin P, Berney, Daniel M, Bernhart, Stephan H, Berrios, Mario, Bersani, Samantha, Betancourt, Miguel, Bhandari, Vinayak, Bhosle, Shriram G, Biankin, Andrew V, Bieg, Matthias, Bigner, Darell, Binder, Hans, Birney, Ewan, Birrer, Michael, Biswas, Nidhan K, Bjerkehagen, Bodil, Bodenheimer, Tom, Boice, Lori, Bonizzato, Giada, De Bono, Johann S, Boot, Arnoud, Bootwalla, Moiz S, Borg, Ake, Borkhardt, Arndt, Borozan, Ivan, Borst, Christoph, Bosenberg, Marcus, Bosio, Mattia, Boultwood, Jacqueline, Bourque, Guillaume, Bova, G Steven, Bowen, David T, Bowlby, Reanne, Bowtell, David DL, Boyault, Sandrine, Boyce, Rich, Boyd, Jeffrey, Brazma, Alvis, Brennan, Paul, Brewer, Daniel S, Brinkman, Arie B, Bristow, Robert G, Broaddus, Russell R, Brock, Jane E, Brock, Malcolm, Broeks, Annegien, Brooks, Angela N, Brooks, Denise, Brors, Benedikt, Bruxner, Timothy JC, Bruzos, Alicia L, Buchanan, Alex, Buchhalter, Ivo, Buchholz, Christiane, Bullman, Susan, Burke, Hazel, Burkhardt, Birgit, Burns, Kathleen H, Busanovich, John, Bustamante, Carlos D, Butler, Adam P, Butte, Atul J, Byrne, Niall J, Børresen-Dale, Anne-Lise, Caesar-Johnson, Samantha J, Cafferkey, Andy, Cahill, Declan, Calabrese, Claudia, Caldas, Carlos, Calvo, Fabien, Camacho, Niedzica, Campo, Elias, Cantù, Cinzia, Cao, Shaolong, Carey, Thomas E, Carlsen, Rebecca, Cataldo, Ivana, Cazzola, Mario, Cebon, Jonathan, Cerfolio, Robert, Chadwick, Dianne E, Chalmers, Don, Chan, Kin, Chan-Seng-Yue, Michelle, Chandan, Vishal S, Chang, David K, Chanock, Stephen J, Chantrill, Lorraine A, Chateigner, Aurélien, Chatterjee, Nilanjan, Chayama, Kazuaki, Chen, Hsiao-Wei, Chen, Jieming, Chen, Yiwen, Chen, Zhaohong, Cherniack, Andrew D, Chien, Jeremy, Chiew, Yoke-Eng, Chin, Suet-Feung, Cho, Juok, Cho, Sunghoon, Choi, Wan, Chomienne, Christine, Chong, Zechen, Choo, Su Pin, Chou, Angela, Christ, Angelika N, Christie, Elizabeth L, Chuah, Eric, Cibulskis, Carrie, Cibulskis, Kristian, Cingarlini, Sara, Clapham, Peter, Claviez, Alexander, Cleary, Sean, Cloonan, Nicole, Cmero, Marek, Collins, Colin C, Connor, Ashton A, Cooke, Susanna L, Cooper, Colin S, Cope, Leslie, Corbo, Vincenzo, Cordes, Matthew G, Cordner, Stephen M, Cortés-Ciriano, Isidro, Covington, Kyle, Cowin, Prue A, Craft, Brian, Craft, David, Creighton, Chad J, Cun, Yupeng, Curley, Erin, Cutcutache, Ioana, Czajka, Karolina, Czerniak, Bogdan, Dagg, Rebecca A, Danilova, Ludmila, Davi, Maria Vittoria, Davidson, Natalie R, Davies, Helen, Davis, Ian J, Davis-Dusenbery, Brandi N, Dawson, Kevin J, De La Vega, Francisco M, De Paoli-Iseppi, Ricardo, Defreitas, Timothy, Dei Tos, Angelo P, Delaneau, Olivier, Demchok, John A, Demeulemeester, Jonas, Demidov, German M, Demircioğlu, Deniz, Dennis, Nening M, Denroche, Robert E, Dentro, Stefan C, Desai, Nikita, Deshpande, Vikram, Deshwar, Amit G, Desmedt, Christine, Dhalla, Noreen, Dhani, Neesha C, Dhir, Rajiv, DiBiase, Anthony, Ding, Li, Ding, Shuai, Dinh, Huy Q, Dirix, Luc, Doddapaneni, HarshaVardhan, Donmez, Nilgun, Dow, Michelle T, Drapkin, Ronny, Drechsel, Oliver, Drews, Ruben M, Serge, Serge, Dudderidge, Tim, Dueso-Barroso, Ana, Dunford, Andrew J, Dunn, Michael, Dursi, Lewis Jonathan, Duthie, Fraser R, Dutton-Regester, Ken, Eagles, Jenna, Easton, Douglas F, Edmonds, Stuart, Edwards, Paul A, Edwards, Sandra E, Eeles, Rosalind A, Ehinger, Anna, Eils, Juergen, Eils, Roland, El-Naggar, Adel, Eldridge, Matthew, Ellrott, Kyle, Erkek, Serap, Escaramis, Georgia, Espiritu, Shadrielle MG, Estivill, Xavier, Etemadmoghadam, Dariush, Eyfjord, Jorunn E, Faltas, Bishoy M, Fan, Daiming, Fan, Yu, Faquin, William C, Farcas, Claudiu, Fassan, Matteo, Fatima, Aquila, Favero, Francesco, Fayzullaev, Nodirjon, Felau, Ina, Fereday, Sian, Ferguson, Martin L, Ferretti, Vincent, Field, Matthew A, Finocchiaro, Gaetano, Fisher, Cyril, Fittall, Matthew W, Fitzgerald, Anna, Fitzgerald, Rebecca C, Flanagan, Adrienne M, Fleshner, Neil E, Flicek, Paul, Foekens, John A, Fong, Kwun M, Foster, Christopher S, Fraser, Michael, Frazer, Scott, Frenkel-Morgenstern, Milana, Friedman, William, Fronick, Catrina C, Fujimoto, Akihiro, Fujita, Masashi, Fukayama, Masashi, Fulton, Lucinda A, Fulton, Robert S, Furuta, Mayuko, Futreal, P Andrew, Füllgrabe, Anja, Gabriel, Stacey B, Gallinger, Steven, Gao, Jianjiong, Gao, Shengjie, Garraway, Levi, Garred, Øystein, Garrison, Erik, Gehlenborg, Nils, Gelpi, Josep LL, George, Joshy, Gerhard, Daniela S, Gerhauser, Clarissa, Gershenwald, Jeffrey E, Gerstung, Moritz, Ghori, Mohammed, Ghossein, Ronald, Giama, Nasra H, Gibbs, Richard A, Gibson, Bob, Gill, Anthony J, Gill, Pelvender, Giri, Dilip D, Glodzik, Dominik, Gnanapragasam, Vincent J, Goebler, Maria Elisabeth, Goldman, Mary J, Gomez, Carmen, Gonzalez, Santiago, Gordenin, Dmitry A, Gossage, James, Gotoh, Kunihito, Govindan, Ramaswamy, Grabau, Dorthe, Graham, Janet S, Grant, Robert C, Green, Anthony R, Green, Eric, Greger, Liliana, Grehan, Nicola, Grimaldi, Sonia, Grimmond, Sean M, Grossman, Robert L, Grundhoff, Adam, Gundem, Gunes, Gupta, Manaswi, Gupta, Shailja, Gut, Marta, Göke, Jonathan, Ha, Gavin, Haake, Andrea, Haas, Siegfried, Haase, Kerstin, Haber, James E, Habermann, Nina, Hach, Faraz, Haider, Syed, Hama, Natsuko, Hamdy, Freddie C, Hamilton, Anne, Han, Leng, Hanna, George B, Hansmann, Martin, Harismendy, Olivier, Harliwong, Ivon, Harrington, Eoghan, Hasegawa, Takanori, Haussler, David, Hawkins, Steve, Hayami, Shinya, Hayashi, Shuto, Hayes, D Neil, Hayes, Stephen J, Hayward, Nicholas K, Hazell, Steven, He, Yao, Heath, Allison P, Heath, Simon C, Hedley, David, Hegde, Apurva M, Heiman, David I, Heinold, Michael C, Heins, Zachary, Heisler, Lawrence E, Hellstrom-Lindberg, Eva, Heo, Seong Gu, Hepperla, Austin J, Heredia-Genestar, José María, Hersey, Peter, Hilmarsdottir, Holmfridur, Hinton, Jonathan, Hirano, Satoshi, Hiraoka, Nobuyoshi, Hoadley, Katherine A, Hoell, Jessica I, Hoffmann, Steve, Hofmann, Oliver, Holbrook, Andrea, Holik, Aliaksei Z, Hollingsworth, Michael A, Holmes, Oliver, Holt, Robert A, Hong, Eun Pyo, Hong, Jongwhi H, Hooijer, Gerrit K, Hosoda, Fumie, Hou, Yong, Hovestadt, Volker, Howat, William, Hoyle, Alan P, Hruban, Ralph H, Hu, Jianhong, Hu, Taobo, Hua, Xing, Huang, Kuan-lin, Huang, Mei, Huang, Mi Ni, Huang, Vincent, Huang, Yi, Huber, Wolfgang, Hudson, Thomas J, Hummel, Michael, Hung, Jillian A, Huntsman, David, Hupp, Ted R, Huse, Jason, Huska, Matthew R, Hutter, Barbara, Hutter, Carolyn M, Hübschmann, Daniel, Iacobuzio-Donahue, Christine A, Imbusch, Charles David, Imielinski, Marcin, Imoto, Seiya, Isaacs, William B, Ishikawa, Shumpei, Iskar, Murat, Islam, SM Ashiqul, Ittmann, Michael, Ivkovic, Sinisa, Jacquemier, Jocelyne, Jakrot, Valerie, Jamieson, Nigel B, Jang, Gun Ho, Jang, Se Jin, Jayaseelan, Joy C, Jayasinghe, Reyka, Jefferys, Stuart R, Jegalian, Karine, Jennings, Jennifer L, Jeon, Seung-Hyup, Jerman, Lara, Ji, Yuan, Jiao, Wei, Johansson, Peter A, Johns, Amber L, Johns, Jeremy, Jolly, Clemency, Joly, Yann, Jonasson, Jon G, Jones, Corbin D, Jones, David R, Jones, David TW, Jones, Nic, Jones, Steven JM, Jonkers, Jos, Ju, Young Seok, Juhl, Hartmut, Jung, Jongsun, Juul, Sissel, Jäger, Natalie, Kabbe, Rolf, Kaiser, Vera B, Kakavand, Hojabr, Kalimuthu, Sangeetha, von Kalle, Christof, Kang, Koo Jeong, Karaszi, Katalin, Karlan, Beth, Karlić, Rosa, Karsch, Dennis, Kasaian, Katayoon, Kassahn, Karin S, Katai, Hitoshi, Kato, Mamoru, Katoh, Hiroto, Kawakami, Yoshiiku, Kay, Jonathan D, Kazakoff, Stephen H, Kazanov, Marat D, Keays, Maria, Kebebew, Electron, Kefford, Richard F, Kench, James G, Kennedy, Catherine J, Kerssemakers, Jules NA, Khoo, David, Khoo, Vincent, Khuntikeo, Narong, Kilpinen, Helena, Kim, Hark Kyun, Kim, Hyung-Lae, Kim, Hyung-Yong, Kim, Hyunghwan, Kim, Jihoon, King, Tari A, Klapper, Wolfram, Kleinheinz, Kortine, Klimczak, Leszek J, Knappskog, Stian, Kneba, Michael, Knoppers, Bartha M, Koh, Youngil, Komura, Daisuke, Komura, Mitsuhiro, Kong, Gu, Kool, Marcel, Korchina, Viktoriya, Korshunov, Andrey, Koscher, Michael, Koster, Roelof, Kote-Jarai, Zsofia, Koures, Antonios, Kovacevic, Milena, Kremeyer, Barbara, Kretzmer, Helene, Kreuz, Markus, Krishnamurthy, Savitri, Kube, Dieter, Kumar, Kiran, Kumar, Pardeep, Kumar, Yogesh, Kundra, Ritika, Kübler, Kirsten, Küppers, Ralf, Lagergren, Jesper, Lai, Phillip H, Laird, Peter W, Lakhani, Sunil R, Lalansingh, Christopher M, Lalonde, Emilie, Lamaze, Fabien C, Lambert, Adam, Lander, Eric, Landgraf, Pablo, Landoni, Luca, Langerød, Anita, Larsimont, Denis, Larsson, Erik, Lathrop, Mark, Lau, Loretta MS, Lawerenz, Chris, Lawlor, Rita T, Lazar, Alexander J, Lazic, Ana Mijalkovic, Le, Xuan, Lee, Darlene, Lee, Eunjung Alice, Lee, Hee Jin, Lee, Jake June-Koo, Lee, Jeong-Yeon, Lee, Juhee, Lee, Ming Ta Michael, Lee-Six, Henry, Lehrach, Hans, Lenze, Dido, Leonard, Conrad R, Leongamornlert, Daniel A, Leshchiner, Ignaty, Letourneau, Louis, Letunic, Ivica, Levine, Douglas A, Lewis, Lora, Ley, Tim, Li, Chang, Li, Constance H, Li, Haiyan Irene, Li, Jun, Li, Lin, Li, Siliang, Li, Xiaobo, Li, Xinyue, Li, Yilong, Liang, Han, Liang, Sheng-Ben, Lichter, Peter, Lin, Pei, Linehan, WM, Lingjærde, Ole Christian, Liu, Dongbing, Liu, Fei-Fei Fei, Liu, Fenglin, Liu, Jia, Liu, Xingmin, Livingstone, Julie, Livitz, Dimitri, Livni, Naomi, Loeffler, Markus, Long, Georgina V, Lopez-Guillermo, Armando, Louis, David N, Lovat, Laurence B, Lu, Yiling, Lu, Yong-Jie, Lu, Youyong, Luchini, Claudio, Lungu, Ilinca, Luo, Xuemei, Luxton, Hayley J, Lynch, Andy G, Lype, Lisa, López, Cristina, López-Otín, Carlos, Z, Eric, Ma, Yussanne, MacGrogan, Gaetan, MacRae, Shona, Macintyre, Geoff, Maejima, Kazuhiro, Mafficini, Andrea, Maglinte, Dennis T, Maitra, Arindam, Majumder, Partha P, Malcovati, Luca, Malikic, Salem, Malleo, Giuseppe, Mann, Graham J, Mantovani-Löffler, Luisa, Marchegiani, Giovanni, Mardis, Elaine R, Margolin, Adam A, Marin, Maximillian G, Markowetz, Florian, Markowski, Julia, Marks, Jeffrey, Marques-Bonet, Tomas, Marra, Marco A, Marsden, Luke, Martens, John WM, Martin, Sancha, Martin-Subero, Jose I, Mashl, R Jay, Massie, Charlie E, Matthew, Thomas J, Matthews, Lucy, Mayer, Erik, Mayes, Simon, Mayo, Michael, Mbabaali, Faridah, McCune, Karen, McDermott, Ultan, McLellan, Michael D, McPherson, John D, McPherson, John R, McPherson, Treasa A, Meier, Samuel R, Meng, Alice, Meng, Shaowu, Menzies, Andrew, Merrett, Neil D, Merson, Sue, Meyerson, Matthew, Mieczkowski, Piotr A, Mihaiescu, George L, Mijalkovic, Sanja, Mikkelsen, Tom, Milella, Michele, Mileshkin, Linda, Miller, Christopher A, Miller, David K, Miller, Jessica K, Mills, Gordon B, Milovanovic, Ana, Minner, Sarah, Miotto, Marco, Arnau, Gisela Mir, Mirabello, Lisa, Mitchell, Chris, Mitchell, Thomas J, Miyano, Satoru, Miyoshi, Naoki, Mizuno, Shinichi, Molnár-Gábor, Fruzsina, Moore, Malcolm J, Moore, Richard A, Morganella, Sandro, Morris, Quaid D, Morrison, Carl, Mose, Lisle E, Moser, Catherine D, Mungall, Andrew J, Mungall, Karen, Musgrove, Elizabeth A, Mustonen, Ville, Mutch, David, Muyas, Francesc, Muzny, Donna M, Muñoz, Alfonso, Myers, Jerome, Myklebost, Ola, Möller, Peter, Nagae, Genta, Nagrial, Adnan M, Nahal-Bose, Hardeep K, Nakagama, Hitoshi, Nakamura, Hiromi, Nakamura, Toru, Nakano, Kaoru, Nandi, Tannistha, Nangalia, Jyoti, Nastic, Mia, Navarro, Arcadi, Navarro, Fabio CP, Neal, David E, Nettekoven, Gerd, Newell, Felicity, Newhouse, Steven J, Newton, Yulia, Ng, Alvin Wei Tian, Ng, Anthony, Nicholson, Jonathan, Nicol, David, Nie, Yongzhan, Nielsen, G Petur, Nik-Zainal, Serena, Noble, Michael S, Nones, Katia, Northcott, Paul A, Notta, Faiyaz, O’Connor, Brian D, O’Donnell, Peter, O’Donovan, Maria, O’Meara, Sarah, O’Neill, Brian Patrick, O’Neill, J Robert, Ocana, David, Ochoa, Angelica, Oesper, Layla, Ogden, Christopher, Ohdan, Hideki, Ohi, Kazuhiro, Ohno-Machado, Lucila, Oien, Karin A, Ojesina, Akinyemi I, Ojima, Hidenori, Okusaka, Takuji, Omberg, Larsson, Ong, Choon Kiat, Ossowski, Stephan, Ott, German, Ouellette, BF Francis, P’ng, Christine, Paiella, Salvatore, Pairojkul, Chawalit, Pajic, Marina, Pan-Hammarström, Qiang, Papaemmanuil, Elli, Papatheodorou, Irene, Paramasivam, Nagarajan, Park, Ji Wan, Park, Joong-Won, Park, Peter J, Parker, Joel S, Parsons, Simon L, Pass, Harvey, Pasternack, Danielle, Pastore, Alessandro, Patch, Ann-Marie, Pauporté, Iris, Pea, Antonio, Pearson, John V, Pedamallu, Chandra Sekhar, Pederzoli, Paolo, Peifer, Martin, Pennell, Nathan A, Perou, Charles M, Perry, Marc D, Petersen, Gloria M, Peto, Myron, Petrelli, Nicholas, Petryszak, Robert, Pfister, Stefan M, Phillips, Mark, Pickett, Hilda A, Pihl, Todd D, Pillay, Nischalan, Pinder, Sarah, Pinese, Mark, Pinho, Andreia V, Pitkänen, Esa, Pivot, Xavier, Piñeiro-Yáñez, Elena, Planko, Laura, Plass, Christoph, Polak, Paz, Popescu, Irinel, Potapova, Olga, Prasad, Aparna, Preston, Shaun R, Prinz, Manuel, Pritchard, Antonia L, Prokopec, Stephenie D, Provenzano, Elena, Puente, Xose S, Puig, Sonia, Puiggròs, Montserrat, Pupo, Gulietta M, Purdie, Colin A, Quinn, Michael C, Rabionet, Raquel, Rader, Janet S, Radlwimmer, Bernhard, Radovic, Petar, Raeder, Benjamin, Raine, Keiran M, Ramakrishna, Manasa, Ramakrishnan, Kamna, Ramalingam, Suresh, Rathmell, W Kimryn, Rausch, Tobias, Reifenberger, Guido, Reis-Filho, Jorge, Reuter, Victor, Reynolds, Sheila M, Riazalhosseini, Yasser, Richardson, Andrea L, Richter, Julia, Ringel, Matthew, Ringnér, Markus, Rino, Yasushi, Rippe, Karsten, Roach, Jeffrey, Roberts, Lewis R, Roberts, Nicola D, Roberts, Steven A, Robertson, A Gordon, Robertson, Alan J, Rodriguez, Javier Bartolomé, Rodriguez-Martin, Bernardo, Rodríguez-González, F Germán, Roehrl, Michael HA, Rohde, Marius, Rokutan, Hirofumi, Romieu, Gilles, Rooman, Ilse, Roques, Tom, Rosebrock, Daniel, Rosenberg, Mara, Rosenstiel, Philip C, Rosenwald, Andreas, Rowe, Edward W, Royo, Romina, Rozen, Steven G, Rubanova, Yulia, Rudneva, Vasilisa A, Rusev, Borislav C, Ruzzenente, Andrea, Rätsch, Gunnar, Sabelnykova, Veronica Y, Sadeghi, Sara, Saini, Natalie, Saito-Adachi, Mihoko, Salcedo, Adriana, Salgado, Roberto, Sallari, Richard, Saller, Charles, Salvia, Roberto, Sam, Michelle, Samra, Jaswinder S, Sanchez-Vega, Francisco, Sanders, Grant, Sarin, Rajiv, Sarrafi, Iman, Sasaki-Oku, Aya, Sauer, Torill, Sauter, Guido, Saw, Robyn PM, Scardoni, Maria, Scarlett, Christopher J, Scarpa, Aldo, Scelo, Ghislaine, Schadendorf, Dirk, Schein, Jacqueline E, Schilhabel, Markus B, Schlesner, Matthias, Schlomm, Thorsten, Schmidt, Heather K, Schramm, Sarah-Jane, Schreiber, Stefan, Schultz, Nikolaus, Schwarz, Roland F, Scolyer, Richard A, Scott, David, Scully, Ralph, Seethala, Raja, Segre, Ayellet V, Selander, Iris, Semple, Colin A, Senbabaoglu, Yasin, Sengupta, Subhajit, Sereni, Elisabetta, Serra, Stefano, Sgroi, Dennis C, Shah, Nimish C, Shahabi, Sagedeh, Shang, Catherine A, Shang, Ping, Shelton, Troy, Shen, Hui, Shepherd, Rebecca, Shi, Ruian, Shi, Yan, Shiah, Yu-Jia, Shibata, Tatsuhiro, Shih, Juliann, Shimizu, Eigo, Shimizu, Kiyo, Shin, Seung Jun, Shiraishi, Yuichi, Shmaya, Tal, Shmulevich, Ilya, Shorser, Solomon I, Short, Charles, Shringarpure, Suyash S, Shriver, Craig, Siebert, Reiner, Sieuwerts, Anieta M, Signoretti, Sabina, Sikora, Katarzyna O, Simbolo, Michele, Simon, Ronald, Simons, Janae V, Simpson, Jared T, Simpson, Peter T, Singer, Samuel, Sipahimalani, Payal, Skelly, Tara J, Smid, Marcel, Smith, Jaclyn, Smith-McCune, Karen, Socci, Nicholas D, Sofia, Heidi J, Soloway, Matthew G, Song, Lei, Sood, Anil K, Sothi, Sharmila, Sotiriou, Christos, Soulette, Cameron M, Span, Paul N, Spellman, Paul T, Sperandio, Nicola, Spillane, Andrew J, Spiro, Oliver, Spring, Jonathan, Staaf, Johan, Stadler, Peter F, Staib, Peter, Stark, Stefan G, Stebbings, Lucy, Stefánsson, Ólafur Andri, Stegle, Oliver, Stenhouse, Alasdair, Stewart, Chip, Stilgenbauer, Stephan, Stobbe, Miranda D, Stratton, Michael R, Stretch, Jonathan R, Struck, Adam J, Stunnenberg, Henk G, Su, Hong, Su, Xiaoping, Sun, Ren X, Sungalee, Stephanie, Susak, Hana, Suzuki, Akihiro, Sweep, Fred, Szczepanowski, Monika, Sültmann, Holger, Yugawa, Takashi, Tam, Angela, Tan, Benita Kiat Tee, Tan, Donghui, Tan, Patrick, Tanaka, Hiroko, Taniguchi, Hirokazu, Tanskanen, Tomas J, Tarabichi, Maxime, Tarnuzzer, Roy, Tarpey, Patrick, Taschuk, Morgan L, Tatsuno, Kenji, Tavaré, Simon, Taylor, Darrin F, Taylor-Weiner, Amaro, Teague, Jon W, Teh, Bin Tean, Tembe, Varsha, Temes, Javier, Thai, Kevin, Thayer, Sarah P, Thiessen, Nina, Thomas, Gilles, Thomas, Sarah, Thompson, Alan, Thompson, Alastair M, Thompson, John FF, Thompson, R Houston, Thorne, Heather, Thorne, Leigh B, Thorogood, Adrian, Tijanic, Nebojsa, Timms, Lee E, Tirabosco, Roberto, Tojo, Marta, Tommasi, Stefania, Toon, Christopher W, Toprak, Umut H, Torrents, David, Tortora, Giampaolo, Tost, Jörg, Totoki, Yasushi, Townend, David, Traficante, Nadia, Treilleux, Isabelle, Trotta, Jean-Rémi, Trümper, Lorenz HP, Tsao, Ming, MC Tubio, Jose, Tucker, Olga, Turkington, Richard, Turner, Daniel J, Tutt, Andrew, Ueno, Masaki, Ueno, Naoto T, Umbricht, Christopher, Underwood, Timothy J, Urban, Lara, Urushidate, Tomoko, Ushiku, Tetsuo, Van Den Berg, David J, Van Laere, Steven, Van Loo, Peter, Van Meir, Erwin G, Van den Eynden, Gert G, Van der Kwast, Theodorus, Vasudev, Naveen, Vedururu, Ravikiran, Veluvolu, Umadevi, Vembu, Shankar, Vermeulen, Peter, Verrill, Clare, Viari, Alain, Vicente, David, Vicentini, Caterina, 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Vijver, Marc J, and Veer, L van’t
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Human Biology & Physiology ,Ecology,Evolution & Ethology ,Tumour Biology ,Genetics & Genomics ,Structural Biology & Biophysics ,Computational & Systems Biology - Abstract
Multi-omics datasets represent distinct aspects of the central dogma of molecular biology. Such high-dimensional molecular profiles pose challenges to data interpretation and hypothesis generation. ActivePathways is an integrative method that discovers significantly enriched pathways across multiple datasets using statistical data fusion, rationalizes contributing evidence and highlights associated genes. As part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2658 cancers across 38 tumor types, we integrated genes with coding and non-coding mutations and revealed frequently mutated pathways and additional cancer genes with infrequent mutations. We also analyzed prognostic molecular pathways by integrating genomic and transcriptomic features of 1780 breast cancers and highlighted associations with immune response and anti-apoptotic signaling. Integration of ChIP-seq and RNA-seq data for master regulators of the Hippo pathway across normal human tissues identified processes of tissue regeneration and stem cell regulation. ActivePathways is a versatile method that improves systems-level understanding of cellular organization in health and disease through integration of multiple molecular datasets and pathway annotations.
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- 2023
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21. Pathway and network analysis of more than 2500 whole cancer genomes
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Human Biology & Physiology ,Ecology,Evolution & Ethology ,Tumour Biology ,Genetics & Genomics ,Structural Biology & Biophysics ,Computational & Systems Biology - Abstract
The catalog of cancer driver mutations in protein-coding genes has greatly expanded in the past decade. However, non-coding cancer driver mutations are less well-characterized and only a handful of recurrent non-coding mutations, most notably TERT promoter mutations, have been reported. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2658 cancer across 38 tumor types, we perform multi-faceted pathway and network analyses of non-coding mutations across 2583 whole cancer genomes from 27 tumor types compiled by the ICGC/TCGA PCAWG project that was motivated by the success of pathway and network analyses in prioritizing rare mutations in protein-coding genes. While few non-coding genomic elements are recurrently mutated in this cohort, we identify 93 genes harboring non-coding mutations that cluster into several modules of interacting proteins. Among these are promoter mutations associated with reduced mRNA expression in TP53, TLE4, and TCF4. We find that biological processes had variable proportions of coding and non-coding mutations, with chromatin remodeling and proliferation pathways altered primarily by coding mutations, while developmental pathways, including Wnt and Notch, altered by both coding and non-coding mutations. RNA splicing is primarily altered by non-coding mutations in this cohort, and samples containing non-coding mutations in well-known RNA splicing factors exhibit similar gene expression signatures as samples with coding mutations in these genes. These analyses contribute a new repertoire of possible cancer genes and mechanisms that are altered by non-coding mutations and offer insights into additional cancer vulnerabilities that can be investigated for potential therapeutic treatments.
- Published
- 2023
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22. Divergent mutational processes distinguish hypoxic and normoxic tumours
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Human Biology & Physiology ,Ecology,Evolution & Ethology ,Tumour Biology ,Genetics & Genomics ,Structural Biology & Biophysics ,Computational & Systems Biology - Abstract
Many primary tumours have low levels of molecular oxygen (hypoxia), and hypoxic tumours respond poorly to therapy. Pan-cancer molecular hallmarks of tumour hypoxia remain poorly understood, with limited comprehension of its associations with specific mutational processes, non-coding driver genes and evolutionary features. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2658 cancers across 38 tumour types, we quantify hypoxia in 1188 tumours spanning 27 cancer types. Elevated hypoxia associates with increased mutational load across cancer types, irrespective of underlying mutational class. The proportion of mutations attributed to several mutational signatures of unknown aetiology directly associates with the level of hypoxia, suggesting underlying mutational processes for these signatures. At the gene level, driver mutations in TP53, MYC and PTEN are enriched in hypoxic tumours, and mutations in PTEN interact with hypoxia to direct tumour evolutionary trajectories. Overall, hypoxia plays a critical role in shaping the genomic and evolutionary landscapes of cancer.
- Published
- 2023
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23. Genomic footprints of activated telomere maintenance mechanisms in cancer
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Christian
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Human Biology & Physiology ,Ecology,Evolution & Ethology ,Tumour Biology ,Genetics & Genomics ,Structural Biology & Biophysics ,Computational & Systems Biology - Abstract
Cancers require telomere maintenance mechanisms for unlimited replicative potential. They achieve this through TERT activation or alternative telomere lengthening associated with ATRX or DAXX loss. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, we dissect whole-genome sequencing data of over 2500 matched tumor-control samples from 36 different tumor types aggregated within the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium to characterize the genomic footprints of these mechanisms. While the telomere content of tumors with ATRX or DAXX mutations (ATRX/DAXXtrunc) is increased, tumors with TERT modifications show a moderate decrease of telomere content. One quarter of all tumor samples contain somatic integrations of telomeric sequences into non-telomeric DNA. This fraction is increased to 80% prevalence in ATRX/DAXXtrunc tumors, which carry an aberrant telomere variant repeat (TVR) distribution as another genomic marker. The latter feature includes enrichment or depletion of the previously undescribed singleton TVRs TTCGGG and TTTGGG, respectively. Our systematic analysis provides new insight into the recurrent genomic alterations associated with telomere maintenance mechanisms in cancer.
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- 2023
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24. Evaluation of metabolomic changes during neoadjuvant chemotherapy combined with bevacizumab in breast cancer using MR spectroscopy
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Euceda, Leslie R., Haukaas, Tonje H., Giskeødegård, Guro F., Vettukattil, Riyas, Engel, Jasper, Silwal-Pandit, Laxmi, Lundgren, Steinar, Borgen, Elin, Garred, Øystein, Postma, Geert, Buydens, Lutgarde M. C., Børresen-Dale, Anne-Lise, Engebraaten, Olav, and Bathen, Tone F.
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- 2017
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25. Prognostic significance of S100A4-expression and subcellular localization in early-stage breast cancer
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Egeland, Eivind Valen, Boye, Kjetil, Park, Daehoon, Synnestvedt, Marit, Sauer, Torill, Naume, Bjørn, Borgen, Elin, Mælandsmo, Gunhild M., Sauer, Torill, Geisler, Jürgen, Hofvind, Solveig, Bathen, Tone F., Borgen, Elin, Børresen‐Dale, Anne‐Lise, Engebråten, Olav, Fodstad, Øystein, Garred, Øystein, Geitvik, Gry A., Kåresen, Rolf, Naume, Bjørn, Mælandsmo, Gunhild M., Russnes, Hege G., Schlichting, Ellen, Sørlie, Therese, Lingjærde, Ole C., Kristensen, Vessela N., Sahlberg, Kristine K., Skjerven, Helle K., Fritzman, Britt, and The Oslo Breast Cancer Consortium (OSBREAC)
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- 2017
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26. LIMT is a novel metastasis inhibiting lncRNA suppressed by EGF and downregulated in aggressive breast cancer
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Sas‐Chen, Aldema, Aure, Miriam R, Leibovich, Limor, Carvalho, Silvia, Enuka, Yehoshua, Körner, Cindy, Polycarpou‐Schwarz, Maria, Lavi, Sara, Nevo, Nava, Kuznetsov, Yuri, Yuan, Justin, Azuaje, Francisco, Ulitsky, Igor, Diederichs, Sven, Wiemann, Stefan, Yakhini, Zohar, Kristensen, Vessela N, Børresen‐Dale, Anne‐Lise, Yarden, Yosef, Sauer, Torill, Geisler, Jürgen, Hofvind, Solveig, Bathen, Tone F, Borgen, Elin, Engebråten, Olav, Fodstad, Øystein, Garred, Øystein, Geitvik, Gry Aarum, Kåresen, Rolf, Naume, Bjørn, Mælandsmo, Gunhild Mari, Russnes, Hege G, Schlichting, Ellen, Sørlie, Therese, Lingjærde, Ole Christian, Sahlberg, Kristine Kleivi, Skjerven, Helle Kristine, and Fritzman, Britt
- Published
- 2016
- Full Text
- View/download PDF
27. Erratum: Inflammation of mammary adipose tissue occurs in overweight and obese patients exhibiting early-stage breast cancer
- Author
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Vaysse, Charlotte, Lømo, Jon, Garred, Øystein, Fjeldheim, Frøydis, Lofteroed, Trygve, Schlichting, Ellen, McTiernan, Anne, Frydenberg, Hanne, Husøy, Anders, Lundgren, Steinar, Fagerland, Morten W., Richardsen, Elin, Wist, Erik A., Muller, Catherine, and Thune, Inger
- Published
- 2017
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28. Sample Preparation Approach Influences PAM50 Risk of Recurrence Score in Early Breast Cancer
- Author
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Lien, Tonje, primary, Ohnstad, Hege, additional, Lingjærde, Ole, additional, Vallon-Christersson, Johan, additional, Aaserud, Marit, additional, Sveli, My, additional, Borg, Åke, additional, OSBREAC, on, additional, Garred, Øystein, additional, Borgen, Elin, additional, Naume, Bjørn, additional, Russnes, Hege, additional, and Sørlie, Therese, additional
- Published
- 2021
- Full Text
- View/download PDF
29. Retrograde Transport from the Golgi Complex to the ER of Both Shiga Toxin and the Nontoxic Shiga B-Fragment Is Regulated by Butyric Acid and cAMP
- Author
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Sandvig, Kirsten, Ryd, Marie, Garred, Øystein, Schweda, Elke, Holm, Pernille Kaae, and van Deurs, Bo
- Published
- 1994
30. RAB5A expression is a predictive biomarker for trastuzumab emtansine in breast cancer
- Author
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Engebraaten, Olav, primary, Yau, Christina, additional, Berg, Kristian, additional, Borgen, Elin, additional, Garred, Øystein, additional, Berstad, Maria E.B., additional, Fremstedal, Ane S.V., additional, De Michele, Angela, additional, van’t Veer, Laura, additional, Esserman, Laura, additional, and Weyergang, Anette, additional
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- 2021
- Full Text
- View/download PDF
31. Subtype and cell type specific expression of lncRNAs provide insight into breast cancer.
- Author
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Bjørklund, Sunniva Stordal, Aure, Miriam Ragle, Häkkinen, Jari, Vallon-Christersson, Johan, Kumar, Surendra, Evensen, Katrine Bull, Fleischer, Thomas, Tost, Jörg, OSBREAC, Bathen, Tone F., Borgen, Elin, Børresen-Dale, Anne-Lise, Engebråten, Olav, Fritzman, Britt, Hartmann-Johnsen, Olaf Johan, Garred, Øystein, Geisler, Jürgen, Geitvik, Gry Aarum, Hofvind, Solveig, and Kåresen, Rolf
- Subjects
BREAST cancer ,LINCRNA ,CARCINOGENESIS ,REGULATOR genes ,GENETIC transcription regulation ,CANCER cells - Abstract
Long non-coding RNAs (lncRNAs) are involved in breast cancer pathogenesis through chromatin remodeling, transcriptional and post-transcriptional gene regulation. We report robust associations between lncRNA expression and breast cancer clinicopathological features in two population-based cohorts: SCAN-B and TCGA. Using co-expression analysis of lncRNAs with protein coding genes, we discovered three distinct clusters of lncRNAs. In silico cell type deconvolution coupled with single-cell RNA-seq analyses revealed that these three clusters were driven by cell type specific expression of lncRNAs. In one cluster lncRNAs were expressed by cancer cells and were mostly associated with the estrogen signaling pathways. In the two other clusters, lncRNAs were expressed either by immune cells or fibroblasts of the tumor microenvironment. To further investigate the cis-regulatory regions driving lncRNA expression in breast cancer, we identified subtype-specific transcription factor (TF) occupancy at lncRNA promoters. We also integrated lncRNA expression with DNA methylation data to identify long-range regulatory regions for lncRNA which were validated using ChiA-Pet-Pol2 loops. lncRNAs play an important role in shaping the gene regulatory landscape in breast cancer. We provide a detailed subtype and cell type-specific expression of lncRNA, which improves the understanding of underlying transcriptional regulation in breast cancer. Long non-coding RNAs (lncRNAs) have been shown to be involved in breast cancer pathogenesis through regulation of multiple steps of gene expression. lncRNA expression patterns are also associated with breast cancer clinicopathological features in large population-based cohorts. [ABSTRACT FROM AUTHOR]
- Published
- 2022
- Full Text
- View/download PDF
32. Germline HOXB13 mutations p.G84E and p.R217C do not confer an increased breast cancer risk
- Author
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Liu, Jingjing, Prager - van der Smissen, Wendy J. C., Collée, J. Margriet, Bolla, Manjeet K., Wang, Qin, Michailidou, Kyriaki, Dennis, Joe, Ahearn, Thomas U., Aittomäki, Kristiina, Ambrosone, Christine B., Andrulis, Irene L., Anton-Culver, Hoda, Antonenkova, Natalia N., Arndt, Volker, Arnold, Norbert, Aronson, Kristan J., Augustinsson, Annelie, Auvinen, Päivi, Becher, Heiko, Beckmann, Matthias W., Behrens, Sabine, Bermisheva, Marina, Bernstein, Leslie, Bogdanova, Natalia V., Bogdanova-Markov, Nadja, Bojesen, Stig E., Brauch, Hiltrud, Brenner, Hermann, Briceno, Ignacio, Brucker, Sara Y., Brüning, Thomas, Burwinkel, Barbara, Cai, Qiuyin, Cai, Hui, Campa, Daniele, Canzian, Federico, Castelao, Jose E., Chang-Claude, Jenny, Chanock, Stephen J., Choi, Ji-Yeob, Christiaens, Melissa, Clarke, Christine L., Couch, Fergus J., Czene, Kamila, Daly, Mary B., Devilee, Peter, dos-Santos-Silva, Isabel, Dwek, Miriam, Eccles, Diana M., Eliassen, A. Heather, Fasching, Peter A., Figueroa, Jonine, Flyger, Henrik, Fritschi, Lin, Gago-Dominguez, Manuela, Gapstur, Susan M., García-Closas, Montserrat, García-Sáenz, José A., Gaudet, Mia M., Giles, Graham G., Goldberg, Mark S., Goldgar, David E., Guénel, Pascal, Haiman, Christopher A., Håkansson, Niclas, Hall, Per, Harrington, Patricia A., Hart, Steven N., Hartman, Mikael, Hillemanns, Peter, Hopper, John L., Hou, Ming-Feng, Hunter, David J., Huo, Dezheng, Ito, Hidemi, Iwasaki, Motoki, Jakimovska, Milena, Jakubowska, Anna, John, Esther M., Kaaks, Rudolf, Kang, Daehee, Keeman, Renske, Khusnutdinova, Elza, Kim, Sung-Won, Kraft, Peter, Kristensen, Vessela N., Kurian, Allison W., Le Marchand, Loic, Li, Jingmei, Lindblom, Annika, Lophatananon, Artitaya, Luben, Robert N., Lubiński, Jan, Mannermaa, Arto, Manoochehri, Mehdi, Manoukian, Siranoush, Margolin, Sara, Mariapun, Shivaani, Matsuo, Keitaro, Maurer, Tabea, Mavroudis, Dimitrios, Meindl, Alfons, Menon, Usha, Milne, Roger L., Muir, Kenneth, Mulligan, Anna Marie, Neuhausen, Susan L., Nevanlinna, Heli, Offit, Kenneth, Olopade, Olufunmilayo I., Olson, Janet E., Olsson, Håkan, Orr, Nick, Park, Sue K., Peterlongo, Paolo, Peto, Julian, Plaseska-Karanfilska, Dijana, Presneau, Nadege, Rack, Brigitte, Rau-Murthy, Rohini, Rennert, Gad, Rennert, Hedy S., Rhenius, Valerie, Romero, Atocha, Ruebner, Matthias, Saloustros, Emmanouil, Schmutzler, Rita K., Schneeweiss, Andreas, Scott, Christopher, Shah, Mitul, Shen, Chen-Yang, Shu, Xiao-Ou, Simard, Jacques, Sohn, Christof, Southey, Melissa C., Spinelli, John J., Tamimi, Rulla M., Tapper, William J., Teo, Soo H., Terry, Mary Beth, Torres, Diana, Truong, Thérèse, Untch, Michael, Vachon, Celine M., van Asperen, Christi J., Wolk, Alicja, Yamaji, Taiki, Zheng, Wei, Ziogas, Argyrios, Ziv, Elad, Torres-Mejía, Gabriela, Dörk, Thilo, Swerdlow, Anthony J., Hamann, Ute, Schmidt, Marjanka K., Dunning, Alison M., Pharoah, Paul D. P., Easton, Douglas F., Hooning, Maartje J., Martens, John W. M., Hollestelle, Antoinette, Sahlberg, Kristine K., Børresen-Dale, Anne-Lise, Ottestad, Lars, Kåresen, Rolf, Schlichting, Ellen, Holmen, Marit Muri, Sauer, Toril, Haakensen, Vilde, Engebråten, Olav, Naume, Bjørn, Fosså, Alexander, Kiserud, Cecile E., Reinertsen, Kristin V., Helland, Åslaug, Riis, Margit, Geisler, Jürgen, Alnæs, Grethe I. Grenaker, Bathen, Tone F., Borgen, Elin, Fritzman, Britt, Garred, Øystein, Geitvik, Gry Aarum, Hofvind, Solveig, Langerød, Anita, Lingjærde, Ole Christian, Mælandsmo, Gunhild Mari, Russnes, Hege G, Skjerven, Helle Kristine, Sørlie, Therese, Clarke, Christine, Marsh, Deborah, Scott, Rodney, Baxter, Robert, Yip, Desmond, Carpenter, Jane, Davis, Alison, Pathmanathan, Nirmala, Simpson, Peter, Graham, Dinny, Sachchithananthan, Mythily, and Apollo - University of Cambridge Repository
- Subjects
631/67 ,631/208 ,article ,skin and connective tissue diseases ,692/499 ,692/4028 - Abstract
In breast cancer, high levels of homeobox protein Hox-B13 (HOXB13) have been associated with disease progression of ER-positive breast cancer patients and resistance to tamoxifen treatment. Since HOXB13 p.G84E is a prostate cancer risk allele, we evaluated the association between HOXB13 germline mutations and breast cancer risk in a previous study consisting of 3,270 familial non-BRCA1/2 breast cancer cases and 2,327 controls from the Netherlands. Although both recurrent HOXB13 mutations p.G84E and p.R217C were not associated with breast cancer risk, the risk estimation for p.R217C was not very precise. To provide more conclusive evidence regarding the role of HOXB13 in breast cancer susceptibility, we here evaluated the association between HOXB13 mutations and increased breast cancer risk within 81 studies of the international Breast Cancer Association Consortium containing 68,521 invasive breast cancer patients and 54,865 controls. Both HOXB13 p.G84E and p.R217C did not associate with the development of breast cancer in European women, neither in the overall analysis (OR = 1.035, 95% CI = 0.859–1.246, P = 0.718 and OR = 0.798, 95% CI = 0.482–1.322, P = 0.381 respectively), nor in specific high-risk subgroups or breast cancer subtypes. Thus, although involved in breast cancer progression, HOXB13 is not a material breast cancer susceptibility gene.
- Published
- 2020
33. Integrated differential DNA methylation and gene expression of formalin-fixed paraffin-embedded uveal melanoma specimens identifies genes associated with early metastasis and poor prognosis
- Author
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Ness, Charlotte, primary, Katta, Kirankumar, additional, Garred, Øystein, additional, Kumar, Theresa, additional, Olstad, Ole Kristoffer, additional, Petrovski, Goran, additional, Moe, Morten C., additional, and Noer, Agate, additional
- Published
- 2021
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34. Immune phenotype of tumor microenvironment predicts response to bevacizumab in neoadjuvant treatment ofER‐positive breast cancer
- Author
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Lippe Gythfeldt, Hedda, primary, Lien, Tonje, additional, Tekpli, Xavier, additional, Silwal‐Pandit, Laxmi, additional, Borgen, Elin, additional, Garred, Øystein, additional, Skjerven, Helle, additional, Schlichting, Ellen, additional, Lundgren, Steinar, additional, Wist, Erik, additional, Naume, Bjørn, additional, Kristensen, Vessela, additional, Børresen‐Dale, Anne‐Lise, additional, Lingjærde, Ole Christian, additional, and Engebraaten, Olav, additional
- Published
- 2020
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- View/download PDF
35. Coagulation factor V is a marker of tumor-infiltrating immune cells in breast cancer
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Tinholt, Mari, primary, Stavik, Benedicte, additional, Tekpli, Xavier, additional, Garred, Øystein, additional, Borgen, Elin, additional, Kristensen, Vessela, additional, Sahlberg, Kristine Kleivi, additional, Sandset, Per Morten, additional, and Iversen, Nina, additional
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- 2020
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- View/download PDF
36. Breast cancer metastasis: immune profiling of lymph nodes reveals exhaustion of effector T cells and immunosuppression.
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Rye, Inga Hansine, Huse, Kanutte, Josefsson, Sarah E., Kildal, Wanja, Danielsen, Håvard E., Schlichting, Ellen, Garred, Øystein, Riis, Margit L., OSBREAC, Lingjærde, Ole Christian, Myklebust, June H., and Russnes, Hege G.
- Abstract
Sentinel lymph nodes are the first nodes draining the lymph from a breast and could reveal early changes in the host immune system upon dissemination of breast cancer cells. To investigate this, we performed single‐cell immune profiling of lymph nodes with and without metastatic cells. Whereas no significant changes were observed for B‐cell and natural killer (NK)‐cell subsets, metastatic lymph nodes had a significantly increased frequency of CD8 T cells and a skewing toward an effector/memory phenotype of CD4 and CD8 T cells, suggesting an ongoing immune response. Additionally, metastatic lymph nodes had an increased frequency of TIGIT (T‐cell immunoreceptor with Ig and ITIM domains)‐positive T cells with suppressed TCR signaling compared with non‐metastatic nodes, indicating exhaustion of effector T cells, and an increased frequency of regulatory T cells (Tregs) with an activated phenotype. T‐cell alterations correlated with the percentage of metastatic tumor cells, reflecting the presence of metastatic tumor cells driving T effector cells toward exhaustion and promoting immunosuppression by recruitment or increased differentiation toward Tregs. These results show that immune suppression occurs already in early stages of tumor progression. [ABSTRACT FROM AUTHOR]
- Published
- 2022
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- View/download PDF
37. EGFR Gene Copy Number Heterogeneity in Fine-Needle Aspiration Cytology From Breast Carcinomas Determined by Chromogenic In Situ Hybridization
- Author
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Sauer, Torill, Beraki, Kahsai, Noren, Tove, Garred, Øystein, and Næss, Oddvar
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- 2005
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38. Reconstitution of Clathrin-Independent Endocytosis at the Apical Domain of Permeabilized MDCK II cells: Requirement for a Rho-Family GTPase
- Author
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Garred, Øystein, Rodal, Siv Kjersti, van Deurs, Bo, and Sandvig, Kirsten
- Published
- 2001
39. Serum levels of inflammation‐related markers and metabolites predict response to neoadjuvant chemotherapy with and without bevacizumab in breast cancers
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Nome, Marianne E., primary, Euceda, Leslie R., additional, Jabeen, Shakila, additional, Debik, Julia, additional, Bathen, Tone F., additional, Giskeødegård, Guro F., additional, Taskén, Kristin A., additional, Mælandsmo, Gunhild M., additional, Halvorsen, Bente, additional, Yndestad, Arne, additional, Borgen, Elin, additional, Garred, Øystein, additional, Aukrust, Pål, additional, Ueland, Thor, additional, Engebraaten, Olav, additional, Kristensen, Vessela N., additional, and Tekpli, Xavier, additional
- Published
- 2019
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- View/download PDF
40. Assessing Treatment Response and Prognosis by Serum and Tissue Metabolomics in Breast Cancer Patients
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Debik, Julia, primary, Euceda, Leslie R., additional, Lundgren, Steinar, additional, Gythfeldt, Hedda von der Lippe, additional, Garred, Øystein, additional, Borgen, Elin, additional, Engebraaten, Olav, additional, Bathen, Tone F., additional, and Giskeødegård, Guro F., additional
- Published
- 2019
- Full Text
- View/download PDF
41. Toward Personalized Computer Simulation of Breast Cancer Treatment: A Multiscale Pharmacokinetic and Pharmacodynamic Model Informed by Multitype Patient Data
- Author
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Lai, Xiaoran, primary, Geier, Oliver M., additional, Fleischer, Thomas, additional, Garred, Øystein, additional, Borgen, Elin, additional, Funke, Simon W., additional, Kumar, Surendra, additional, Rognes, Marie E., additional, Seierstad, Therese, additional, Børresen-Dale, Anne-Lise, additional, Kristensen, Vessela N., additional, Engebraaten, Olav, additional, Köhn-Luque, Alvaro, additional, and Frigessi, Arnoldo, additional
- Published
- 2019
- Full Text
- View/download PDF
42. Inflammation of mammary adipose tissue occurs in overweight and obese patients exhibiting early-stage breast cancer
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Vaysse, Charlotte, Lømo, Jon, Garred, Øystein, Fjeldheim, Frøydis Nyborg, Lofterød, Trygve, Schlichting, Ellen, McTiernan, Anne, Frydenberg, Hanne, Husøy, Anders, Lundgren, Steinar, Fagerland, Morten W, Richardsen, Elin, Wist, Erik, Muller, Catherine, and Thune, Inger
- Subjects
VDP::Medisinske Fag: 700::Klinisk medisinske fag: 750::Onkologi: 762 ,VDP::Medical disciplines: 700::Clinical medical disciplines: 750::Oncology: 762 ,Neoplasms. Tumors. Oncology. Including cancer and carcinogens ,RC254-282 ,Article - Abstract
Growing evidence indicates that adiposity is associated with breast cancer risk and negatively affects breast cancer recurrence and survival, a paracrine role of mammary adipose tissue being very likely in this process. In contrast to other adipose depots, occurrence of a sub-inflammatory state of mammary adipose tissue defined by dying adipocytes surrounded by macrophages forming crown-like structures in overweight and obese subjects, remains only partially described. In a general population of breast cancer patients (107 patients) mostly undergoing breast-conserving surgery, we found a positive association between patient’s body composition, breast adipocytes size, and presence of crown-like structures in mammary adipose tissue close to the tumor. Overweight (BMI: 25.0–29.9 kg/m2) and obese (BMI ≥ 30.0 kg/m2) patients have 3.2 and 6.9 times higher odds ratio of crown-like structures respectively, compared with normal weight patients. The relatively small increase in adipocyte size in crown-like structures positive vs. negative patients suggests that mammary adipose tissue inflammation might occur early during hypertrophy. Our results further highlight that body mass index is an adequate predictor of the presence of crown-like structures in mammary adipose tissue among postmenopausal women, whereas in premenopausal women truncal fat percentage might be more predictive, suggesting that mammary adipose tissue inflammation is more likely to occur in patients exhibiting visceral obesity. Finally, the presence of crown-like structures was positively associated with systemic markers such as the Triglyceride/High-density lipoprotein-cholesterol ratio serum C-reactive protein and glucose/(HbA1c) glycated Haemoglobin. These compelling results demonstrate that excess adiposity, even in overweight patients, is associated with mammary adipose tissue inflammation, an event that could contribute to breast cancer development and progression., Immunology: Weight tied to inflammation in fat surrounding tumor Overweight and obese women with breast cancer show more inflammation in their mammary fat tissue, creating an environment favorable to tumor growth. In a study performed at the Oslo University Hospital, Norway, Charlotte Vaysse and colleagues characterized the fat cells found close to the breast tumors of 107 patients with early-stage disease. The researchers showed that overweight and obese women were more likely to have clusters of pro-inflammatory macrophage cells within the fat tissue close to the tumors than normal weight women. They further divided the patients according to whether they’d gone through menopause or not, and found that body mass index was a good predictor of fat cell inflammatory status in postmenopausal women, whereas belly fat percentage was a more accurate measure for premenopausal women. The inflammation brought on by excess weight may contribute to breast cancer development and progression.
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- 2017
43. Personalized Computer Simulations of Breast Cancer Tumors Treated with Neoadjuvant Chemotherapy and Bevacizumab
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Köhn-Luque, Alvaro, Xiaoran Lai, Geier, Oliver M, Garred, Øystein, Fleischer, Thomas, Vitelli, Valeria, Zucknick, Manuela, Seierstad, Therese, Borgen, Elin, Børresen-Dale, Anne Lise, Kristesen, Vessela N, Engebråten, Olav, and Frigessi, Arnoldo
- Abstract
Poster presented at Personalized Cancer Care Symposium, Oslo 2016: http://pccradiumhospital.org/
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- 2017
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44. Immune phenotype of tumor microenvironment predicts response to bevacizumab in neoadjuvant treatment of ER‐positive breast cancer.
- Author
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Lippe Gythfeldt, Hedda, Lien, Tonje, Tekpli, Xavier, Silwal‐Pandit, Laxmi, Borgen, Elin, Garred, Øystein, Skjerven, Helle, Schlichting, Ellen, Lundgren, Steinar, Wist, Erik, Naume, Bjørn, Kristensen, Vessela, Børresen‐Dale, Anne‐Lise, Lingjærde, Ole Christian, and Engebraaten, Olav
- Subjects
TRIPLE-negative breast cancer ,TUMOR microenvironment ,EPIDERMAL growth factor receptors ,KILLER cells ,BREAST cancer ,ESTROGEN receptors - Abstract
Antiangiogenic drugs are potentially a useful supplement to neoadjuvant chemotherapy for a subgroup of patients with human epidermal growth factor receptor 2 (HER2) negative breast cancer, but reliable biomarkers for improved response are lacking. Here, we report on a randomized phase II clinical trial to study the added effect of bevacizumab in neoadjuvant chemotherapy with FEC100 (5‐fluorouracil, epirubicin and cyclophosphamide) and taxanes (n = 132 patients). Gene expression from the tumors was obtained before neoadjuvant treatment, and treatment response was evaluated by residual cancer burden (RCB) at time of surgery. Bevacizumab increased the proportion of complete responders (RCB class 0) from 5% to 20% among patients with estrogen receptor (ER) positive tumors (P =.02). Treatment with bevacizumab was associated with improved 8‐year disease‐free survival (P =.03) among the good responders (RCB class 0 or I). Patients treated with paclitaxel (n = 45) responded better than those treated with docetaxel (n = 21; P =.03). Improved treatment response was associated with higher proliferation rate and an immune phenotype characterized by high presence of classically activated M1 macrophages, activated NK cells and memory activated CD4 T cells. Treatment with bevacizumab increased the number of adverse events, including hemorrhage, hypertension, infection and febrile neutropenia, but despite this, the ECOG status was not affected. What's new? The molecular effects of antiangiogenic therapy are largely unknown. In this neoadjuvant clinical trial studying the anti‐VEGF monoclonal antibody bevacizumab, the authors demonstrated increased response in tumors with immune gene upregulation, using a 770‐gene immune panel. Specific immune cell types were identified as determinants of drug response. Moreover, the results suggested improved recurrence‐free survival in patients achieving a favorable response after neoadjuvant antiangiogenic therapy in combination with chemotherapy. [ABSTRACT FROM AUTHOR]
- Published
- 2020
- Full Text
- View/download PDF
45. Contrasting DCIS and invasive breast cancer by subtype suggests basal-like DCIS as distinct lesions.
- Author
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Bergholtz, Helga, Lien, Tonje G., Swanson, David M., Frigessi, Arnoldo, Oslo Breast Cancer Research Consortium (OSBREAC), Bathen, Tone F., Borgen, Elin, Børresen-Dale, Anne Lise, Engebråten, Olav, Garred, Øystein, Geisler, Jürgen, Geitvik, Gry Aarum, Hartmann-Johnsen, Olaf Johan, Hofvind, Solveig, Kristensen, Vessela N., Langerød, Anita, Lingjærde, Ole Christian, Mælandsmo, Gunhild Mari, Naume, Bjørn, and Russnes, Hege
- Published
- 2020
- Full Text
- View/download PDF
46. DNA copy number motifs are strong and independent predictors of survival in breast cancer.
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Pladsen, Arne V., Nilsen, Gro, Rueda, Oscar M., Aure, Miriam R., Borgan, Ørnulf, Liestøl, Knut, Vitelli, Valeria, Frigessi, Arnoldo, Langerød, Anita, Mathelier, Anthony, OSBREAC, Bathen, Tone F., Borgen, Elin, Børresen-Dale, Anne-Lise, Engebråten, Olav, Fritzman, Britt, Garred, Øystein, Geisler, Jürgen, Geitvik, Gry Aarum, and Hofvind, Solveig
- Subjects
DNA copy number variations ,BREAST cancer ,GENOMES ,DNA replication ,DNA repair - Abstract
Somatic copy number alterations are a frequent sign of genome instability in cancer. A precise characterization of the genome architecture would reveal underlying instability mechanisms and provide an instrument for outcome prediction and treatment guidance. Here we show that the local spatial behavior of copy number profiles conveys important information about this architecture. Six filters were defined to characterize regional traits in copy number profiles, and the resulting Copy Aberration Regional Mapping Analysis (CARMA) algorithm was applied to tumors in four breast cancer cohorts (n = 2919). The derived motifs represent a layer of information that complements established molecular classifications of breast cancer. A score reflecting presence or absence of motifs provided a highly significant independent prognostic predictor. Results were consistent between cohorts. The nonsite-specific occurrence of the detected patterns suggests that CARMA captures underlying replication and repair defects and could have a future potential in treatment stratification. Pladsen et al. develop Copy Aberration Regional Mapping Analysis (CARMA), an algorithm that derives motifs for copy number profiles in breast cancers by integrating several features, to predict breast cancer prognosis and stratifications. Their algorithm can detect replication and repair defects and can be used in personalized medicine. [ABSTRACT FROM AUTHOR]
- Published
- 2020
- Full Text
- View/download PDF
47. Serum levels of inflammation‐related markers and metabolites predict response to neoadjuvant chemotherapy with and without bevacizumab in breast cancers.
- Author
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Nome, Marianne E., Euceda, Leslie R., Jabeen, Shakila, Debik, Julia, Bathen, Tone F., Giskeødegård, Guro F., Taskén, Kristin A., Mælandsmo, Gunhild M., Halvorsen, Bente, Yndestad, Arne, Borgen, Elin, Garred, Øystein, Aukrust, Pål, Ueland, Thor, Engebraaten, Olav, Kristensen, Vessela N., and Tekpli, Xavier
- Subjects
ACUTE phase proteins ,CANCER chemotherapy ,PENTRAXINS ,BREAST cancer ,METABOLITES ,ENDOTHELIAL growth factors ,BEVACIZUMAB ,NEOADJUVANT chemotherapy - Abstract
Angiogenesis is necessary for tumor growth and has been targeted in breast cancer; however, it is unclear which patients will respond and benefit from antiangiogenic therapy. We report noninvasive monitoring of patient response to neoadjuvant chemotherapy given alone or in combination with anti‐vascular endothelial growth factor (bevacizumab) in a randomized clinical trial. At four time points during neoadjuvant chemotherapy ± bevacizumab of receptor tyrosine‐protein kinase erbB‐2‐negative breast cancers, we measured metabolites and inflammation‐related markers in patient's serum. We report significant changes in the levels of several molecules induced by bevacizumab, the most prominent being an increase in pentraxin 3 (PTX3) and von Willebrand factor (VWF). Serum levels of AXL, VWF and pulmonary and activation‐regulated cytokine (PARC/CCL18) reflected response to chemotherapy alone or in combination with bevacizumab. We further analyzed serum cytokines in relation to tumor characteristics such as gene expression, tumor metabolites and tumor infiltrating leukocytes. We found that VWF and growth‐differentiation factor 15 tumor mRNA levels correlated with their respective serum protein levels suggesting that these cytokines may be produced by tumors and outflow to the bloodstream while influencing the tumor microenvironment locally. Finally, we used binomial logistic regression which allowed to predict patient's response using only 10 noninvasive biomarkers. Our study highlights the potential of monitoring circulating levels of cytokines and metabolites during breast cancer therapy. What's new? How inflammatory markers and metabolites mold the tumor microenvironment, especially angiogenesis, is still poorly understood. Here the authors tested the response of patients with breast cancer to neoadjuvant chemotherapy with or without the angiogenesis inhibitor bevacizumab. They identified 10 non‐invasive biomarkers that predict therapy response, including the acute phase protein pentraxin‐3 and hemostasis regulator von Willebrand factor that were specifically upregulated by bevacizumab treatment. The authors suggest that these factors could be further targeted to potentiate antiangiogenic therapies in breast cancer and beyond. [ABSTRACT FROM AUTHOR]
- Published
- 2020
- Full Text
- View/download PDF
48. Towards personalized computer simulation of breast cancer treatment: a multi-scale pharmacokinetic and pharmacodynamic model informed by multi-type patient data
- Author
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Lai, Xiaoran, primary, Geier, Oliver M, additional, Fleischer, Thomas, additional, Garred, Øystein, additional, Borgen, Elin, additional, Funke, Simon Wolfgang, additional, Kumar, Surendra, additional, Elisabeth Rognes, Marie, additional, Seierstad, Therese, additional, Børresen-Dale, Anne-Lise, additional, Kristensen, Vessela N., additional, Engebraaten, Olav, additional, Köhn-Luque, Alvaro, additional, and Frigessi, Arnoldo, additional
- Published
- 2018
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- View/download PDF
49. Additional file 2: Table S2. of Lipoprotein subfractions by nuclear magnetic resonance are associated with tumor characteristics in breast cancer
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Flote, Vidar, Riyas Vettukattil, Bathen, Tone, Egeland, Thore, McTiernan, Anne, Frydenberg, Hanne, Husøy, Anders, Finstad, Sissi, Lømo, Jon, Garred, Øystein, Schlichting, Ellen, Wist, Erik, and Thune, Inger
- Abstract
Principal Component analysis (PCA); the association between tumor characteristics and lipoprotein subfractions by NMR among estrogen receptor positive (n = 52). (DOCX 16 kb)
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- 2016
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50. The Longitudinal Transcriptional Response to Neoadjuvant Chemotherapy with and without Bevacizumab in Breast Cancer
- Author
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Silwal-Pandit, Laxmi, primary, Nord, Silje, additional, von der Lippe Gythfeldt, Hedda, additional, Møller, Elen K., additional, Fleischer, Thomas, additional, Rødland, Einar, additional, Krohn, Marit, additional, Borgen, Elin, additional, Garred, Øystein, additional, Olsen, Tone, additional, Vu, Phuong, additional, Skjerven, Helle, additional, Fangberget, Anne, additional, Holmen, Marit M., additional, Schlitchting, Ellen, additional, Wille, Elisabeth, additional, Nordberg Stokke, Mette, additional, Moen Vollan, Hans Kristian, additional, Kristensen, Vessela, additional, Langerød, Anita, additional, Lundgren, Steinar, additional, Wist, Erik, additional, Naume, Bjørn, additional, Lingjærde, Ole Christian, additional, Børresen-Dale, Anne-Lise, additional, and Engebraaten, Olav, additional
- Published
- 2017
- Full Text
- View/download PDF
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