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645 results on '"Grigoriadis, Anita"'

1. Deep Multi-Scale U-Net Architecture and Label-Noise Robust Training Strategies for Histopathological Image Segmentation

Author

Kurian, Nikhil Cherian, Lohan, Amit, Verghese, Gregory, Dharamshi, Nimish, Meena, Swati, Li, Mengyuan, Liu, Fangfang, Gillet, Cheryl, Rane, Swapnil, Grigoriadis, Anita, and Sethi, Amit

Subjects
Electrical Engineering and Systems Science - Image and Video Processing, Computer Science - Computer Vision and Pattern Recognition
Abstract

Although the U-Net architecture has been extensively used for segmentation of medical images, we address two of its shortcomings in this work. Firstly, the accuracy of vanilla U-Net degrades when the target regions for segmentation exhibit significant variations in shape and size. Even though the U-Net already possesses some capability to analyze features at various scales, we propose to explicitly add multi-scale feature maps in each convolutional module of the U-Net encoder to improve segmentation of histology images. Secondly, the accuracy of a U-Net model also suffers when the annotations for supervised learning are noisy or incomplete. This can happen due to the inherent difficulty for a human expert to identify and delineate all instances of specific pathology very precisely and accurately. We address this challenge by introducing auxiliary confidence maps that emphasize less on the boundaries of the given target regions. Further, we utilize the bootstrapping properties of the deep network to address the missing annotation problem intelligently. In our experiments on a private dataset of breast cancer lymph nodes, where the primary task was to segment germinal centres and sinus histiocytosis, we observed substantial improvement over a U-Net baseline based on the two proposed augmentations., Comment: 12 pages, 4 figures , 2 tables ,Added Attention UNet Results, Added Sinus and Germinal Center overlay images, Modified paper format, Fixed Title typos

Published
2022

6. Genomic analysis defines clonal relationships of ductal carcinoma in situ and recurrent invasive breast cancer

Author

Lips, Esther H., Kumar, Tapsi, Megalios, Anargyros, Visser, Lindy L., Sheinman, Michael, Fortunato, Angelo, Shah, Vandna, Hoogstraat, Marlous, Sei, Emi, Mallo, Diego, Roman-Escorza, Maria, Ahmed, Ahmed A., Xu, Mingchu, van den Belt-Dusebout, Alexandra W., Brugman, Wim, Casasent, Anna K., Clements, Karen, Davies, Helen R., Fu, Liping, Grigoriadis, Anita, Hardman, Timothy M., King, Lorraine M., Krete, Marielle, Kristel, Petra, de Maaker, Michiel, Maley, Carlo C., Marks, Jeffrey R., Menegaz, Brian A., Mulder, Lennart, Nieboer, Frank, Nowinski, Salpie, Pinder, Sarah, Quist, Jelmar, Salinas-Souza, Carolina, Schaapveld, Michael, Schmidt, Marjanka K., Shaaban, Abeer M., Shami, Rana, Sridharan, Mathini, Zhang, John, Stobart, Hilary, Collyar, Deborah, Nik-Zainal, Serena, Wessels, Lodewyk F. A., Hwang, E. Shelley, Navin, Nicholas E., Futreal, P. Andrew, Thompson, Alastair M., Wesseling, Jelle, and Sawyer, Elinor J.

Published
2022
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8. TGF-β1 potentiates Vγ9Vδ2 T cell adoptive immunotherapy of cancer

Author

Beatson, Richard E., Parente-Pereira, Ana C., Halim, Leena, Cozzetto, Domenico, Hull, Caroline, Whilding, Lynsey M., Martinez, Olivier, Taylor, Chelsea A., Obajdin, Jana, Luu Hoang, Kim Ngan, Draper, Benjamin, Iqbal, Ayesha, Hardiman, Tom, Zabinski, Tomasz, Man, Francis, de Rosales, Rafael T.M., Xie, Jinger, Aswad, Fred, Achkova, Daniela, Joseph, Chung-Yang Ricardo, Ciprut, Sara, Adami, Antonella, Roider, Helge G., Hess-Stumpp, Holger, Győrffy, Balázs, Quist, Jelmar, Grigoriadis, Anita, Sommer, Anette, Tutt, Andrew N.J., Davies, David M., and Maher, John

Published
2021
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9. Synergistic T cell signaling by 41BB and CD28 is optimally achieved by membrane proximal positioning within parallel chimeric antigen receptors

Author

Muliaditan, Tamara, Halim, Leena, Whilding, Lynsey M., Draper, Benjamin, Achkova, Daniela Y., Kausar, Fahima, Glover, Maya, Bechman, Natasha, Arulappu, Appitha, Sanchez, Jenifer, Flaherty, Katie R., Obajdin, Jana, Grigoriadis, Kristiana, Antoine, Pierre, Larcombe-Young, Daniel, Hull, Caroline M., Buus, Richard, Gordon, Peter, Grigoriadis, Anita, Davies, David M., Schurich, Anna, and Maher, John

Published
2021
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10. Anti-EGFR antibody-drug conjugate carrying an inhibitor targeting CDK restricts triple-negative breast cancer growth

Author

Cheung, Anthony, primary, Chenoweth, Alicia M., additional, Johansson, Annelie, additional, Laddach, Roman, additional, Guppy, Naomi, additional, Trendell, Jennifer, additional, Esapa, Benjamina, additional, Mavousian, Antranik, additional, Navarro-Llinas, Blanca, additional, Haider, Syed, additional, Romero-Clavijo, Pablo, additional, Hoffmann, Ricarda M., additional, Andriollo, Paolo, additional, Rahman, Khondaker Miraz, additional, Jackson, Paul, additional, Tsoka, Sophia, additional, Irshad, Sheeba, additional, Roxanis, Ioannis, additional, Grigoriadis, Anita, additional, Thurston, David E., additional, Lord, Christopher J., additional, Tutt, Andrew N.J., additional, and Karagiannis, Sophia N., additional

Published
2024
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12. Image-based multiplex immune profiling of cancer tissues: translational implications. A report of the International Immuno-oncology Biomarker Working Group on Breast Cancer

Author

Pathologie, Cancer, Jahangir, Chowdhury Arif, Page, David B., Broeckx, Glenn, Gonzalez, Claudia A., Burke, Caoimbhe, Murphy, Clodagh, Reis-Filho, Jorge S., Ly, Amy, Harms, Paul W., Gupta, Rajarsi R., Vieth, Michael, Hida, Akira I., Kahila, Mohamed, Kos, Zuzana, van Diest, Paul J., Verbandt, Sara, Thagaard, Jeppe, Khiroya, Reena, Abduljabbar, Khalid, Acosta Haab, Gabriela, Acs, Balazs, Adams, Sylvia, Almeida, Jonas S., Alvarado-Cabrero, Isabel, Azmoudeh-Ardalan, Farid, Badve, Sunil, Baharun, Nurkhairul Bariyah, Bellolio, Enrique R., Bheemaraju, Vydehi, Blenman, Kim R.M., Botinelly Mendonça Fujimoto, Luciana, Burgues, Octavio, Chardas, Alexandros, Cheang, Maggie Chon U., Ciompi, Francesco, Cooper, Lee A.D., Coosemans, An, Corredor, Germán, Dantas Portela, Flavio Luis, Deman, Frederik, Demaria, Sandra, Dudgeon, Sarah N., Elghazawy, Mahmoud, Fernandez-Martín, Claudio, Fineberg, Susan, Fox, Stephen B., Giltnane, Jennifer M., Gnjatic, Sacha, Gonzalez-Ericsson, Paula I., Grigoriadis, Anita, Halama, Niels, Hanna, Matthew G., Harbhajanka, Aparna, Hart, Steven N., Hartman, Johan, Hewitt, Stephen, Horlings, Hugo M., Husain, Zaheed, Irshad, Sheeba, Janssen, Emiel A.M., Kataoka, Tatsuki R., Kawaguchi, Kosuke, Khramtsov, Andrey I., Kiraz, Umay, Kirtani, Pawan, Kodach, Liudmila L., Korski, Konstanty, Akturk, Guray, Scott, Ely, Kovács, Anikó, Lænkholm, Anne Vibeke, Lang-Schwarz, Corinna, Larsimont, Denis, Lennerz, Jochen K., Lerousseau, Marvin, Li, Xiaoxian, Madabhushi, Anant, Maley, Sai K., Manur Narasimhamurthy, Vidya, Marks, Douglas K., McDonald, Elizabeth S., Mehrotra, Ravi, Michiels, Stefan, Kharidehal, Durga, Minhas, Fayyaz ul Amir Afsar, Mittal, Shachi, Moore, David A., Mushtaq, Shamim, Nighat, Hussain, Papathomas, Thomas, Penault-Llorca, Frederique, Perera, Rashindrie D., Pinard, Christopher J., Pinto-Cardenas, Juan Carlos, Pruneri, Giancarlo, Pusztai, Lajos, Rajpoot, Nasir Mahmood, Rapoport, Bernardo Leon, Rau, Tilman T., Ribeiro, Joana M., Rimm, David, Vincent-Salomon, Anne, Saltz, Joel, Sayed, Shahin, Hytopoulos, Evangelos, Mahon, Sarah, Siziopikou, Kalliopi P., Sotiriou, Christos, Stenzinger, Albrecht, Sughayer, Maher A., Sur, Daniel, Symmans, Fraser, Tanaka, Sunao, Taxter, Timothy, Tejpar, Sabine, Teuwen, Jonas, Thompson, E. Aubrey, Tramm, Trine, Tran, William T., van der Laak, Jeroen, Verghese, Gregory E., Viale, Giuseppe, Wahab, Noorul, Walter, Thomas, Waumans, Yannick, Wen, Hannah Y., Yang, Wentao, Yuan, Yinyin, Bartlett, John, Loibl, Sibylle, Denkert, Carsten, Savas, Peter, Loi, Sherene, Specht Stovgaard, Elisabeth, Salgado, Roberto, Gallagher, William M., Rahman, Arman, Pathologie, Cancer, Jahangir, Chowdhury Arif, Page, David B., Broeckx, Glenn, Gonzalez, Claudia A., Burke, Caoimbhe, Murphy, Clodagh, Reis-Filho, Jorge S., Ly, Amy, Harms, Paul W., Gupta, Rajarsi R., Vieth, Michael, Hida, Akira I., Kahila, Mohamed, Kos, Zuzana, van Diest, Paul J., Verbandt, Sara, Thagaard, Jeppe, Khiroya, Reena, Abduljabbar, Khalid, Acosta Haab, Gabriela, Acs, Balazs, Adams, Sylvia, Almeida, Jonas S., Alvarado-Cabrero, Isabel, Azmoudeh-Ardalan, Farid, Badve, Sunil, Baharun, Nurkhairul Bariyah, Bellolio, Enrique R., Bheemaraju, Vydehi, Blenman, Kim R.M., Botinelly Mendonça Fujimoto, Luciana, Burgues, Octavio, Chardas, Alexandros, Cheang, Maggie Chon U., Ciompi, Francesco, Cooper, Lee A.D., Coosemans, An, Corredor, Germán, Dantas Portela, Flavio Luis, Deman, Frederik, Demaria, Sandra, Dudgeon, Sarah N., Elghazawy, Mahmoud, Fernandez-Martín, Claudio, Fineberg, Susan, Fox, Stephen B., Giltnane, Jennifer M., Gnjatic, Sacha, Gonzalez-Ericsson, Paula I., Grigoriadis, Anita, Halama, Niels, Hanna, Matthew G., Harbhajanka, Aparna, Hart, Steven N., Hartman, Johan, Hewitt, Stephen, Horlings, Hugo M., Husain, Zaheed, Irshad, Sheeba, Janssen, Emiel A.M., Kataoka, Tatsuki R., Kawaguchi, Kosuke, Khramtsov, Andrey I., Kiraz, Umay, Kirtani, Pawan, Kodach, Liudmila L., Korski, Konstanty, Akturk, Guray, Scott, Ely, Kovács, Anikó, Lænkholm, Anne Vibeke, Lang-Schwarz, Corinna, Larsimont, Denis, Lennerz, Jochen K., Lerousseau, Marvin, Li, Xiaoxian, Madabhushi, Anant, Maley, Sai K., Manur Narasimhamurthy, Vidya, Marks, Douglas K., McDonald, Elizabeth S., Mehrotra, Ravi, Michiels, Stefan, Kharidehal, Durga, Minhas, Fayyaz ul Amir Afsar, Mittal, Shachi, Moore, David A., Mushtaq, Shamim, Nighat, Hussain, Papathomas, Thomas, Penault-Llorca, Frederique, Perera, Rashindrie D., Pinard, Christopher J., Pinto-Cardenas, Juan Carlos, Pruneri, Giancarlo, Pusztai, Lajos, Rajpoot, Nasir Mahmood, Rapoport, Bernardo Leon, Rau, Tilman T., Ribeiro, Joana M., Rimm, David, Vincent-Salomon, Anne, Saltz, Joel, Sayed, Shahin, Hytopoulos, Evangelos, Mahon, Sarah, Siziopikou, Kalliopi P., Sotiriou, Christos, Stenzinger, Albrecht, Sughayer, Maher A., Sur, Daniel, Symmans, Fraser, Tanaka, Sunao, Taxter, Timothy, Tejpar, Sabine, Teuwen, Jonas, Thompson, E. Aubrey, Tramm, Trine, Tran, William T., van der Laak, Jeroen, Verghese, Gregory E., Viale, Giuseppe, Wahab, Noorul, Walter, Thomas, Waumans, Yannick, Wen, Hannah Y., Yang, Wentao, Yuan, Yinyin, Bartlett, John, Loibl, Sibylle, Denkert, Carsten, Savas, Peter, Loi, Sherene, Specht Stovgaard, Elisabeth, Salgado, Roberto, Gallagher, William M., and Rahman, Arman

Published
2024

13. Image-based multiplex immune profiling of cancer tissues:translational implications. A report of the International Immuno-oncology Biomarker Working Group on Breast Cancer

Author

Jahangir, Chowdhury Arif, Page, David B., Broeckx, Glenn, Gonzalez, Claudia A., Burke, Caoimbhe, Murphy, Clodagh, Reis-Filho, Jorge S., Ly, Amy, Harms, Paul W., Gupta, Rajarsi R., Vieth, Michael, Hida, Akira I., Kahila, Mohamed, Kos, Zuzana, van Diest, Paul J., Verbandt, Sara, Thagaard, Jeppe, Khiroya, Reena, Abduljabbar, Khalid, Acosta Haab, Gabriela, Acs, Balazs, Adams, Sylvia, Almeida, Jonas S., Alvarado-Cabrero, Isabel, Azmoudeh-Ardalan, Farid, Badve, Sunil, Baharun, Nurkhairul Bariyah, Bellolio, Enrique R., Bheemaraju, Vydehi, Blenman, Kim R.M., Botinelly Mendonça Fujimoto, Luciana, Burgues, Octavio, Chardas, Alexandros, Cheang, Maggie Chon U., Ciompi, Francesco, Cooper, Lee A.D., Coosemans, An, Corredor, Germán, Dantas Portela, Flavio Luis, Deman, Frederik, Demaria, Sandra, Dudgeon, Sarah N., Elghazawy, Mahmoud, Fernandez-Martín, Claudio, Fineberg, Susan, Fox, Stephen B., Giltnane, Jennifer M., Gnjatic, Sacha, Gonzalez-Ericsson, Paula I., Grigoriadis, Anita, Halama, Niels, Hanna, Matthew G., Harbhajanka, Aparna, Hart, Steven N., Hartman, Johan, Hewitt, Stephen, Horlings, Hugo M., Husain, Zaheed, Irshad, Sheeba, Janssen, Emiel A.M., Kataoka, Tatsuki R., Kawaguchi, Kosuke, Khramtsov, Andrey I., Kiraz, Umay, Kirtani, Pawan, Kodach, Liudmila L., Korski, Konstanty, Akturk, Guray, Scott, Ely, Kovács, Anikó, Lænkholm, Anne Vibeke, Lang-Schwarz, Corinna, Larsimont, Denis, Lennerz, Jochen K., Lerousseau, Marvin, Li, Xiaoxian, Madabhushi, Anant, Maley, Sai K., Manur Narasimhamurthy, Vidya, Marks, Douglas K., McDonald, Elizabeth S., Mehrotra, Ravi, Michiels, Stefan, Kharidehal, Durga, Minhas, Fayyaz ul Amir Afsar, Mittal, Shachi, Moore, David A., Mushtaq, Shamim, Nighat, Hussain, Papathomas, Thomas, Penault-Llorca, Frederique, Perera, Rashindrie D., Pinard, Christopher J., Pinto-Cardenas, Juan Carlos, Pruneri, Giancarlo, Pusztai, Lajos, Rajpoot, Nasir Mahmood, Rapoport, Bernardo Leon, Rau, Tilman T., Ribeiro, Joana M., Rimm, David, Vincent-Salomon, Anne, Saltz, Joel, Sayed, Shahin, Hytopoulos, Evangelos, Mahon, Sarah, Siziopikou, Kalliopi P., Sotiriou, Christos, Stenzinger, Albrecht, Sughayer, Maher A., Sur, Daniel, Symmans, Fraser, Tanaka, Sunao, Taxter, Timothy, Tejpar, Sabine, Teuwen, Jonas, Thompson, E. Aubrey, Tramm, Trine, Tran, William T., van der Laak, Jeroen, Verghese, Gregory E., Viale, Giuseppe, Wahab, Noorul, Walter, Thomas, Waumans, Yannick, Wen, Hannah Y., Yang, Wentao, Yuan, Yinyin, Bartlett, John, Loibl, Sibylle, Denkert, Carsten, Savas, Peter, Loi, Sherene, Specht Stovgaard, Elisabeth, Salgado, Roberto, Gallagher, William M., Rahman, Arman, Jahangir, Chowdhury Arif, Page, David B., Broeckx, Glenn, Gonzalez, Claudia A., Burke, Caoimbhe, Murphy, Clodagh, Reis-Filho, Jorge S., Ly, Amy, Harms, Paul W., Gupta, Rajarsi R., Vieth, Michael, Hida, Akira I., Kahila, Mohamed, Kos, Zuzana, van Diest, Paul J., Verbandt, Sara, Thagaard, Jeppe, Khiroya, Reena, Abduljabbar, Khalid, Acosta Haab, Gabriela, Acs, Balazs, Adams, Sylvia, Almeida, Jonas S., Alvarado-Cabrero, Isabel, Azmoudeh-Ardalan, Farid, Badve, Sunil, Baharun, Nurkhairul Bariyah, Bellolio, Enrique R., Bheemaraju, Vydehi, Blenman, Kim R.M., Botinelly Mendonça Fujimoto, Luciana, Burgues, Octavio, Chardas, Alexandros, Cheang, Maggie Chon U., Ciompi, Francesco, Cooper, Lee A.D., Coosemans, An, Corredor, Germán, Dantas Portela, Flavio Luis, Deman, Frederik, Demaria, Sandra, Dudgeon, Sarah N., Elghazawy, Mahmoud, Fernandez-Martín, Claudio, Fineberg, Susan, Fox, Stephen B., Giltnane, Jennifer M., Gnjatic, Sacha, Gonzalez-Ericsson, Paula I., Grigoriadis, Anita, Halama, Niels, Hanna, Matthew G., Harbhajanka, Aparna, Hart, Steven N., Hartman, Johan, Hewitt, Stephen, Horlings, Hugo M., Husain, Zaheed, Irshad, Sheeba, Janssen, Emiel A.M., Kataoka, Tatsuki R., Kawaguchi, Kosuke, Khramtsov, Andrey I., Kiraz, Umay, Kirtani, Pawan, Kodach, Liudmila L., Korski, Konstanty, Akturk, Guray, Scott, Ely, Kovács, Anikó, Lænkholm, Anne Vibeke, Lang-Schwarz, Corinna, Larsimont, Denis, Lennerz, Jochen K., Lerousseau, Marvin, Li, Xiaoxian, Madabhushi, Anant, Maley, Sai K., Manur Narasimhamurthy, Vidya, Marks, Douglas K., McDonald, Elizabeth S., Mehrotra, Ravi, Michiels, Stefan, Kharidehal, Durga, Minhas, Fayyaz ul Amir Afsar, Mittal, Shachi, Moore, David A., Mushtaq, Shamim, Nighat, Hussain, Papathomas, Thomas, Penault-Llorca, Frederique, Perera, Rashindrie D., Pinard, Christopher J., Pinto-Cardenas, Juan Carlos, Pruneri, Giancarlo, Pusztai, Lajos, Rajpoot, Nasir Mahmood, Rapoport, Bernardo Leon, Rau, Tilman T., Ribeiro, Joana M., Rimm, David, Vincent-Salomon, Anne, Saltz, Joel, Sayed, Shahin, Hytopoulos, Evangelos, Mahon, Sarah, Siziopikou, Kalliopi P., Sotiriou, Christos, Stenzinger, Albrecht, Sughayer, Maher A., Sur, Daniel, Symmans, Fraser, Tanaka, Sunao, Taxter, Timothy, Tejpar, Sabine, Teuwen, Jonas, Thompson, E. Aubrey, Tramm, Trine, Tran, William T., van der Laak, Jeroen, Verghese, Gregory E., Viale, Giuseppe, Wahab, Noorul, Walter, Thomas, Waumans, Yannick, Wen, Hannah Y., Yang, Wentao, Yuan, Yinyin, Bartlett, John, Loibl, Sibylle, Denkert, Carsten, Savas, Peter, Loi, Sherene, Specht Stovgaard, Elisabeth, Salgado, Roberto, Gallagher, William M., and Rahman, Arman

Abstract

Recent advances in the field of immuno-oncology have brought transformative changes in the management of cancer patients. The immune profile of tumours has been found to have key value in predicting disease prognosis and treatment response in various cancers. Multiplex immunohistochemistry and immunofluorescence have emerged as potent tools for the simultaneous detection of multiple protein biomarkers in a single tissue section, thereby expanding opportunities for molecular and immune profiling while preserving tissue samples. By establishing the phenotype of individual tumour cells when distributed within a mixed cell population, the identification of clinically relevant biomarkers with high-throughput multiplex immunophenotyping of tumour samples has great potential to guide appropriate treatment choices. Moreover, the emergence of novel multi-marker imaging approaches can now provide unprecedented insights into the tumour microenvironment, including the potential interplay between various cell types. However, there are significant challenges to widespread integration of these technologies in daily research and clinical practice. This review addresses the challenges and potential solutions within a structured framework of action from a regulatory and clinical trial perspective. New developments within the field of immunophenotyping using multiplexed tissue imaging platforms and associated digital pathology are also described, with a specific focus on translational implications across different subtypes of cancer.

Published
2024

14. Fusobacterium is toxic for head and neck squamous cell carcinoma and its presence may determine a better prognosis.

Author

Chander, Anjali, Iacovacci, Jacopo, Pellon, Aize, Kataria, Rhadika, Grigoriadis, Anita, Maher, John, Sears, Cynthia, Bachrach, Gilad, Urbano, Teresa Guerrero, Lei, Mary, Petkar, Imran, Kong, Anthony, Ng, Tony, Orlandi, Ester, Iacovelli, Nicola Alessandro, De Cecco, Loris, Serafini, Mara Serena, Moyes, David, Rancati, Tiziana, and Ferreira, Miguel Reis

Published
2024
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16. Supplementary Data from Natural History of Germline BRCA1 Mutated and BRCA Wild-type Triple-negative Breast Cancer

Author

Gardi, Nilesh, primary, Chaubal, Rohan, primary, Parab, Pallavi, primary, Pachakar, Sunil, primary, Kulkarni, Suyash, primary, Shet, Tanuja, primary, Joshi, Shalaka, primary, Kembhavi, Yogesh, primary, Chandrani, Pratik, primary, Quist, Jelmar, primary, Kowtal, Pradnya, primary, Grigoriadis, Anita, primary, Sarin, Rajiv, primary, Govindarajan, Raman, primary, and Gupta, Sudeep, primary

Published
2024
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17. Supplementary Table S4 from Natural History of Germline BRCA1 Mutated and BRCA Wild-type Triple-negative Breast Cancer

Author

Gardi, Nilesh, primary, Chaubal, Rohan, primary, Parab, Pallavi, primary, Pachakar, Sunil, primary, Kulkarni, Suyash, primary, Shet, Tanuja, primary, Joshi, Shalaka, primary, Kembhavi, Yogesh, primary, Chandrani, Pratik, primary, Quist, Jelmar, primary, Kowtal, Pradnya, primary, Grigoriadis, Anita, primary, Sarin, Rajiv, primary, Govindarajan, Raman, primary, and Gupta, Sudeep, primary

Published
2024
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18. Supplementary figure S2 from Natural History of Germline BRCA1 Mutated and BRCA Wild-type Triple-negative Breast Cancer

Author

Gardi, Nilesh, primary, Chaubal, Rohan, primary, Parab, Pallavi, primary, Pachakar, Sunil, primary, Kulkarni, Suyash, primary, Shet, Tanuja, primary, Joshi, Shalaka, primary, Kembhavi, Yogesh, primary, Chandrani, Pratik, primary, Quist, Jelmar, primary, Kowtal, Pradnya, primary, Grigoriadis, Anita, primary, Sarin, Rajiv, primary, Govindarajan, Raman, primary, and Gupta, Sudeep, primary

Published
2024
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19. FIGURE 1 from Natural History of Germline BRCA1 Mutated and BRCA Wild-type Triple-negative Breast Cancer

Author

Gardi, Nilesh, primary, Chaubal, Rohan, primary, Parab, Pallavi, primary, Pachakar, Sunil, primary, Kulkarni, Suyash, primary, Shet, Tanuja, primary, Joshi, Shalaka, primary, Kembhavi, Yogesh, primary, Chandrani, Pratik, primary, Quist, Jelmar, primary, Kowtal, Pradnya, primary, Grigoriadis, Anita, primary, Sarin, Rajiv, primary, Govindarajan, Raman, primary, and Gupta, Sudeep, primary

Published
2024
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20. FIGURE 4 from Natural History of Germline BRCA1 Mutated and BRCA Wild-type Triple-negative Breast Cancer

Author

Gardi, Nilesh, primary, Chaubal, Rohan, primary, Parab, Pallavi, primary, Pachakar, Sunil, primary, Kulkarni, Suyash, primary, Shet, Tanuja, primary, Joshi, Shalaka, primary, Kembhavi, Yogesh, primary, Chandrani, Pratik, primary, Quist, Jelmar, primary, Kowtal, Pradnya, primary, Grigoriadis, Anita, primary, Sarin, Rajiv, primary, Govindarajan, Raman, primary, and Gupta, Sudeep, primary

Published
2024
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21. FIGURE 3 from Natural History of Germline BRCA1 Mutated and BRCA Wild-type Triple-negative Breast Cancer

Author

Gardi, Nilesh, primary, Chaubal, Rohan, primary, Parab, Pallavi, primary, Pachakar, Sunil, primary, Kulkarni, Suyash, primary, Shet, Tanuja, primary, Joshi, Shalaka, primary, Kembhavi, Yogesh, primary, Chandrani, Pratik, primary, Quist, Jelmar, primary, Kowtal, Pradnya, primary, Grigoriadis, Anita, primary, Sarin, Rajiv, primary, Govindarajan, Raman, primary, and Gupta, Sudeep, primary

Published
2024
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22. FIGURE 2 from Natural History of Germline BRCA1 Mutated and BRCA Wild-type Triple-negative Breast Cancer

Author

Gardi, Nilesh, primary, Chaubal, Rohan, primary, Parab, Pallavi, primary, Pachakar, Sunil, primary, Kulkarni, Suyash, primary, Shet, Tanuja, primary, Joshi, Shalaka, primary, Kembhavi, Yogesh, primary, Chandrani, Pratik, primary, Quist, Jelmar, primary, Kowtal, Pradnya, primary, Grigoriadis, Anita, primary, Sarin, Rajiv, primary, Govindarajan, Raman, primary, and Gupta, Sudeep, primary

Published
2024
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23. Supplementary Materials and Methods from Natural History of Germline BRCA1 Mutated and BRCA Wild-type Triple-negative Breast Cancer

Author

Gardi, Nilesh, primary, Chaubal, Rohan, primary, Parab, Pallavi, primary, Pachakar, Sunil, primary, Kulkarni, Suyash, primary, Shet, Tanuja, primary, Joshi, Shalaka, primary, Kembhavi, Yogesh, primary, Chandrani, Pratik, primary, Quist, Jelmar, primary, Kowtal, Pradnya, primary, Grigoriadis, Anita, primary, Sarin, Rajiv, primary, Govindarajan, Raman, primary, and Gupta, Sudeep, primary

Published
2024
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24. TABLE 2 from Natural History of Germline BRCA1 Mutated and BRCA Wild-type Triple-negative Breast Cancer

Author

Gardi, Nilesh, primary, Chaubal, Rohan, primary, Parab, Pallavi, primary, Pachakar, Sunil, primary, Kulkarni, Suyash, primary, Shet, Tanuja, primary, Joshi, Shalaka, primary, Kembhavi, Yogesh, primary, Chandrani, Pratik, primary, Quist, Jelmar, primary, Kowtal, Pradnya, primary, Grigoriadis, Anita, primary, Sarin, Rajiv, primary, Govindarajan, Raman, primary, and Gupta, Sudeep, primary

Published
2024
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25. Data from Natural History of Germline BRCA1 Mutated and BRCA Wild-type Triple-negative Breast Cancer

Author

Gardi, Nilesh, primary, Chaubal, Rohan, primary, Parab, Pallavi, primary, Pachakar, Sunil, primary, Kulkarni, Suyash, primary, Shet, Tanuja, primary, Joshi, Shalaka, primary, Kembhavi, Yogesh, primary, Chandrani, Pratik, primary, Quist, Jelmar, primary, Kowtal, Pradnya, primary, Grigoriadis, Anita, primary, Sarin, Rajiv, primary, Govindarajan, Raman, primary, and Gupta, Sudeep, primary

Published
2024
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26. TABLE 1 from Natural History of Germline BRCA1 Mutated and BRCA Wild-type Triple-negative Breast Cancer

Author

Gardi, Nilesh, primary, Chaubal, Rohan, primary, Parab, Pallavi, primary, Pachakar, Sunil, primary, Kulkarni, Suyash, primary, Shet, Tanuja, primary, Joshi, Shalaka, primary, Kembhavi, Yogesh, primary, Chandrani, Pratik, primary, Quist, Jelmar, primary, Kowtal, Pradnya, primary, Grigoriadis, Anita, primary, Sarin, Rajiv, primary, Govindarajan, Raman, primary, and Gupta, Sudeep, primary

Published
2024
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27. Natural History of Germline BRCA1 Mutated and BRCA Wild-type Triple-negative Breast Cancer

Author

Gardi, Nilesh, primary, Chaubal, Rohan, additional, Parab, Pallavi, additional, Pachakar, Sunil, additional, Kulkarni, Suyash, additional, Shet, Tanuja, additional, Joshi, Shalaka, additional, Kembhavi, Yogesh, additional, Chandrani, Pratik, additional, Quist, Jelmar, additional, Kowtal, Pradnya, additional, Grigoriadis, Anita, additional, Sarin, Rajiv, additional, Govindarajan, Raman, additional, and Gupta, Sudeep, additional

Published
2024
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28. Image‐based multiplex immune profiling of cancer tissues: translational implications. A report of the International Immuno‐oncology Biomarker Working Group on Breast Cancer

Author

Jahangir, Chowdhury Arif, primary, Page, David B, additional, Broeckx, Glenn, additional, Gonzalez, Claudia A, additional, Burke, Caoimbhe, additional, Murphy, Clodagh, additional, Reis‐Filho, Jorge S, additional, Ly, Amy, additional, Harms, Paul W, additional, Gupta, Rajarsi R, additional, Vieth, Michael, additional, Hida, Akira I, additional, Kahila, Mohamed, additional, Kos, Zuzana, additional, van Diest, Paul J, additional, Verbandt, Sara, additional, Thagaard, Jeppe, additional, Khiroya, Reena, additional, Abduljabbar, Khalid, additional, Acosta Haab, Gabriela, additional, Acs, Balazs, additional, Adams, Sylvia, additional, Almeida, Jonas S, additional, Alvarado‐Cabrero, Isabel, additional, Azmoudeh‐Ardalan, Farid, additional, Badve, Sunil, additional, Baharun, Nurkhairul Bariyah, additional, Bellolio, Enrique R, additional, Bheemaraju, Vydehi, additional, Blenman, Kim RM, additional, Botinelly Mendonça Fujimoto, Luciana, additional, Burgues, Octavio, additional, Chardas, Alexandros, additional, Cheang, Maggie Chon U, additional, Ciompi, Francesco, additional, Cooper, Lee AD, additional, Coosemans, An, additional, Corredor, Germán, additional, Dantas Portela, Flavio Luis, additional, Deman, Frederik, additional, Demaria, Sandra, additional, Dudgeon, Sarah N, additional, Elghazawy, Mahmoud, additional, Fernandez‐Martín, Claudio, additional, Fineberg, Susan, additional, Fox, Stephen B, additional, Giltnane, Jennifer M, additional, Gnjatic, Sacha, additional, Gonzalez‐Ericsson, Paula I, additional, Grigoriadis, Anita, additional, Halama, Niels, additional, Hanna, Matthew G, additional, Harbhajanka, Aparna, additional, Hart, Steven N, additional, Hartman, Johan, additional, Hewitt, Stephen, additional, Horlings, Hugo M, additional, Husain, Zaheed, additional, Irshad, Sheeba, additional, Janssen, Emiel AM, additional, Kataoka, Tatsuki R, additional, Kawaguchi, Kosuke, additional, Khramtsov, Andrey I, additional, Kiraz, Umay, additional, Kirtani, Pawan, additional, Kodach, Liudmila L, additional, Korski, Konstanty, additional, Akturk, Guray, additional, Scott, Ely, additional, Kovács, Anikó, additional, Lænkholm, Anne‐Vibeke, additional, Lang‐Schwarz, Corinna, additional, Larsimont, Denis, additional, Lennerz, Jochen K, additional, Lerousseau, Marvin, additional, Li, Xiaoxian, additional, Madabhushi, Anant, additional, Maley, Sai K, additional, Manur Narasimhamurthy, Vidya, additional, Marks, Douglas K, additional, McDonald, Elizabeth S, additional, Mehrotra, Ravi, additional, Michiels, Stefan, additional, Kharidehal, Durga, additional, Minhas, Fayyaz ul Amir Afsar, additional, Mittal, Shachi, additional, Moore, David A, additional, Mushtaq, Shamim, additional, Nighat, Hussain, additional, Papathomas, Thomas, additional, Penault‐Llorca, Frederique, additional, Perera, Rashindrie D, additional, Pinard, Christopher J, additional, Pinto‐Cardenas, Juan Carlos, additional, Pruneri, Giancarlo, additional, Pusztai, Lajos, additional, Rajpoot, Nasir Mahmood, additional, Rapoport, Bernardo Leon, additional, Rau, Tilman T, additional, Ribeiro, Joana M, additional, Rimm, David, additional, Vincent‐Salomon, Anne, additional, Saltz, Joel, additional, Sayed, Shahin, additional, Hytopoulos, Evangelos, additional, Mahon, Sarah, additional, Siziopikou, Kalliopi P, additional, Sotiriou, Christos, additional, Stenzinger, Albrecht, additional, Sughayer, Maher A, additional, Sur, Daniel, additional, Symmans, Fraser, additional, Tanaka, Sunao, additional, Taxter, Timothy, additional, Tejpar, Sabine, additional, Teuwen, Jonas, additional, Thompson, E Aubrey, additional, Tramm, Trine, additional, Tran, William T, additional, van der Laak, Jeroen, additional, Verghese, Gregory E, additional, Viale, Giuseppe, additional, Wahab, Noorul, additional, Walter, Thomas, additional, Waumans, Yannick, additional, Wen, Hannah Y, additional, Yang, Wentao, additional, Yuan, Yinyin, additional, Bartlett, John, additional, Loibl, Sibylle, additional, Denkert, Carsten, additional, Savas, Peter, additional, Loi, Sherene, additional, Specht Stovgaard, Elisabeth, additional, Salgado, Roberto, additional, Gallagher, William M, additional, and Rahman, Arman, additional

Published
2024
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31. Genomic Complexity Profiling Reveals That HORMAD1 Overexpression Contributes to Homologous Recombination Deficiency in Triple-Negative Breast Cancers

Author

Watkins, Johnathan, Weekes, Daniel, Shah, Vandna, Gazinska, Patrycja, Joshi, Shalaka, Sidhu, Bhavna, Gillett, Cheryl, Pinder, Sarah, Vanoli, Fabio, Jasin, Maria, Mayrhofer, Markus, Isaksson, Anders, Cheang, Maggie CU, Mirza, Hasan, Frankum, Jessica, Lord, Christopher J, Ashworth, Alan, Vinayak, Shaveta, Ford, James M, Telli, Melinda L, Grigoriadis, Anita, and Tutt, Andrew NJ

Subjects
Human Genome, Cancer, Biotechnology, Genetics, Breast Cancer, 2.1 Biological and endogenous factors, Aetiology, Allelic Imbalance, Antineoplastic Combined Chemotherapy Protocols, Cell Cycle Proteins, Cell Line, Tumor, Cell Nucleus, Cell Survival, Chromosomal Instability, Cluster Analysis, DNA Copy Number Variations, Drug Resistance, Neoplasm, Gene Expression, Gene Expression Profiling, Gene Silencing, Genomics, Homologous Recombination, Humans, Platinum, Polymorphism, Single Nucleotide, RNA, Small Interfering, Triple Negative Breast Neoplasms, Oncology and Carcinogenesis
Abstract

UnlabelledTriple-negative breast cancers (TNBC) are characterized by a wide spectrum of genomic alterations, some of which might be caused by defects in DNA repair processes such as homologous recombination (HR). Despite this understanding, associating particular patterns of genomic instability with response to therapy has been challenging. Here, we show that allelic-imbalanced copy-number aberrations (AiCNA) are more prevalent in TNBCs that respond to platinum-based chemotherapy, thus providing a candidate predictive biomarker for this disease. Furthermore, we show that a high level of AiCNA is linked with elevated expression of a meiosis-associated gene, HORMAD1. Elevated HORMAD1 expression suppresses RAD51-dependent HR and drives the use of alternative forms of DNA repair, the generation of AiCNAs, as well as sensitizing cancer cells to HR-targeting therapies. Our data therefore provide a mechanistic association between HORMAD1 expression, a specific pattern of genomic instability, and an association with response to platinum-based chemotherapy in TNBC.SignificancePrevious studies have shown correlation between mutational "scars" and sensitivity to platinums extending beyond associations with BRCA1/2 mutation, but do not elucidate the mechanism. Here, a novel allele-specific copy-number characterization of genome instability identifies and functionally validates the inappropriate expression of the meiotic gene HORMAD1 as a driver of HR deficiency in TNBC, acting to induce allelic imbalance and moderate platinum and PARP inhibitor sensitivity with implications for the use of such "scars" and expression of meiotic genes as predictive biomarkers.

Published
2015

32. Figure 4 from Integrated Multimodal Analyses of DNA Damage Response and Immune Markers as Predictors of Response in Metastatic Triple-Negative Breast Cancer in the TNT Trial (NCT00532727)

Author

Tovey, Holly, primary, Sipos, Orsolya, primary, Parker, Joel S., primary, Hoadley, Katherine A., primary, Quist, Jelmar, primary, Kernaghan, Sarah, primary, Kilburn, Lucy, primary, Salgado, Roberto, primary, Loi, Sherene, primary, Kennedy, Richard D., primary, Roxanis, Ioannis, primary, Gazinska, Patrycja, primary, Pinder, Sarah E., primary, Bliss, Judith, primary, Perou, Charles M., primary, Haider, Syed, primary, Grigoriadis, Anita, primary, Tutt, Andrew, primary, and Cheang, Maggie Chon U., primary

Published
2023
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33. Figure 2 from Integrated Multimodal Analyses of DNA Damage Response and Immune Markers as Predictors of Response in Metastatic Triple-Negative Breast Cancer in the TNT Trial (NCT00532727)

Author

Tovey, Holly, primary, Sipos, Orsolya, primary, Parker, Joel S., primary, Hoadley, Katherine A., primary, Quist, Jelmar, primary, Kernaghan, Sarah, primary, Kilburn, Lucy, primary, Salgado, Roberto, primary, Loi, Sherene, primary, Kennedy, Richard D., primary, Roxanis, Ioannis, primary, Gazinska, Patrycja, primary, Pinder, Sarah E., primary, Bliss, Judith, primary, Perou, Charles M., primary, Haider, Syed, primary, Grigoriadis, Anita, primary, Tutt, Andrew, primary, and Cheang, Maggie Chon U., primary

Published
2023
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34. Supplementary Figure S1 from Integrated Multimodal Analyses of DNA Damage Response and Immune Markers as Predictors of Response in Metastatic Triple-Negative Breast Cancer in the TNT Trial (NCT00532727)

Author

Tovey, Holly, primary, Sipos, Orsolya, primary, Parker, Joel S., primary, Hoadley, Katherine A., primary, Quist, Jelmar, primary, Kernaghan, Sarah, primary, Kilburn, Lucy, primary, Salgado, Roberto, primary, Loi, Sherene, primary, Kennedy, Richard D., primary, Roxanis, Ioannis, primary, Gazinska, Patrycja, primary, Pinder, Sarah E., primary, Bliss, Judith, primary, Perou, Charles M., primary, Haider, Syed, primary, Grigoriadis, Anita, primary, Tutt, Andrew, primary, and Cheang, Maggie Chon U., primary

Published
2023
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35. Table 1 from Integrated Multimodal Analyses of DNA Damage Response and Immune Markers as Predictors of Response in Metastatic Triple-Negative Breast Cancer in the TNT Trial (NCT00532727)

Author

Tovey, Holly, primary, Sipos, Orsolya, primary, Parker, Joel S., primary, Hoadley, Katherine A., primary, Quist, Jelmar, primary, Kernaghan, Sarah, primary, Kilburn, Lucy, primary, Salgado, Roberto, primary, Loi, Sherene, primary, Kennedy, Richard D., primary, Roxanis, Ioannis, primary, Gazinska, Patrycja, primary, Pinder, Sarah E., primary, Bliss, Judith, primary, Perou, Charles M., primary, Haider, Syed, primary, Grigoriadis, Anita, primary, Tutt, Andrew, primary, and Cheang, Maggie Chon U., primary

Published
2023
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36. Supplementary Table S3 from Integrated Multimodal Analyses of DNA Damage Response and Immune Markers as Predictors of Response in Metastatic Triple-Negative Breast Cancer in the TNT Trial (NCT00532727)

Author

Tovey, Holly, primary, Sipos, Orsolya, primary, Parker, Joel S., primary, Hoadley, Katherine A., primary, Quist, Jelmar, primary, Kernaghan, Sarah, primary, Kilburn, Lucy, primary, Salgado, Roberto, primary, Loi, Sherene, primary, Kennedy, Richard D., primary, Roxanis, Ioannis, primary, Gazinska, Patrycja, primary, Pinder, Sarah E., primary, Bliss, Judith, primary, Perou, Charles M., primary, Haider, Syed, primary, Grigoriadis, Anita, primary, Tutt, Andrew, primary, and Cheang, Maggie Chon U., primary

Published
2023
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37. Data from Integrated Multimodal Analyses of DNA Damage Response and Immune Markers as Predictors of Response in Metastatic Triple-Negative Breast Cancer in the TNT Trial (NCT00532727)

Author

Tovey, Holly, primary, Sipos, Orsolya, primary, Parker, Joel S., primary, Hoadley, Katherine A., primary, Quist, Jelmar, primary, Kernaghan, Sarah, primary, Kilburn, Lucy, primary, Salgado, Roberto, primary, Loi, Sherene, primary, Kennedy, Richard D., primary, Roxanis, Ioannis, primary, Gazinska, Patrycja, primary, Pinder, Sarah E., primary, Bliss, Judith, primary, Perou, Charles M., primary, Haider, Syed, primary, Grigoriadis, Anita, primary, Tutt, Andrew, primary, and Cheang, Maggie Chon U., primary

Published
2023
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38. Figure 3 from Integrated Multimodal Analyses of DNA Damage Response and Immune Markers as Predictors of Response in Metastatic Triple-Negative Breast Cancer in the TNT Trial (NCT00532727)

Author

Tovey, Holly, primary, Sipos, Orsolya, primary, Parker, Joel S., primary, Hoadley, Katherine A., primary, Quist, Jelmar, primary, Kernaghan, Sarah, primary, Kilburn, Lucy, primary, Salgado, Roberto, primary, Loi, Sherene, primary, Kennedy, Richard D., primary, Roxanis, Ioannis, primary, Gazinska, Patrycja, primary, Pinder, Sarah E., primary, Bliss, Judith, primary, Perou, Charles M., primary, Haider, Syed, primary, Grigoriadis, Anita, primary, Tutt, Andrew, primary, and Cheang, Maggie Chon U., primary

Published
2023
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39. Figure 5 from Integrated Multimodal Analyses of DNA Damage Response and Immune Markers as Predictors of Response in Metastatic Triple-Negative Breast Cancer in the TNT Trial (NCT00532727)

Author

Tovey, Holly, primary, Sipos, Orsolya, primary, Parker, Joel S., primary, Hoadley, Katherine A., primary, Quist, Jelmar, primary, Kernaghan, Sarah, primary, Kilburn, Lucy, primary, Salgado, Roberto, primary, Loi, Sherene, primary, Kennedy, Richard D., primary, Roxanis, Ioannis, primary, Gazinska, Patrycja, primary, Pinder, Sarah E., primary, Bliss, Judith, primary, Perou, Charles M., primary, Haider, Syed, primary, Grigoriadis, Anita, primary, Tutt, Andrew, primary, and Cheang, Maggie Chon U., primary

Published
2023
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40. Figure 1 from Integrated Multimodal Analyses of DNA Damage Response and Immune Markers as Predictors of Response in Metastatic Triple-Negative Breast Cancer in the TNT Trial (NCT00532727)

Author

Tovey, Holly, primary, Sipos, Orsolya, primary, Parker, Joel S., primary, Hoadley, Katherine A., primary, Quist, Jelmar, primary, Kernaghan, Sarah, primary, Kilburn, Lucy, primary, Salgado, Roberto, primary, Loi, Sherene, primary, Kennedy, Richard D., primary, Roxanis, Ioannis, primary, Gazinska, Patrycja, primary, Pinder, Sarah E., primary, Bliss, Judith, primary, Perou, Charles M., primary, Haider, Syed, primary, Grigoriadis, Anita, primary, Tutt, Andrew, primary, and Cheang, Maggie Chon U., primary

Published
2023
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41. 1240: Fusobacterium associates with a better prognosis and radiosensitizes head and neck cancers

Author

Chander, Anjali Rani, Iacovacci, Jacopo, Rodriguez, Aize Pellon, Butterworth, Victoria, Kataria, Radhika, Grigoriadis, Anita, Orlandi, Ester, Iacovelli, Nicola Alessandro, De Cecco, Loris, Serafini, Mara Serena, Urbano, Teresa Guerrero, Kong, Anthony, Lei, Mary, Petkar, Imran, Ng, Tony, Bachrach, Gilad, Sears, Cynthia, Moyes, David, Rancati, Tiziana, and Ferreira, Miguel Reis

Published
2024
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42. Spatial analyses of immune cell infiltration in cancer: current methods and future directions. A report of the International Immuno‐Oncology Biomarker Working Group on Breast Cancer

Author

Page, David B, primary, Broeckx, Glenn, additional, Jahangir, Chowdhury Arif, additional, Verbandt, Sara, additional, Gupta, Rajarsi R, additional, Thagaard, Jeppe, additional, Khiroya, Reena, additional, Kos, Zuzana, additional, Abduljabbar, Khalid, additional, Acosta Haab, Gabriela, additional, Acs, Balazs, additional, Almeida, Jonas S, additional, Alvarado‐Cabrero, Isabel, additional, Azmoudeh‐Ardalan, Farid, additional, Badve, Sunil, additional, Baharun, Nurkhairul Bariyah, additional, Bellolio, Enrique R, additional, Bheemaraju, Vydehi, additional, Blenman, Kim RM, additional, Botinelly Mendonça Fujimoto, Luciana, additional, Burgues, Octavio, additional, Cheang, Maggie Chon U, additional, Ciompi, Francesco, additional, Cooper, Lee AD, additional, Coosemans, An, additional, Corredor, Germán, additional, Dantas Portela, Flavio Luis, additional, Deman, Frederik, additional, Demaria, Sandra, additional, Dudgeon, Sarah N, additional, Elghazawy, Mahmoud, additional, Ely, Scott, additional, Fernandez‐Martín, Claudio, additional, Fineberg, Susan, additional, Fox, Stephen B, additional, Gallagher, William M, additional, Giltnane, Jennifer M, additional, Gnjatic, Sacha, additional, Gonzalez‐Ericsson, Paula I, additional, Grigoriadis, Anita, additional, Halama, Niels, additional, Hanna, Matthew G, additional, Harbhajanka, Aparna, additional, Hardas, Alexandros, additional, Hart, Steven N, additional, Hartman, Johan, additional, Hewitt, Stephen, additional, Hida, Akira I, additional, Horlings, Hugo M, additional, Husain, Zaheed, additional, Hytopoulos, Evangelos, additional, Irshad, Sheeba, additional, Janssen, Emiel AM, additional, Kahila, Mohamed, additional, Kataoka, Tatsuki R, additional, Kawaguchi, Kosuke, additional, Kharidehal, Durga, additional, Khramtsov, Andrey I, additional, Kiraz, Umay, additional, Kirtani, Pawan, additional, Kodach, Liudmila L, additional, Korski, Konstanty, additional, Kovács, Anikó, additional, Laenkholm, Anne‐Vibeke, additional, Lang‐Schwarz, Corinna, additional, Larsimont, Denis, additional, Lennerz, Jochen K, additional, Lerousseau, Marvin, additional, Li, Xiaoxian, additional, Ly, Amy, additional, Madabhushi, Anant, additional, Maley, Sai K, additional, Manur Narasimhamurthy, Vidya, additional, Marks, Douglas K, additional, McDonald, Elizabeth S, additional, Mehrotra, Ravi, additional, Michiels, Stefan, additional, Minhas, Fayyaz ul Amir Afsar, additional, Mittal, Shachi, additional, Moore, David A, additional, Mushtaq, Shamim, additional, Nighat, Hussain, additional, Papathomas, Thomas, additional, Penault‐Llorca, Frederique, additional, Perera, Rashindrie D, additional, Pinard, Christopher J, additional, Pinto‐Cardenas, Juan Carlos, additional, Pruneri, Giancarlo, additional, Pusztai, Lajos, additional, Rahman, Arman, additional, Rajpoot, Nasir Mahmood, additional, Rapoport, Bernardo Leon, additional, Rau, Tilman T, additional, Reis‐Filho, Jorge S, additional, Ribeiro, Joana M, additional, Rimm, David, additional, Salomon, Anne‐Vincent, additional, Salto‐Tellez, Manuel, additional, Saltz, Joel, additional, Sayed, Shahin, additional, Siziopikou, Kalliopi P, additional, Sotiriou, Christos, additional, Stenzinger, Albrecht, additional, Sughayer, Maher A, additional, Sur, Daniel, additional, Symmans, Fraser, additional, Tanaka, Sunao, additional, Taxter, Timothy, additional, Tejpar, Sabine, additional, Teuwen, Jonas, additional, Thompson, E Aubrey, additional, Tramm, Trine, additional, Tran, William T, additional, van der Laak, Jeroen, additional, van Diest, Paul J, additional, Verghese, Gregory E, additional, Viale, Giuseppe, additional, Vieth, Michael, additional, Wahab, Noorul, additional, Walter, Thomas, additional, Waumans, Yannick, additional, Wen, Hannah Y, additional, Yang, Wentao, additional, Yuan, Yinyin, additional, Adams, Sylvia, additional, Bartlett, John Mark Seaverns, additional, Loibl, Sibylle, additional, Denkert, Carsten, additional, Savas, Peter, additional, Loi, Sherene, additional, Salgado, Roberto, additional, Specht Stovgaard, Elisabeth, additional, Akturk, Guray, additional, and Bouchmaa, Najat, additional

Published
2023
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43. Pitfalls in machine learning‐based assessment of tumor‐infiltrating lymphocytes in breast cancer: a report of the international immuno‐oncology biomarker working group

Author

Thagaard, Jeppe, primary, Broeckx, Glenn, additional, Page, David B, additional, Jahangir, Chowdhury Arif, additional, Verbandt, Sara, additional, Kos, Zuzana, additional, Gupta, Rajarsi, additional, Khiroya, Reena, additional, Abduljabbar, Khalid, additional, Acosta Haab, Gabriela, additional, Acs, Balazs, additional, Akturk, Guray, additional, Almeida, Jonas S, additional, Alvarado‐Cabrero, Isabel, additional, Amgad, Mohamed, additional, Azmoudeh‐Ardalan, Farid, additional, Badve, Sunil, additional, Baharun, Nurkhairul Bariyah, additional, Balslev, Eva, additional, Bellolio, Enrique R, additional, Bheemaraju, Vydehi, additional, Blenman, Kim RM, additional, Botinelly Mendonça Fujimoto, Luciana, additional, Bouchmaa, Najat, additional, Burgues, Octavio, additional, Chardas, Alexandros, additional, Chon U Cheang, Maggie, additional, Ciompi, Francesco, additional, Cooper, Lee AD, additional, Coosemans, An, additional, Corredor, Germán, additional, Dahl, Anders B, additional, Dantas Portela, Flavio Luis, additional, Deman, Frederik, additional, Demaria, Sandra, additional, Doré Hansen, Johan, additional, Dudgeon, Sarah N, additional, Ebstrup, Thomas, additional, Elghazawy, Mahmoud, additional, Fernandez‐Martín, Claudio, additional, Fox, Stephen B, additional, Gallagher, William M, additional, Giltnane, Jennifer M, additional, Gnjatic, Sacha, additional, Gonzalez‐Ericsson, Paula I, additional, Grigoriadis, Anita, additional, Halama, Niels, additional, Hanna, Matthew G, additional, Harbhajanka, Aparna, additional, Hart, Steven N, additional, Hartman, Johan, additional, Hauberg, Søren, additional, Hewitt, Stephen, additional, Hida, Akira I, additional, Horlings, Hugo M, additional, Husain, Zaheed, additional, Hytopoulos, Evangelos, additional, Irshad, Sheeba, additional, Janssen, Emiel AM, additional, Kahila, Mohamed, additional, Kataoka, Tatsuki R, additional, Kawaguchi, Kosuke, additional, Kharidehal, Durga, additional, Khramtsov, Andrey I, additional, Kiraz, Umay, additional, Kirtani, Pawan, additional, Kodach, Liudmila L, additional, Korski, Konstanty, additional, Kovács, Anikó, additional, Laenkholm, Anne‐Vibeke, additional, Lang‐Schwarz, Corinna, additional, Larsimont, Denis, additional, Lennerz, Jochen K, additional, Lerousseau, Marvin, additional, Li, Xiaoxian, additional, Ly, Amy, additional, Madabhushi, Anant, additional, Maley, Sai K, additional, Manur Narasimhamurthy, Vidya, additional, Marks, Douglas K, additional, McDonald, Elizabeth S, additional, Mehrotra, Ravi, additional, Michiels, Stefan, additional, Minhas, Fayyaz ul Amir Afsar, additional, Mittal, Shachi, additional, Moore, David A, additional, Mushtaq, Shamim, additional, Nighat, Hussain, additional, Papathomas, Thomas, additional, Penault‐Llorca, Frederique, additional, Perera, Rashindrie D, additional, Pinard, Christopher J, additional, Pinto‐Cardenas, Juan Carlos, additional, Pruneri, Giancarlo, additional, Pusztai, Lajos, additional, Rahman, Arman, additional, Rajpoot, Nasir Mahmood, additional, Rapoport, Bernardo Leon, additional, Rau, Tilman T, additional, Reis‐Filho, Jorge S, additional, Ribeiro, Joana M, additional, Rimm, David, additional, Roslind, Anne, additional, Vincent‐Salomon, Anne, additional, Salto‐Tellez, Manuel, additional, Saltz, Joel, additional, Sayed, Shahin, additional, Scott, Ely, additional, Siziopikou, Kalliopi P, additional, Sotiriou, Christos, additional, Stenzinger, Albrecht, additional, Sughayer, Maher A, additional, Sur, Daniel, additional, Fineberg, Susan, additional, Symmans, Fraser, additional, Tanaka, Sunao, additional, Taxter, Timothy, additional, Tejpar, Sabine, additional, Teuwen, Jonas, additional, Thompson, E Aubrey, additional, Tramm, Trine, additional, Tran, William T, additional, van der Laak, Jeroen, additional, van Diest, Paul J, additional, Verghese, Gregory E, additional, Viale, Giuseppe, additional, Vieth, Michael, additional, Wahab, Noorul, additional, Walter, Thomas, additional, Waumans, Yannick, additional, Wen, Hannah Y, additional, Yang, Wentao, additional, Yuan, Yinyin, additional, Zin, Reena Md, additional, Adams, Sylvia, additional, Bartlett, John, additional, Loibl, Sibylle, additional, Denkert, Carsten, additional, Savas, Peter, additional, Loi, Sherene, additional, Salgado, Roberto, additional, and Specht Stovgaard, Elisabeth, additional

Published
2023
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45. Integrated Multimodal Analyses of DNA Damage Response and Immune Markers as Predictors of Response in Metastatic Triple-Negative Breast Cancer in the TNT Trial (NCT00532727)

Author

Tovey, Holly, primary, Sipos, Orsolya, additional, Parker, Joel S., additional, Hoadley, Katherine A., additional, Quist, Jelmar, additional, Kernaghan, Sarah, additional, Kilburn, Lucy, additional, Salgado, Roberto, additional, Loi, Sherene, additional, Kennedy, Richard D., additional, Roxanis, Ioannis, additional, Gazinska, Patrycja, additional, Pinder, Sarah E., additional, Bliss, Judith, additional, Perou, Charles M., additional, Haider, Syed, additional, Grigoriadis, Anita, additional, Tutt, Andrew, additional, and Cheang, Maggie Chon U., additional

Published
2023
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46. Regulator of G-protein signalling 2 mRNA is differentially expressed in mammary epithelial subpopulations and over-expressed in the majority of breast cancers

Author

Smalley, Matthew J, Iravani, Marjan, Leao, Maria, Grigoriadis, Anita, Kendrick, Howard, Dexter, Tim, Fenwick, Kerry, Regan, Joseph L, Britt, Kara, McDonald, Sarah, Lord, Christopher J, MacKay, Alan, and Ashworth, Alan

Subjects
Biomedical and Clinical Sciences, Oncology and Carcinogenesis, Genetics, Biotechnology, Breast Cancer, Stem Cell Research, Cancer, Underpinning research, Aetiology, 1.1 Normal biological development and functioning, 2.1 Biological and endogenous factors, Animals, Breast Neoplasms, Epithelial Cells, Female, Flow Cytometry, GTP-Binding Proteins, Gene Expression Profiling, Gene Expression Regulation, Neoplastic, Mammary Glands, Animal, Mice, Oligonucleotide Array Sequence Analysis, RGS Proteins, RNA, Messenger, Receptors, Oxytocin, Reverse Transcriptase Polymerase Chain Reaction, Signal Transduction, Up-Regulation, Oncology & Carcinogenesis, Oncology and carcinogenesis
Abstract

IntroductionTo understand which signalling pathways become deregulated in breast cancer, it is necessary to identify functionally significant gene expression patterns in the stem, progenitor, transit amplifying and differentiated cells of the mammary epithelium. We have previously used the markers 33A10, CD24 and Sca-1 to identify mouse mammary epithelial cell subpopulations. We now investigate the relationship between cells expressing these markers and use gene expression microarray analysis to identify genes differentially expressed in the cell populations.MethodsFreshly isolated primary mouse mammary epithelial cells were separated on the basis of staining with the 33A10 antibody and an alpha-Sca-1 antibody. The populations identified were profiled using gene expression microarray analysis. Gene expression patterns were confirmed on normal mouse and human mammary epithelial subpopulations and were examined in a panel of breast cancer samples and cell lines.ResultsAnalysis of the separated populations demonstrated that Sca-1- 33A10High stained cells were estrogen receptor alpha (Esr1)- luminal epithelial cells, whereas Sca-1+ 33A10Low/- stained cells were a mix of nonepithelial cells and Esr1+ epithelial cells. Analysis of the gene expression data identified the gene Rgs2 (regulator of G-protein signalling 2) as being highly expressed in the Sca-1- 33A10Low/- population, which included myoepithelial/basal cells. RGS2 has previously been described as a regulator of angiotensin II receptor signalling. Gene expression analysis by quantitative real-time RT-PCR of cells separated on the basis of CD24 and Sca-1 expression confirmed that Rgs2 was more highly expressed in mouse myoepithelial/basal mammary cells than luminal cells. This expression pattern was conserved in normal human breast cells. Functional analysis demonstrated RGS2 to be a modulator of oxytocin receptor signalling. The potential significance of RGS2 expression in breast cancer was demonstrated by semi-quantitative RT-PCR analysis, data mining and quantitative real-time RT-PCR approaches, which showed that RGS2 was expressed in the majority of solid breast cancers at much higher levels than in normal human mammary cells.ConclusionMolecular analysis of prospectively isolated mammary epithelial cells identified RGS2 as a modulator of oxytocin receptor signalling, which is highly expressed in the myoepithelial cells. The RGS2 gene, but not the oxytocin receptor, was also shown to be over-expressed in the majority of breast cancers, identifying the product of this gene, or the pathway(s) it regulates, as potentially significant therapeutic targets.

Published
2007

47. Establishment of the epithelial-specific transcriptome of normal and malignant human breast cells based on MPSS and array expression data

Author

Grigoriadis, Anita, Mackay, Alan, Reis-Filho, Jorge S, Steele, Dawn, Iseli, Christian, Stevenson, Brian J, Jongeneel, C Victor, Valgeirsson, Haukur, Fenwick, Kerry, Iravani, Marjan, Leao, Maria, Simpson, Andrew JG, Strausberg, Robert L, Jat, Parmjit S, Ashworth, Alan, Neville, A Munro, and O'Hare, Michael J

Subjects
Cancer, Genetics, Human Genome, Biotechnology, Breast Cancer, 4.1 Discovery and preclinical testing of markers and technologies, Detection, screening and diagnosis, 2.1 Biological and endogenous factors, Aetiology, Biomarkers, Tumor, Breast, Breast Neoplasms, Cell Adhesion Molecules, Cells, Cultured, Epithelial Cells, Female, Gene Expression Profiling, Humans, Oligonucleotide Array Sequence Analysis, Prognosis, Transcription, Genetic, Tumor Cells, Cultured, Oncology and Carcinogenesis, Oncology & Carcinogenesis
Abstract

IntroductionDiverse microarray and sequencing technologies have been widely used to characterise the molecular changes in malignant epithelial cells in breast cancers. Such gene expression studies to identify markers and targets in tumour cells are, however, compromised by the cellular heterogeneity of solid breast tumours and by the lack of appropriate counterparts representing normal breast epithelial cells.MethodsMalignant neoplastic epithelial cells from primary breast cancers and luminal and myoepithelial cells isolated from normal human breast tissue were isolated by immunomagnetic separation methods. Pools of RNA from highly enriched preparations of these cell types were subjected to expression profiling using massively parallel signature sequencing (MPSS) and four different genome wide microarray platforms. Functional related transcripts of the differential tumour epithelial transcriptome were used for gene set enrichment analysis to identify enrichment of luminal and myoepithelial type genes. Clinical pathological validation of a small number of genes was performed on tissue microarrays.ResultsMPSS identified 6,553 differentially expressed genes between the pool of normal luminal cells and that of primary tumours substantially enriched for epithelial cells, of which 98% were represented and 60% were confirmed by microarray profiling. Significant expression level changes between these two samples detected only by microarray technology were shown by 4,149 transcripts, resulting in a combined differential tumour epithelial transcriptome of 8,051 genes. Microarray gene signatures identified a comprehensive list of 907 and 955 transcripts whose expression differed between luminal epithelial cells and myoepithelial cells, respectively. Functional annotation and gene set enrichment analysis highlighted a group of genes related to skeletal development that were associated with the myoepithelial/basal cells and upregulated in the tumour sample. One of the most highly overexpressed genes in this category, that encoding periostin, was analysed immunohistochemically on breast cancer tissue microarrays and its expression in neoplastic cells correlated with poor outcome in a cohort of poor prognosis estrogen receptor-positive tumours.ConclusionUsing highly enriched cell populations in combination with multiplatform gene expression profiling studies, a comprehensive analysis of molecular changes between the normal and malignant breast tissue was established. This study provides a basis for the identification of novel and potentially important targets for diagnosis, prognosis and therapy in breast cancer.

Published
2006

48. Carboplatin in BRCA1/2-mutated and triple-negative breast cancer BRCAness subgroups: the TNT Trial

Author

Tutt, Andrew, Tovey, Holly, Cheang, Maggie Chon U., Kernaghan, Sarah, Kilburn, Lucy, Gazinska, Patrycja, Owen, Julie, Abraham, Jacinta, Barrett, Sophie, Barrett-Lee, Peter, Brown, Robert, Chan, Stephen, Dowsett, Mitchell, Flanagan, James M, Fox, Lisa, Grigoriadis, Anita, Gutin, Alexander, Harper-Wynne, Catherine, Hatton, Matthew Q., Hoadley, Katherine A., Parikh, Jyoti, Parker, Peter, Perou, Charles M., Roylance, Rebecca, Shah, Vandna, Shaw, Adam, Smith, Ian E., Timms, Kirsten M., Wardley, Andrew M., Wilson, Gregory, Gillett, Cheryl, Lanchbury, Jerry S., Ashworth, Alan, Rahman, Nazneen, Harries, Mark, Ellis, Paul, Pinder, Sarah E., and Bliss, Judith M.

Published
2018
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49. Multiscale deep learning framework captures systemic immune features in lymph nodes predictive of triple negative breast cancer outcome in large‐scale studies

Author

Verghese, Gregory, primary, Li, Mengyuan, additional, Liu, Fangfang, additional, Lohan, Amit, additional, Kurian, Nikhil Cherian, additional, Meena, Swati, additional, Gazinska, Patrycja, additional, Shah, Aekta, additional, Oozeer, Aasiyah, additional, Chan, Terry, additional, Opdam, Mark, additional, Linn, Sabine, additional, Gillett, Cheryl, additional, Alberts, Elena, additional, Hardiman, Thomas, additional, Jones, Samantha, additional, Thavaraj, Selvam, additional, Jones, J Louise, additional, Salgado, Roberto, additional, Pinder, Sarah E, additional, Rane, Swapnil, additional, Sethi, Amit, additional, and Grigoriadis, Anita, additional

Published
2023
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