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1. Proteomic understanding of SARS-CoV-2 infection and COVID-19: Biological, diagnostic, and therapeutic perspectives

Author

Al-Ejeh, Fares, primary, Merhi, Maysaloun, additional, Al-Muftah, Mariam, additional, Fernandes, Queenie, additional, Al-Zaidan, Lobna, additional, Bedhiafi, Takwa, additional, Mestiri, Sarra, additional, Moustafa, Dina, additional, Taib, Nassiba, additional, Inchakalody, Varghese, additional, Raza, Afsheen, additional, Uddin, Shahab, additional, and Dermime, Said, additional

Published
2023
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2. Contributors

Author

Agni, Megha Bhat, primary, Al-Ejeh, Fares, additional, Ali, Amjad, additional, Al-Muftah, Mariam, additional, Alvarenga, Taís Aparecida, additional, Al-Zaidan, Lobna, additional, Anu, K.R., additional, Anwer, Farha, additional, Arif, Maryum, additional, Awan, Hayeqa Shahwar, additional, Bandyopadhyay, Anindya, additional, Baralić, Katarina, additional, Barbosa, Bruno Henrique Groenner, additional, Barh, Debmalya, additional, Barnes, Christopher, additional, Basheer, Amina, additional, Bedhiafi, Takwa, additional, Bhardwaj, Tulika, additional, Bozic, Dragica, additional, Carmona, Elenice Valentim, additional, Chandra, Subhash, additional, Chapin, Nathaniel, additional, Chaudhry, Almas, additional, Chlamydas, Sarantis, additional, Coppock, Harry, additional, Cornillot, Emmanuel, additional, da Fonseca, Simone Gonçalves, additional, Gowda, Damodara, additional, Das, Subham, additional, Dasgupta, Santanu, additional, Dermime, Said, additional, dos Santos Alves, Daniela Fernanda, additional, Đukić-Ćosić, Danijela, additional, Duran, Erika Christiane Marocco, additional, Fernandes, Queenie, additional, Fernandez-Martinez, Juan Luis, additional, Ferreira, Ana Cláudia Barbosa Honório, additional, Ferreira, Danton Diego, additional, Frutos, Roger, additional, Garbati, Michael, additional, Gardinassi, Luiz Gustavo, additional, Gourgoulianis, Konstantinos I., additional, Hassan, Mubashir, additional, Hegde, Pramukh Subrahmanya, additional, Inchakalody, Varghese, additional, Joseph, Alex, additional, Joshi, Tushar, additional, Kancharla, Nagesh, additional, Kaur, Bineypreet, additional, Kaur, Jaspreet, additional, Kellarai, Adithi, additional, Kloczkowski, Andrzej, additional, Libotte, Gustavo Barbosa, additional, de Lima, Davi Vinícius, additional, Lobato, Fran Sérgio, additional, Ludhiadch, Abhilash, additional, Lugo Reyes, Saul O., additional, Lundstrom, Kenneth, additional, Maiti, Amit K., additional, Mathpal, Shalini, additional, Merhi, Maysaloun, additional, Mestiri, Sarra, additional, Mohamed, Mostafa M., additional, de Moraes Lopes, Maria Helena Baena, additional, Moustafa, Dina, additional, Munshi, Anjana, additional, Naz, Anam, additional, Nessiem, Mina A., additional, Özdemir, Mehmet, additional, Platt, Gustavo Mendes, additional, Pratiwi, Sari Eka, additional, Rahman, Abdur, additional, Raza, Afsheen, additional, Rodríguez, Demóstenes Zegarra, additional, Sales-Campos, Helioswilton, additional, Santos, Luis Otávio, additional, Sarkar, Shreya, additional, Schuller, Björn W., additional, Sen, Rwik, additional, Shahid, Fatima, additional, Sharma, Priyanka, additional, Siddique, Abubakar, additional, Siddique, Ammara, additional, Somvanshi, Pallavi, additional, Souza, Camila Oliveira Silva, additional, Tahir, Syeda Duaa, additional, Taib, Nassiba, additional, Tamta, Sushma, additional, Uddin, Shahab, additional, Uğur, Ayşe Rüveyda, additional, Vavougios, George D., additional, Waseem, Maaz, additional, Yadav, Umesh Prasad, additional, Yiannakopoulou, Eugenia Ch., additional, Ysrafil, Ysrafil, additional, Zaheer, Tahreem, additional, Zarogiannis, Sotirios G., additional, and Živančević, Katarina, additional

Published
2023
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3. Genome-wide association and transcriptome studies identify target genes and risk loci for breast cancer.

Author

Ferreira, Manuel A, Gamazon, Eric R, Al-Ejeh, Fares, Aittomäki, Kristiina, Andrulis, Irene L, Anton-Culver, Hoda, Arason, Adalgeir, Arndt, Volker, Aronson, Kristan J, Arun, Banu K, Asseryanis, Ella, Azzollini, Jacopo, Balmaña, Judith, Barnes, Daniel R, Barrowdale, Daniel, Beckmann, Matthias W, Behrens, Sabine, Benitez, Javier, Bermisheva, Marina, Białkowska, Katarzyna, Blomqvist, Carl, Bogdanova, Natalia V, Bojesen, Stig E, Bolla, Manjeet K, Borg, Ake, Brauch, Hiltrud, Brenner, Hermann, Broeks, Annegien, Burwinkel, Barbara, Caldés, Trinidad, Caligo, Maria A, Campa, Daniele, Campbell, Ian, Canzian, Federico, Carter, Jonathan, Carter, Brian D, Castelao, Jose E, Chang-Claude, Jenny, Chanock, Stephen J, Christiansen, Hans, Chung, Wendy K, Claes, Kathleen BM, Clarke, Christine L, EMBRACE Collaborators, GC-HBOC Study Collaborators, GEMO Study Collaborators, Couch, Fergus J, Cox, Angela, Cross, Simon S, Czene, Kamila, Daly, Mary B, de la Hoya, Miguel, Dennis, Joe, Devilee, Peter, Diez, Orland, Dörk, Thilo, Dunning, Alison M, Dwek, Miriam, Eccles, Diana M, Ejlertsen, Bent, Ellberg, Carolina, Engel, Christoph, Eriksson, Mikael, Fasching, Peter A, Fletcher, Olivia, Flyger, Henrik, Friedman, Eitan, Frost, Debra, Gabrielson, Marike, Gago-Dominguez, Manuela, Ganz, Patricia A, Gapstur, Susan M, Garber, Judy, García-Closas, Montserrat, García-Sáenz, José A, Gaudet, Mia M, Giles, Graham G, Glendon, Gord, Godwin, Andrew K, Goldberg, Mark S, Goldgar, David E, González-Neira, Anna, Greene, Mark H, Gronwald, Jacek, Guénel, Pascal, Haiman, Christopher A, Hall, Per, Hamann, Ute, He, Wei, Heyworth, Jane, Hogervorst, Frans BL, Hollestelle, Antoinette, Hoover, Robert N, Hopper, John L, Hulick, Peter J, Humphreys, Keith, Imyanitov, Evgeny N, ABCTB Investigators, HEBON Investigators, and BCFR Investigators

Subjects
EMBRACE Collaborators, GC-HBOC Study Collaborators, GEMO Study Collaborators, ABCTB Investigators, HEBON Investigators, BCFR Investigators, Humans, Breast Neoplasms, Genetic Predisposition to Disease, Gene Expression Profiling, Quantitative Trait Loci, Female, Genome-Wide Association Study, Prevention, Cancer, Human Genome, Aging, Breast Cancer, Genetics, Biotechnology, 2.1 Biological and endogenous factors
Abstract

Genome-wide association studies (GWAS) have identified more than 170 breast cancer susceptibility loci. Here we hypothesize that some risk-associated variants might act in non-breast tissues, specifically adipose tissue and immune cells from blood and spleen. Using expression quantitative trait loci (eQTL) reported in these tissues, we identify 26 previously unreported, likely target genes of overall breast cancer risk variants, and 17 for estrogen receptor (ER)-negative breast cancer, several with a known immune function. We determine the directional effect of gene expression on disease risk measured based on single and multiple eQTL. In addition, using a gene-based test of association that considers eQTL from multiple tissues, we identify seven (and four) regions with variants associated with overall (and ER-negative) breast cancer risk, which were not reported in previous GWAS. Further investigation of the function of the implicated genes in breast and immune cells may provide insights into the etiology of breast cancer.

Published
2019

4. Epigenome erosion and SOX10 drive neural crest phenotypic mimicry in triple-negative breast cancer

Author

Saunus, Jodi M., De Luca, Xavier M., Northwood, Korinne, Raghavendra, Ashwini, Hasson, Alexander, McCart Reed, Amy E., Lim, Malcolm, Lal, Samir, Vargas, A. Cristina, Kutasovic, Jamie R., Dalley, Andrew J., Miranda, Mariska, Kalaw, Emarene, Kalita-de Croft, Priyakshi, Gresshoff, Irma, Al-Ejeh, Fares, Gee, Julia M. W., Ormandy, Chris, Khanna, Kum Kum, Beesley, Jonathan, Chenevix-Trench, Georgia, Green, Andrew R., Rakha, Emad A., Ellis, Ian O., Nicolau, Jr, Dan V., Simpson, Peter T., and Lakhani, Sunil R.

Published
2022
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5. Prognostic tools and candidate drugs based on plasma proteomics of patients with severe COVID-19 complications

Author

Al-Nesf, Maryam A. Y., Abdesselem, Houari B., Bensmail, Ilham, Ibrahim, Shahd, Saeed, Walaa A. H., Mohammed, Sara S. I., Razok, Almurtada, Alhussain, Hashim, Aly, Reham M. A., Al Maslamani, Muna, Ouararhni, Khalid, Khatib, Mohamad Y., Hssain, Ali Ait, Omrani, Ali S., Al-Kaabi, Saad, Al Khal, Abdullatif, Al-Thani, Asmaa A., Samsam, Waseem, Farooq, Abdulaziz, Al-Suwaidi, Jassim, Al-Maadheed, Mohammed, Al-Siddiqi, Heba H., Butler, Alexandra E., Decock, Julie V., Mohamed-Ali, Vidya, and Al-Ejeh, Fares

Published
2022
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6. A transcriptome-wide association study of 229,000 women identifies new candidate susceptibility genes for breast cancer

Author

Wu, Lang, Shi, Wei, Long, Jirong, Guo, Xingyi, Michailidou, Kyriaki, Beesley, Jonathan, Bolla, Manjeet K, Shu, Xiao-Ou, Lu, Yingchang, Cai, Qiuyin, Al-Ejeh, Fares, Rozali, Esdy, Wang, Qin, Dennis, Joe, Li, Bingshan, Zeng, Chenjie, Feng, Helian, Gusev, Alexander, Barfield, Richard T, Andrulis, Irene L, Anton-Culver, Hoda, Arndt, Volker, Aronson, Kristan J, Auer, Paul L, Barrdahl, Myrto, Baynes, Caroline, Beckmann, Matthias W, Benitez, Javier, Bermisheva, Marina, Blomqvist, Carl, Bogdanova, Natalia V, Bojesen, Stig E, Brauch, Hiltrud, Brenner, Hermann, Brinton, Louise, Broberg, Per, Brucker, Sara Y, Burwinkel, Barbara, Caldés, Trinidad, Canzian, Federico, Carter, Brian D, Castelao, J Esteban, Chang-Claude, Jenny, Chen, Xiaoqing, Cheng, Ting-Yuan David, Christiansen, Hans, Clarke, Christine L, NBCS Collaborators, Collée, Margriet, Cornelissen, Sten, Couch, Fergus J, Cox, David, Cox, Angela, Cross, Simon S, Cunningham, Julie M, Czene, Kamila, Daly, Mary B, Devilee, Peter, Doheny, Kimberly F, Dörk, Thilo, dos-Santos-Silva, Isabel, Dumont, Martine, Dwek, Miriam, Eccles, Diana M, Eilber, Ursula, Eliassen, A Heather, Engel, Christoph, Eriksson, Mikael, Fachal, Laura, Fasching, Peter A, Figueroa, Jonine, Flesch-Janys, Dieter, Fletcher, Olivia, Flyger, Henrik, Fritschi, Lin, Gabrielson, Marike, Gago-Dominguez, Manuela, Gapstur, Susan M, García-Closas, Montserrat, Gaudet, Mia M, Ghoussaini, Maya, Giles, Graham G, Goldberg, Mark S, Goldgar, David E, González-Neira, Anna, Guénel, Pascal, Hahnen, Eric, Haiman, Christopher A, Håkansson, Niclas, Hall, Per, Hallberg, Emily, Hamann, Ute, Harrington, Patricia, Hein, Alexander, Hicks, Belynda, Hillemanns, Peter, Hollestelle, Antoinette, Hoover, Robert N, Hopper, John L, and Huang, Guanmengqian

Subjects
Biological Sciences, Genetics, Cancer, Breast Cancer, Human Genome, Prevention, Women's Health, Cancer Genomics, Biotechnology, 2.1 Biological and endogenous factors, Generic health relevance, Breast Neoplasms, Case-Control Studies, Female, Gene Expression, Genetic Predisposition to Disease, Genome-Wide Association Study, Humans, Polymorphism, Single Nucleotide, Risk, Transcriptome, NBCS Collaborators, kConFab/AOCS Investigators, Medical and Health Sciences, Developmental Biology, Agricultural biotechnology, Bioinformatics and computational biology
Abstract

The breast cancer risk variants identified in genome-wide association studies explain only a small fraction of the familial relative risk, and the genes responsible for these associations remain largely unknown. To identify novel risk loci and likely causal genes, we performed a transcriptome-wide association study evaluating associations of genetically predicted gene expression with breast cancer risk in 122,977 cases and 105,974 controls of European ancestry. We used data from the Genotype-Tissue Expression Project to establish genetic models to predict gene expression in breast tissue and evaluated model performance using data from The Cancer Genome Atlas. Of the 8,597 genes evaluated, significant associations were identified for 48 at a Bonferroni-corrected threshold of P

Published
2018

7. Identification of ten variants associated with risk of estrogen-receptor-negative breast cancer

Author

Milne, Roger L, Kuchenbaecker, Karoline B, Michailidou, Kyriaki, Beesley, Jonathan, Kar, Siddhartha, Lindström, Sara, Hui, Shirley, Lemaçon, Audrey, Soucy, Penny, Dennis, Joe, Jiang, Xia, Rostamianfar, Asha, Finucane, Hilary, Bolla, Manjeet K, McGuffog, Lesley, Wang, Qin, Aalfs, Cora M, Adams, Marcia, Adlard, Julian, Agata, Simona, Ahmed, Shahana, Ahsan, Habibul, Aittomäki, Kristiina, Al-Ejeh, Fares, Allen, Jamie, Ambrosone, Christine B, Amos, Christopher I, Andrulis, Irene L, Anton-Culver, Hoda, Antonenkova, Natalia N, Arndt, Volker, Arnold, Norbert, Aronson, Kristan J, Auber, Bernd, Auer, Paul L, Ausems, Margreet GEM, Azzollini, Jacopo, Bacot, François, Balmaña, Judith, Barile, Monica, Barjhoux, Laure, Barkardottir, Rosa B, Barrdahl, Myrto, Barnes, Daniel, Barrowdale, Daniel, Baynes, Caroline, Beckmann, Matthias W, Benitez, Javier, Bermisheva, Marina, Bernstein, Leslie, Bignon, Yves-Jean, Blazer, Kathleen R, Blok, Marinus J, Blomqvist, Carl, Blot, William, Bobolis, Kristie, Boeckx, Bram, Bogdanova, Natalia V, Bojesen, Anders, Bojesen, Stig E, Bonanni, Bernardo, Børresen-Dale, Anne-Lise, Bozsik, Aniko, Bradbury, Angela R, Brand, Judith S, Brauch, Hiltrud, Brenner, Hermann, Bressac-de Paillerets, Brigitte, Brewer, Carole, Brinton, Louise, Broberg, Per, Brooks-Wilson, Angela, Brunet, Joan, Brüning, Thomas, Burwinkel, Barbara, Buys, Saundra S, Byun, Jinyoung, Cai, Qiuyin, Caldés, Trinidad, Caligo, Maria A, Campbell, Ian, Canzian, Federico, Caron, Olivier, Carracedo, Angel, Carter, Brian D, Castelao, J Esteban, Castera, Laurent, Caux-Moncoutier, Virginie, Chan, Salina B, Chang-Claude, Jenny, Chanock, Stephen J, Chen, Xiaoqing, Cheng, Ting-Yuan David, Chiquette, Jocelyne, Christiansen, Hans, Claes, Kathleen BM, Clarke, Christine L, Conner, Thomas, Conroy, Don M, and Cook, Jackie

Subjects
Biological Sciences, Genetics, Cancer, Human Genome, Prevention, Breast Cancer, Aging, Estrogen, 2.1 Biological and endogenous factors, Aetiology, BRCA1 Protein, Breast Neoplasms, Female, Genetic Predisposition to Disease, Genome-Wide Association Study, Heterozygote, Humans, Mutation, Polymorphism, Single Nucleotide, Receptors, Estrogen, Risk Factors, White People, ABCTB Investigators, EMBRACE, GEMO Study Collaborators, HEBON, kConFab/AOCS Investigators, NBSC Collaborators, Medical and Health Sciences, Developmental Biology, Agricultural biotechnology, Bioinformatics and computational biology
Abstract

Most common breast cancer susceptibility variants have been identified through genome-wide association studies (GWAS) of predominantly estrogen receptor (ER)-positive disease. We conducted a GWAS using 21,468 ER-negative cases and 100,594 controls combined with 18,908 BRCA1 mutation carriers (9,414 with breast cancer), all of European origin. We identified independent associations at P < 5 × 10-8 with ten variants at nine new loci. At P < 0.05, we replicated associations with 10 of 11 variants previously reported in ER-negative disease or BRCA1 mutation carrier GWAS and observed consistent associations with ER-negative disease for 105 susceptibility variants identified by other studies. These 125 variants explain approximately 16% of the familial risk of this breast cancer subtype. There was high genetic correlation (0.72) between risk of ER-negative breast cancer and breast cancer risk for BRCA1 mutation carriers. These findings may lead to improved risk prediction and inform further fine-mapping and functional work to better understand the biological basis of ER-negative breast cancer.

Published
2017

9. Essential developmental, genomic stability, and tumour suppressor functions of the mouse orthologue of hSSB1/NABP2.

Author

Shi, Wei, Bain, Amanda L, Schwer, Bjoern, Al-Ejeh, Fares, Smith, Corey, Wong, Lee, Chai, Hua, Miranda, Mariska S, Ho, Uda, Kawaguchi, Makoto, Miura, Yutaka, Finnie, John W, Wall, Meaghan, Heierhorst, Jörg, Wicking, Carol, Spring, Kevin J, Alt, Frederick W, and Khanna, Kum Kum

Subjects
B-Lymphocytes, Fibroblasts, Animals, Humans, Mice, Infertility, Male, Chromosome Breakage, Genomic Instability, Carrier Proteins, Nuclear Proteins, Histones, Transcription Factors, Signal Transduction, Spermatogenesis, DNA Repair, Gene Expression Regulation, Developmental, Radiation, Ionizing, Radiation Tolerance, Male, Suppressor of Cytokine Signaling Proteins, DNA Breaks, Double-Stranded, Homologous Recombination, Developmental Biology, Genetics
Abstract

Single-stranded DNA binding proteins (SSBs) regulate multiple DNA transactions, including replication, transcription, and repair. We recently identified SSB1 as a novel protein critical for the initiation of ATM signaling and DNA double-strand break repair by homologous recombination. Here we report that germline Ssb1(-/-) embryos die at birth from respiratory failure due to severe rib cage malformation and impaired alveolar development, coupled with additional skeletal defects. Unexpectedly, Ssb1(-/-) fibroblasts did not exhibit defects in Atm signaling or γ-H2ax focus kinetics in response to ionizing radiation (IR), and B-cell specific deletion of Ssb1 did not affect class-switch recombination in vitro. However, conditional deletion of Ssb1 in adult mice led to increased cancer susceptibility with broad tumour spectrum, impaired male fertility with testicular degeneration, and increased radiosensitivity and IR-induced chromosome breaks in vivo. Collectively, these results demonstrate essential roles of Ssb1 in embryogenesis, spermatogenesis, and genome stability in vivo.

Published
2013

12. Ssb1 and Ssb2 cooperate to regulate mouse hematopoietic stem and progenitor cells by resolving replicative stress

Author

Shi, Wei, Vu, Therese, Boucher, Didier, Biernacka, Anna, Nde, Jules, Pandita, Raj K., Straube, Jasmin, Boyle, Glen M., Al-Ejeh, Fares, Nag, Purba, Jeffery, Jessie, Harris, Janelle L., Bain, Amanda L., Grzelak, Marta, Skrzypczak, Magdalena, Mitra, Abhishek, Dojer, Norbert, Crosetto, Nicola, Cloonan, Nicole, Becherel, Olivier J., Finnie, John, Skaar, Jeffrey R., Walkley, Carl R., Pandita, Tej K., Rowicka, Maga, Ginalski, Krzysztof, Lane, Steven W., and Khanna, Kum Kum

Published
2017
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17. Supplementary Tables from G9a Inhibition Enhances Checkpoint Inhibitor Blockade Response in Melanoma

Author

Kelly, Gregory M., primary, Al-Ejeh, Fares, primary, McCuaig, Robert, primary, Casciello, Francesco, primary, Ahmad Kamal, Nabilah, primary, Ferguson, Blake, primary, Pritchard, Antonia L., primary, Ali, Sayed, primary, Silva, Ines P., primary, Wilmott, James S., primary, Long, Georgina V., primary, Scolyer, Richard A., primary, Rao, Sudha, primary, Hayward, Nicholas K., primary, Gannon, Frank, primary, and Lee, Jason S., primary

Published
2023
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19. Supplementary Figures from G9a Inhibition Enhances Checkpoint Inhibitor Blockade Response in Melanoma

Author

Kelly, Gregory M., primary, Al-Ejeh, Fares, primary, McCuaig, Robert, primary, Casciello, Francesco, primary, Ahmad Kamal, Nabilah, primary, Ferguson, Blake, primary, Pritchard, Antonia L., primary, Ali, Sayed, primary, Silva, Ines P., primary, Wilmott, James S., primary, Long, Georgina V., primary, Scolyer, Richard A., primary, Rao, Sudha, primary, Hayward, Nicholas K., primary, Gannon, Frank, primary, and Lee, Jason S., primary

Published
2023
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23. Multidimensional phenotyping of breast cancer cell lines to guide preclinical research

Author

Saunus, Jodi M., Smart, Chanel E., Kutasovic, Jamie R., Johnston, Rebecca L., Kalita-de Croft, Priyakshi, Miranda, Mariska, Rozali, Esdy N., Vargas, Ana Cristina, Reid, Lynne E., Lorsy, Eva, Cocciardi, Sibylle, Seidens, Tatjana, McCart Reed, Amy E., Dalley, Andrew J., Wockner, Leesa F., Johnson, Julie, Sarkar, Debina, Askarian-Amiri, Marjan E., Simpson, Peter T., Khanna, Kum Kum, Chenevix-Trench, Georgia, Al-Ejeh, Fares, and Lakhani, Sunil R.

Published
2017
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25. EphA3 Maintains Tumorigenicity and Is a Therapeutic Target in Glioblastoma Multiforme

Author

Day, Bryan W., Stringer, Brett W., Al-Ejeh, Fares, Ting, Michael J., Wilson, John, Ensbey, Kathleen S., Jamieson, Paul R., Bruce, Zara C., Lim, Yi Chieh, Offenhäuser, Carolin, Charmsaz, Sara, Cooper, Leanne T., Ellacott, Jennifer K., Harding, Angus, Leveque, Lucie, Inglis, Po, Allan, Suzanne, Walker, David G., Lackmann, Martin, Osborne, Geoffrey, Khanna, Kum Kum, Reynolds, Brent A., Lickliter, Jason D., and Boyd, Andrew W.

Published
2013
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26. Integrated genomic and transcriptomic analysis of human brain metastases identifies alterations of potential clinical significance

Author

Saunus, Jodi M, Quinn, Michael CJ, Patch, Ann-Marie, Pearson, John V, Bailey, Peter J, Nones, Katia, McCart Reed, Amy E, Miller, David, Wilson, Peter J, Al-Ejeh, Fares, Mariasegaram, Mythily, Lau, Queenie, Withers, Teresa, Jeffree, Rosalind L, Reid, Lynne E, Da Silva, Leonard, Matsika, Admire, Niland, Colleen M, Cummings, Margaret C, Bruxner, Timothy JC, Christ, Angelika N, Harliwong, Ivon, Idrisoglu, Senel, Manning, Suzanne, Nourse, Craig, Nourbakhsh, Ehsan, Wani, Shivangi, Anderson, Matthew J, Fink, Lynn J, Holmes, Oliver, Kazakoff, Stephen, Leonard, Conrad, Newell, Felicity, Taylor, Darrin, Waddell, Nick, Wood, Scott, Xu, Qinying, Kassahn, Karin S, Narayanan, Vairavan, Taib, Nur Aishah, Teo, Soo-Hwang, Chow, Yock Ping, kConFab, Jat, Parmjit S, Brandner, Sebastian, Flanagan, Adrienne M, Khanna, Kum Kum, Chenevix-Trench, Georgia, Grimmond, Sean M, Simpson, Peter T, Waddell, Nicola, and Lakhani, Sunil R

Published
2015
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29. Epigenome erosion drives neural crest-like phenotypic mimicry in triple-negative breast cancer and other SOX10+ malignancies

Author

Saunus, Jodi M., primary, De Luca, Xavier M., additional, Northwood, Korinne, additional, Raghavendra, Ashwini, additional, Hasson, Alexander, additional, McCart Reed, Amy E., additional, Lim, Malcolm, additional, Lal, Samir, additional, Vargas, Ana Cristina, additional, Kutasovic, Jamie R., additional, Dalley, Andrew J., additional, Miranda, Mariska, additional, Kalaw, Emarene, additional, Kalita-de Croft, Priyakshi, additional, Gresshoff, Irma, additional, Al-Ejeh, Fares, additional, Gee, Julia M.W., additional, Ormandy, Chris, additional, Khanna, Kum Kum, additional, Beesley, Jonathan, additional, Chenevix-Trench, Georgia, additional, Green, Andrew R., additional, Rakha, Emad A., additional, Ellis, Ian O., additional, Nicolau, Dan V., additional, Simpson, Peter T., additional, and Lakhani, Sunil R., additional

Published
2021
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30. A short ERK5 isoform modulates nucleocytoplasmic shuttling of active ERK5 and associates with poor survival in breast cancer

Author

Miranda, Mariska, primary, Saunus, Jodi M., additional, Akgül, Seçkin, additional, Marjaneh, Mahdi Moradi, additional, Kutasovic, Jamie R., additional, Shi, Wei, additional, Chatterjee, Oishee, additional, Casciello, Francesco, additional, Rozali, Esdy, additional, Handoko, Herlina Y., additional, Wiegmans, Adrian P., additional, Liu, Tianqing, additional, Lee, Jason S., additional, Day, Bryan W., additional, Edwards, Stacey L., additional, French, Juliet D., additional, Reed, Amy E. McCart, additional, Chenevix-Trench, Georgia, additional, Khanna, Kum Kum, additional, Simpson, Peter T., additional, Lakhani, Sunil R., additional, and Al-Ejeh, Fares, additional

Published
2021
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31. Robust prognostic signatures derived from proteomic panel profiling of plasma from patients with severe COVID-19 complications

Author

Al-Nesf, Maryam, primary, Abdesselem, Houari, additional, Bensmail, Ilham, additional, Ibrahim, Shahd, additional, Saeed, Walaa, additional, Mohammed, Sara, additional, Razok, Almurtada, additional, Alhussain, Hashim, additional, Aly, Reham, additional, Maslamani, Muna Al, additional, Ouararhni, Khalid, additional, Khatib, Mohamad, additional, Hssain, Ali Ait, additional, Omrani, Ali, additional, Al-Kaabi, Saad, additional, Khal, Abdullatif Al, additional, Althani, Asma, additional, Samsam, Waseem, additional, Farooq, Abdulaziz, additional, Al-Suwaidi, Jassim, additional, Al-Maadheedh, Mohammed, additional, Al-Siddiqi, Heba, additional, Butler, Alexandra, additional, Decock, Julie, additional, Mohamed-Ali, Vidya, additional, and Al-Ejeh, Fares, additional

Published
2021
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32. G9a Inhibition Enhances Checkpoint Inhibitor Blockade Response in Melanoma

Author

Kelly, Gregory M., primary, Al-Ejeh, Fares, additional, McCuaig, Robert, additional, Casciello, Francesco, additional, Ahmad Kamal, Nabilah, additional, Ferguson, Blake, additional, Pritchard, Antonia L., additional, Ali, Sayed, additional, Silva, Ines P., additional, Wilmott, James S., additional, Long, Georgina V., additional, Scolyer, Richard A., additional, Rao, Sudha, additional, Hayward, Nicholas K., additional, Gannon, Frank, additional, and Lee, Jason S., additional

Published
2021
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34. Differential gene expression of tumor-infiltrating CD8+T cells in advanced versus early-stage colorectal cancer and identification of a gene signature of poor prognosis

Author

Saleh, Reem, primary, Sasidharan Nair, Varun, additional, Toor, Salman M, additional, Taha, Rowaida Z, additional, Murshed, Khaled, additional, Al-Dhaheri, Mahmood, additional, Khawar, Mahwish, additional, Petkar, Mahir Abdulla, additional, Abu Nada, Mohamed, additional, Al-Ejeh, Fares, additional, and Elkord, Eyad, additional

Published
2020
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35. Clinicopathologic significance of nuclear HER4 and phospho-YAP(S127) in human breast cancers and matching brain metastases

Author

Kalita-de Croft, Priyakshi, primary, Lim, Malcolm, additional, Chittoory, Haarika, additional, de Luca, Xavier M., additional, Kutasovic, Jamie R., additional, Day, Bryan W., additional, Al-Ejeh, Fares, additional, Simpson, Peter T., additional, McCart Reed, Amy E., additional, Lakhani, Sunil R., additional, and Saunus, Jodi M., additional

Published
2020
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37. Differential gene expression of tumor-infiltrating CD4+ T cells in advanced versus early stage colorectal cancer and identification of a gene signature of poor prognosis

Author

Sasidharan Nair, Varun, primary, Saleh, Reem, additional, Taha, Rowaida Z, additional, Toor, Salman M, additional, Murshed, Khaled, additional, Ahmed, Ayman A, additional, Kurer, Mohamed A, additional, Abu Nada, Mohamed, additional, Al Ejeh, Fares, additional, and Elkord, Eyad, additional

Published
2020
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39. LobSig, a prognostic signature for ILC

Author

Reed, Amy E McCart, primary, Lal, Samir, additional, Nones, Katia, additional, Kutasovic, Jamie R, additional, Coorey, Craig P, additional, de, Croft Priyakshi Kalita, additional, Dalley, Andrew, additional, Kuo, Luyu, additional, Wockner, Leesa, additional, Robertson, Alan, additional, Ferguson, Kaltin, additional, Niland, Colleen, additional, Sachchithananthan, Mythily, additional, Vargas, Ana Cristina, additional, Miller, Gregory, additional, Black, Debra, additional, Johnson, Julie, additional, Reid, Lynne E, additional, Males, Renique, additional, Gresshoff, Irma, additional, Porter, Alan, additional, Evans, Elizabeth, additional, Saunus, Jodi M, additional, Al-Ejeh, Fares, additional, Pearson, John V, additional, Chenevix-Trench, Georgia, additional, Coin, Lachlan, additional, Waddell, Nicola, additional, Lakhani, Sunil R, additional, and Simpson, Peter T, additional

Published
2019
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41. Secreted cellular prion protein binds doxorubicin and correlates with anthracycline resistance in breast cancer

Author

Wiegmans, Adrian P., primary, Saunus, Jodi M., additional, Ham, Sunyoung, additional, Lobb, Richard J., additional, Kutasovic, Jamie R., additional, Dalley, Andrew J., additional, Miranda, Mariska, additional, Atkinson, Caroline, additional, Foliaki, Simote T., additional, Ferguson, Kaltin, additional, Niland, Colleen, additional, Johnstone, Cameron N., additional, Lewis, Victoria, additional, Collins, Steven, additional, Lakhani, Sunil R., additional, Al-Ejeh, Fares, additional, and Möller, Andreas, additional

Published
2019
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42. Identification of ten variants associated with risk of estrogen-receptor-negative breast cancer

Author

Milne, Roger L., Kuchenbaecker, Karoline B., Michailidou, Kyriaki, Beesley, Jonathan, Kar, Siddhartha, Lindström, Sara, Hui, Shirley, Lemaçon, Audrey, Soucy, Penny, Dennis, Joe, Jiang, Xia, Rostamianfar, Asha, Finucane, Hilary K, Bolla, Manjeet K., McGuffog, Lesley, Wang, Qin, Aalfs, Cora M., Adams, Marcia, Adlard, Julian, Agata, Simona, Ahmed, Shahana, Ahsan, Habibul, Aittomäki, Kristiina, Al-Ejeh, Fares, Allen, Jamie, Ambrosone, Christine B., Amos, Christopher I, Andrulis, Irene L., Anton-Culver, Hoda, Antonenkova, Natalia N., Arndt, Volker, Arnold, Norbert, Aronson, Kristan J, Auber, Bernd, Auer, Paul L., Ausems, Margreet G E M, Azzollini, Jacopo, Bacot, François, Balmaña, Judith, Barile, Monica, Barjhoux, Laure, Barkardottir, Rosa B., Barrdahl, Myrto, Barnes, Daniel R, Barrowdale, Daniel, Baynes, Caroline, Beckmann, Matthias W., Benitez, Javier, Bermisheva, Marina, Bernstein, Leslie, and ABCTB Investigators

Subjects
Heterozygote, Receptors, Estrogen, BRCA1 Protein, Risk Factors, European Continental Ancestry Group, Mutation, Journal Article, Humans, Breast Neoplasms, Female, Genetic Predisposition to Disease, Polymorphism, Single Nucleotide, Genome-Wide Association Study
Abstract

Most common breast cancer susceptibility variants have been identified through genome-wide association studies (GWAS) of predominantly estrogen receptor (ER)-positive disease. We conducted a GWAS using 21,468 ER-negative cases and 100,594 controls combined with 18,908 BRCA1 mutation carriers (9,414 with breast cancer), all of European origin. We identified independent associations at P < 5 × 10-8 with ten variants at nine new loci. At P < 0.05, we replicated associations with 10 of 11 variants previously reported in ER-negative disease or BRCA1 mutation carrier GWAS and observed consistent associations with ER-negative disease for 105 susceptibility variants identified by other studies. These 125 variants explain approximately 16% of the familial risk of this breast cancer subtype. There was high genetic correlation (0.72) between risk of ER-negative breast cancer and breast cancer risk for BRCA1 mutation carriers. These findings may lead to improved risk prediction and inform further fine-mapping and functional work to better understand the biological basis of ER-negative breast cancer.

Published
2017

43. EphA3 Pay-Loaded Antibody Therapeutics for the Treatment of Glioblastoma

Author

Offenhäuser, Carolin, primary, Al-Ejeh, Fares, additional, Puttick, Simon, additional, Ensbey, Kathleen, additional, Bruce, Zara, additional, Jamieson, Paul, additional, Smith, Fiona, additional, Stringer, Brett, additional, Carrington, Benjamin, additional, Fuchs, Adrian, additional, Bell, Craig, additional, Jeffree, Rosalind, additional, Rose, Stephen, additional, Thurecht, Kristofer, additional, Boyd, Andrew, additional, and Day, Bryan, additional

Published
2018
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44. Breast cancer metastasis to gynaecological organs: a clinico‐pathological and molecular profiling study

Author

Kutasovic, Jamie R, primary, McCart Reed, Amy E, additional, Males, Renique, additional, Sim, Sarah, additional, Saunus, Jodi M, additional, Dalley, Andrew, additional, McEvoy, Christopher R, additional, Dedina, Liana, additional, Miller, Gregory, additional, Peyton, Stephen, additional, Reid, Lynne, additional, Lal, Samir, additional, Niland, Colleen, additional, Ferguson, Kaltin, additional, Fellowes, Andrew P, additional, Al‐Ejeh, Fares, additional, Lakhani, Sunil R, additional, Cummings, Margaret C, additional, and Simpson, Peter T, additional

Published
2018
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46. Clinicopathologic significance of nuclear HER4 and phospho-YAP(S 127) in human breast cancers and matching brain metastases.

Author

Kalita-de Croft, Priyakshi, Lim, Malcolm, Chittoory, Haarika, de Luca, Xavier M., Kutasovic, Jamie R., Day, Bryan W., Al-Ejeh, Fares, Simpson, Peter T., McCart Reed, Amy E., Lakhani, Sunil R., and Saunus, Jodi M.

Abstract

Background: Human epidermal growth factor receptor-4 (HER4) and yes-associated protein-1 (YAP) are candidate therapeutic targets in oncology. YAP's transcriptional coactivation function is modulated by the HER4 intracellular domain (HER4-ICD) in vitro, but the clinical relevance of this has not been established. This study investigated the potential for targeting the HER4-YAP pathway in brain metastatic breast cancer. Methods: We performed immuno-phenotypic profiling of pathway markers in a consecutive breast cancer series with 25 years of clinical follow up (n = 371), and patient-matched breast and metastatic brain tumours (n = 91; 30 pairs). Results: Membrane localisation of phospho-HER4 [pHER4(Y1162)] was infrequent in primary breast cancer, but very frequent in brain metastases (5.9% versus 75% positive), where it was usually co-expressed with pHER3(Y1289) (p < 0.05). The presence of YAP in tumour cell nuclei was associated directly with nuclear pERK5(T218/Y210) (p = 0.003). However, relationships with disease-specific survival depended on oestrogen receptor (ER) status. Nuclear pYAP(S127) was associated with smaller, good prognostic ER+ breast tumours (log-rank hazard-ratio 0.53; p = 9.6E−03), but larger, poor prognostic triple-negative cancers (log-rank hazard-ratio 2.78; p = 1.7E−02), particularly when co-expressed with nuclear HER4-ICD (p = 0.02). This phenotype was associated with stemness and mitotic instability markers (vimentin, SOX9, ID1, SPAG5, TTK, geminin; p < 0.05). YAP expression in brain metastases was higher than matched primary tumours; specifically, nuclear pYAP(S127) in ER-negative cases (p < 0.05). Nuclear YAP was detected in ~70% of ER-negative, HER4-activated brain metastases. Discussion: Our findings suggest that the canonical-mechanism where Hippo pathway-mediated phosphorylation of YAP ostensibly excludes it from the nucleus is dysfunctional in breast cancer. The data are consistent with pYAP(S127) having independent transcriptional functions, which may include transducing neuregulin signals in brain metastases. Consistent with mechanistic studies implicating it as an ER co-factor, nuclear pYAP(S127) associations with breast cancer clinical outcomes were dependent on ER status. Conclusion: Preclinical studies investigating HER4 and nuclear YAP combination therapy strategies are warranted. [ABSTRACT FROM AUTHOR]

Published
2020
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47. Differential gene expression of tumor-infiltrating CD4+ T cells in advanced versus early stage colorectal cancer and identification of a gene signature of poor prognosis.

Author

Sasidharan Nair, Varun, Saleh, Reem, Taha, Rowaida Z, Toor, Salman M, Murshed, Khaled, Ahmed, Ayman A, Kurer, Mohamed A, Abu Nada, Mohamed, Al Ejeh, Fares, and Elkord, Eyad

Subjects
CANCER genes, GENE expression, T cells, COLORECTAL cancer, GENE silencing
Abstract

Tumor-infiltrating lymphocytes (TILs) play indispensable roles in the progression and response to treatment of solid tumors. However, the prognostic significance of CD4+ TILs is not fully disclosed in cancers generally and in CRC in particular, mainly due to the existence of different functional subsets of CD4+ T cells. We performed transcriptomic profiling of CD4+ TILs isolated from CRC patients in order to identify differentially expressed genes and their functional pathways in early versus advanced disease stages. We found that in advanced stages, genes related to immune and inflammatory responses, in particular Th1-mediated immune response and cytotoxicity-mediated genes, were downregulated; while epigenetic-mediated silencing genes were upregulated. Interestingly, we identified genes, which were steadily upregulated or downregulated in CD4+ TILs with CRC progression from stage I to IV. Additionally, of the top 200 deregulated genes, 43 upregulated and 64 downregulated genes showed similar deregulation trends in the cancer genome atlas CRC dataset. From these 97 deregulated genes, we identified a "poor prognosis CD4 gene signature (ppCD4sig)". Patients with high ppCD4sig score showed shorter disease-specific survival (DSS) and progression-free interval (PFI). The ppCD4sig was an independent prognostic indicator for DSS (HR = 1.73, 95% CI 1.32–2.27, P = 0.0001) and PFI (HR = 1.75, 95% CI 1.3–2.35, P = 0.0016). Additionally, patients at advanced stages and at a younger age (<55 years) were more likely to have a high ppCD4sig score. Altogether, our data provide novel insights and a unique prognostic gene signature of CD4+ TILs in the CRC microenvironment. [ABSTRACT FROM AUTHOR]

Published
2020
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48. Characterization of a novel breast cancer cell line derived from a metastatic bone lesion of a breast cancer patient

Author

Johnson, Julie, primary, Bessette, Darrell C., additional, Saunus, Jodi M., additional, Smart, Chanel E., additional, Song, Sarah, additional, Johnston, Rebecca L., additional, Cocciardi, Sibylle, additional, Rozali, Esdy N., additional, Johnstone, Cameron N., additional, Vargas, Ana Christina, additional, Kazakoff, Stephen H., additional, BioBank, Victorian Cancer, additional, Khanna, Kum Kum, additional, Lakhani, Sunil R., additional, Chenevix-Trench, Georgia, additional, Simpson, Peter T., additional, Nones, Katia, additional, Waddell, Nicola, additional, and Al-Ejeh, Fares, additional

Published
2018
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50. Long Noncoding RNAs CUPID1 and CUPID2 Mediate Breast Cancer Risk at 11q13 by Modulating the Response to DNA Damage

Author

Betts, Joshua A., primary, Moradi Marjaneh, Mahdi, additional, Al-Ejeh, Fares, additional, Lim, Yi Chieh, additional, Shi, Wei, additional, Sivakumaran, Haran, additional, Tropée, Romain, additional, Patch, Ann-Marie, additional, Clark, Michael B., additional, Bartonicek, Nenad, additional, Wiegmans, Adrian P., additional, Hillman, Kristine M., additional, Kaufmann, Susanne, additional, Bain, Amanda L., additional, Gloss, Brian S., additional, Crawford, Joanna, additional, Kazakoff, Stephen, additional, Wani, Shivangi, additional, Wen, Shu W., additional, Day, Bryan, additional, Möller, Andreas, additional, Cloonan, Nicole, additional, Pearson, John, additional, Brown, Melissa A., additional, Mercer, Timothy R., additional, Waddell, Nicola, additional, Khanna, Kum Kum, additional, Dray, Eloise, additional, Dinger, Marcel E., additional, Edwards, Stacey L., additional, and French, Juliet D., additional

Published
2017
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