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1. GeneFEAST: the pivotal, gene-centric step in functional enrichment analysis interpretation

Author

Taylor, Avigail, Macaulay, Valentine M, Maurya, Anand K, Miossec, Matthieu J, and Buffa, Francesca M

Subjects
Quantitative Biology - Quantitative Methods
Abstract

Summary: GeneFEAST, implemented in Python, is a gene-centric functional enrichment analysis summarisation and visualisation tool that can be applied to large functional enrichment analysis (FEA) results arising from upstream FEA pipelines. It produces a systematic, navigable HTML report, making it easy to identify sets of genes putatively driving multiple enrichments and to explore gene-level quantitative data first used to identify input genes. Further, GeneFEAST can compare FEA results from multiple studies, making it possible, for example, to highlight patterns of gene expression amongst genes commonly differentially expressed in two sets of conditions, and giving rise to shared enrichments under those conditions. GeneFEAST offers a novel, effective way to address the complexities of linking up many overlapping FEA results to their underlying genes and data, advancing gene-centric hypotheses, and providing pivotal information for downstream validation experiments. Availability: GeneFEAST is available at https://github.com/avigailtaylor/GeneFEAST Contact: avigail.taylor@well.ox.ac.uk, Comment: Main text: 3 pages, 1 figure. Supplementary Information: 16 pages, 3 figures, 2 tables, 4 boxes

Published
2023

8. A Phase Ib/II study of IGF-neutralising antibody xentuzumab with enzalutamide in metastatic castration-resistant prostate cancer

Author

Macaulay, Valentine M., primary, Lord, Simon, additional, Hussain, Syed, additional, Maroto, José Pablo, additional, Jones, Robert Hugh, additional, Climent, Miguel Ángel, additional, Cook, Natalie, additional, Lin, Chia-Chi, additional, Wang, Shian-Shiang, additional, Bianchini, Diletta, additional, Bailey, Mark, additional, Schlieker, Laura, additional, Bogenrieder, Thomas, additional, and de Bono, Johann, additional

Published
2023
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9. Aleksic_Supplementary data from Nuclear IGF1R Interacts with Regulatory Regions of Chromatin to Promote RNA Polymerase II Recruitment and Gene Expression Associated with Advanced Tumor Stage

Author

Aleksic, Tamara, primary, Gray, Nicki, primary, Wu, Xiaoning, primary, Rieunier, Guillaume, primary, Osher, Eliot, primary, Mills, Jack, primary, Verrill, Clare, primary, Bryant, Richard J., primary, Han, Cheng, primary, Hutchinson, Kathryn, primary, Lambert, Adam G., primary, Kumar, Rajeev, primary, Hamdy, Freddie C., primary, Weyer-Czernilofsky, Ulrike, primary, Sanderson, Michael P., primary, Bogenrieder, Thomas, primary, Taylor, Stephen, primary, and Macaulay, Valentine M., primary

Published
2023
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12. Aleksic_Supplementary Table S5 from Nuclear IGF1R Interacts with Regulatory Regions of Chromatin to Promote RNA Polymerase II Recruitment and Gene Expression Associated with Advanced Tumor Stage

Author

Aleksic, Tamara, primary, Gray, Nicki, primary, Wu, Xiaoning, primary, Rieunier, Guillaume, primary, Osher, Eliot, primary, Mills, Jack, primary, Verrill, Clare, primary, Bryant, Richard J., primary, Han, Cheng, primary, Hutchinson, Kathryn, primary, Lambert, Adam G., primary, Kumar, Rajeev, primary, Hamdy, Freddie C., primary, Weyer-Czernilofsky, Ulrike, primary, Sanderson, Michael P., primary, Bogenrieder, Thomas, primary, Taylor, Stephen, primary, and Macaulay, Valentine M., primary

Published
2023
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13. Data from Nuclear IGF1R Interacts with Regulatory Regions of Chromatin to Promote RNA Polymerase II Recruitment and Gene Expression Associated with Advanced Tumor Stage

Author

Aleksic, Tamara, primary, Gray, Nicki, primary, Wu, Xiaoning, primary, Rieunier, Guillaume, primary, Osher, Eliot, primary, Mills, Jack, primary, Verrill, Clare, primary, Bryant, Richard J., primary, Han, Cheng, primary, Hutchinson, Kathryn, primary, Lambert, Adam G., primary, Kumar, Rajeev, primary, Hamdy, Freddie C., primary, Weyer-Czernilofsky, Ulrike, primary, Sanderson, Michael P., primary, Bogenrieder, Thomas, primary, Taylor, Stephen, primary, and Macaulay, Valentine M., primary

Published
2023
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14. Supplementary Data from Targeting IGF Perturbs Global Replication through Ribonucleotide Reductase Dysfunction

Author

Rieunier, Guillaume, primary, Wu, Xiaoning, primary, Harris, Letitia E., primary, Mills, Jack V., primary, Nandakumar, Ashwin, primary, Colling, Laura, primary, Seraia, Elena, primary, Hatch, Stephanie B., primary, Ebner, Daniel V., primary, Folkes, Lisa K., primary, Weyer-Czernilofsky, Ulrike, primary, Bogenrieder, Thomas, primary, Ryan, Anderson J., primary, and Macaulay, Valentine M., primary

Published
2023
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15. Data from Targeting IGF Perturbs Global Replication through Ribonucleotide Reductase Dysfunction

Author

Rieunier, Guillaume, primary, Wu, Xiaoning, primary, Harris, Letitia E., primary, Mills, Jack V., primary, Nandakumar, Ashwin, primary, Colling, Laura, primary, Seraia, Elena, primary, Hatch, Stephanie B., primary, Ebner, Daniel V., primary, Folkes, Lisa K., primary, Weyer-Czernilofsky, Ulrike, primary, Bogenrieder, Thomas, primary, Ryan, Anderson J., primary, and Macaulay, Valentine M., primary

Published
2023
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17. Supplementary Figures S1-S6 from Dsh Homolog DVL3 Mediates Resistance to IGFIR Inhibition by Regulating IGF-RAS Signaling

Author

Gao, Shan, primary, Bajrami, Ilirjana, primary, Verrill, Clare, primary, Kigozi, Asha, primary, Ouaret, Djamila, primary, Aleksic, Tamara, primary, Asher, Ruth, primary, Han, Cheng, primary, Allen, Paul, primary, Bailey, Deborah, primary, Feller, Stephan, primary, Kashima, Takeshi, primary, Athanasou, Nicholas, primary, Blay, Jean-Yves, primary, Schmitz, Sandra, primary, Machiels, Jean-Pascal, primary, Upile, Nav, primary, Jones, Terry M., primary, Thalmann, George, primary, Ashraf, Shazad Q., primary, Wilding, Jennifer L., primary, Bodmer, Walter F., primary, Middleton, Mark R., primary, Ashworth, Alan, primary, Lord, Christopher J., primary, and Macaulay, Valentine M., primary

Published
2023
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18. Supplementary Figure Legend from Dsh Homolog DVL3 Mediates Resistance to IGFIR Inhibition by Regulating IGF-RAS Signaling

Author

Gao, Shan, primary, Bajrami, Ilirjana, primary, Verrill, Clare, primary, Kigozi, Asha, primary, Ouaret, Djamila, primary, Aleksic, Tamara, primary, Asher, Ruth, primary, Han, Cheng, primary, Allen, Paul, primary, Bailey, Deborah, primary, Feller, Stephan, primary, Kashima, Takeshi, primary, Athanasou, Nicholas, primary, Blay, Jean-Yves, primary, Schmitz, Sandra, primary, Machiels, Jean-Pascal, primary, Upile, Nav, primary, Jones, Terry M., primary, Thalmann, George, primary, Ashraf, Shazad Q., primary, Wilding, Jennifer L., primary, Bodmer, Walter F., primary, Middleton, Mark R., primary, Ashworth, Alan, primary, Lord, Christopher J., primary, and Macaulay, Valentine M., primary

Published
2023
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20. Supplementary Methods and References from Dsh Homolog DVL3 Mediates Resistance to IGFIR Inhibition by Regulating IGF-RAS Signaling

Author

Gao, Shan, primary, Bajrami, Ilirjana, primary, Verrill, Clare, primary, Kigozi, Asha, primary, Ouaret, Djamila, primary, Aleksic, Tamara, primary, Asher, Ruth, primary, Han, Cheng, primary, Allen, Paul, primary, Bailey, Deborah, primary, Feller, Stephan, primary, Kashima, Takeshi, primary, Athanasou, Nicholas, primary, Blay, Jean-Yves, primary, Schmitz, Sandra, primary, Machiels, Jean-Pascal, primary, Upile, Nav, primary, Jones, Terry M., primary, Thalmann, George, primary, Ashraf, Shazad Q., primary, Wilding, Jennifer L., primary, Bodmer, Walter F., primary, Middleton, Mark R., primary, Ashworth, Alan, primary, Lord, Christopher J., primary, and Macaulay, Valentine M., primary

Published
2023
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22. Supplementary Tables S1-S8 from Dsh Homolog DVL3 Mediates Resistance to IGFIR Inhibition by Regulating IGF-RAS Signaling

Author

Gao, Shan, primary, Bajrami, Ilirjana, primary, Verrill, Clare, primary, Kigozi, Asha, primary, Ouaret, Djamila, primary, Aleksic, Tamara, primary, Asher, Ruth, primary, Han, Cheng, primary, Allen, Paul, primary, Bailey, Deborah, primary, Feller, Stephan, primary, Kashima, Takeshi, primary, Athanasou, Nicholas, primary, Blay, Jean-Yves, primary, Schmitz, Sandra, primary, Machiels, Jean-Pascal, primary, Upile, Nav, primary, Jones, Terry M., primary, Thalmann, George, primary, Ashraf, Shazad Q., primary, Wilding, Jennifer L., primary, Bodmer, Walter F., primary, Middleton, Mark R., primary, Ashworth, Alan, primary, Lord, Christopher J., primary, and Macaulay, Valentine M., primary

Published
2023
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23. Data from Dsh Homolog DVL3 Mediates Resistance to IGFIR Inhibition by Regulating IGF-RAS Signaling

Author

Gao, Shan, primary, Bajrami, Ilirjana, primary, Verrill, Clare, primary, Kigozi, Asha, primary, Ouaret, Djamila, primary, Aleksic, Tamara, primary, Asher, Ruth, primary, Han, Cheng, primary, Allen, Paul, primary, Bailey, Deborah, primary, Feller, Stephan, primary, Kashima, Takeshi, primary, Athanasou, Nicholas, primary, Blay, Jean-Yves, primary, Schmitz, Sandra, primary, Machiels, Jean-Pascal, primary, Upile, Nav, primary, Jones, Terry M., primary, Thalmann, George, primary, Ashraf, Shazad Q., primary, Wilding, Jennifer L., primary, Bodmer, Walter F., primary, Middleton, Mark R., primary, Ashworth, Alan, primary, Lord, Christopher J., primary, and Macaulay, Valentine M., primary

Published
2023
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26. WNT5A-ROR2 axis mediates VEGF dependence of BRAF mutant melanoma

Author

Coupe, Nicholas, primary, Guo, Lina, additional, Bridges, Esther, additional, Campo, Leticia, additional, Espinosa, Olivia, additional, Colling, Richard, additional, Marshall, Andrea, additional, Nandakumar, Ashwin, additional, van Stiphout, Ruud, additional, Buffa, Francesca M., additional, Corrie, Pippa G., additional, Middleton, Mark R., additional, and Macaulay, Valentine M., additional

Published
2022
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32. CHK1 inhibition exacerbates replication stress induced by IGF blockade

Author

Wu, Xiaoning, primary, Seraia, Elena, additional, Hatch, Stephanie B., additional, Wan, Xiao, additional, Ebner, Daniel V., additional, Aroldi, Francesca, additional, Jiang, Yanyan, additional, Ryan, Anderson J., additional, Bogenrieder, Thomas, additional, Weyer-Czernilofsky, Ulrike, additional, Rieunier, Guillaume, additional, and Macaulay, Valentine M., additional

Published
2021
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37. Targeting IGF Perturbs Global Replication through Ribonucleotide Reductase Dysfunction

Author

Rieunier, Guillaume, primary, Wu, Xiaoning, additional, Harris, Letitia E., additional, Mills, Jack V., additional, Nandakumar, Ashwin, additional, Colling, Laura, additional, Seraia, Elena, additional, Hatch, Stephanie B., additional, Ebner, Daniel V., additional, Folkes, Lisa K., additional, Weyer-Czernilofsky, Ulrike, additional, Bogenrieder, Thomas, additional, Ryan, Anderson J., additional, and Macaulay, Valentine M., additional

Published
2021
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38. Aberrant succination of proteins in fumarate hydratase-deficient mice and HLRCC patients is a robust biomarker of mutation status

Author

Bardella, Chiara, El-Bahrawy, Mona, Frizzell, Norma, Adam, Julie, Ternette, Nicola, Hatipoglu, Emine, Howarth, Kimberley, OʼFlaherty, Linda, Roberts, Ian, Turner, Gareth, Taylor, Jennifer, Giaslakiotis, Konstantinos, Macaulay, Valentine M, Harris, Adrian L, Chandra, Ashish, Lehtonen, Heli J, Launonen, Virpi, Aaltonen, Lauri A, Pugh, Christopher W, Mihai, Radu, Trudgian, David, Kessler, Benedikt, Baynes, John W, Ratcliffe, Peter J, Tomlinson, Ian P, and Pollard, Patrick J

Published
2011
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40. IGF targeting perturbs global replication through ribonucleotide reductase dysfunction

Author

Rieunier, Guillaume, primary, Wu, Xiaoning, additional, Harris, Letitia, additional, Mills, Jack, additional, Nandakumar, Ashwin, additional, Colling, Laura, additional, Seraia, Elena, additional, Hatch, Stephanie B., additional, Ebner, Daniel, additional, Folkes, Lisa K., additional, Weyer-Czernilofsky, Ulrike, additional, Bogenrieder, Thomas, additional, Ryan, Anderson J., additional, and Macaulay, Valentine M., additional

Published
2020
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42. TOPK modulates tumour-specific radiosensitivity and correlates with recurrence after prostate radiotherapy

Author

Pirovano, Giacomo, Ashton, Thomas M., Herbert, Katharine J., Bryant, Richard J., Verrill, Clare L., Cerundolo, Lucia, Buffa, Francesca M., Prevo, Remko, Harrap, Iona, Ryan, Anderson J., Macaulay, Valentine, McKenna, William G., and Higgins, Geoff S.

Subjects
Cell Nucleus, Chromosome Aberrations, Male, Mitogen-Activated Protein Kinase Kinases, TOPK, Prostatic Neoplasms, Apoptosis, Cell Cycle Checkpoints, Quinolones, HCT116 Cells, Radiation Tolerance, Survival Rate, PBK, radiosensitivity, Cell Line, Tumor, Gene Knockdown Techniques, cancer, Humans, Neoplasm Recurrence, Local, Translational Therapeutics, Protein Kinase Inhibitors, HeLa Cells
Abstract

Background:\ud Tumour-specific radiosensitising treatments may enhance the efficacy of radiotherapy without exacerbating side effects. In this study we determined the radiation response following depletion or inhibition of TOPK, a mitogen-activated protein kinase kinase family Ser/Thr protein kinase that is upregulated in many cancers.\ud \ud Methods:\ud Radiation response was studied in a wide range of cancer cell lines and normal cells using colony formation assays. The effect on cell cycle progression was assessed and the relationship between TOPK expression and therapeutic efficacy was studied in a cohort of 128 prostate cancer patients treated with radical radiotherapy.\ud \ud Results:\ud TOPK knockdown did not alter radiation response in normal tissues, but significantly enhanced radiosensitivity in cancer cells. This result was recapitulated in TOPK knockout cells and with the TOPK inhibitor, OTS964. TOPK depletion altered the G1/S transition and G2/M arrest in response to radiation. Furthermore, TOPK depletion increased chromosomal aberrations, multinucleation and apoptotic cell death after irradiation. These results suggest a possible role for TOPK in the radiation-induced DNA damage checkpoints. These findings have clinical relevance, as elevated TOPK protein expression was associated with poorer clinical outcomes in prostate cancer patients treated with radical radiotherapy.\ud \ud Conclusions:\ud This study demonstrates that TOPK disruption may cause tumour-specific radiosensitisation in multiple different tumour types.

Published
2017

47. Dual-specificity protein phosphatase DUSP4 regulates response to MEK inhibition in BRAF wild-type melanoma

Author

Gupta, Avinash, primary, Towers, Christopher, additional, Willenbrock, Frances, additional, Brant, Roz, additional, Hodgson, Darren Richard, additional, Sharpe, Alan, additional, Smith, Paul, additional, Cutts, Anthony, additional, Schuh, Anna, additional, Asher, Ruth, additional, Myers, Kevin, additional, Love, Sharon, additional, Collins, Linda, additional, Wise, Adelyn, additional, Middleton, Mark Roy, additional, and Macaulay, Valentine Moya, additional

Published
2019
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