Search

Your search keyword '"Humphries, Matthew"' showing total 263 results
Start Over Author "Humphries, Matthew" Publication Year Range Last 50 years
263 results on '"Humphries, Matthew"'

1. Activation of a cGAS-STING-mediated immune response predicts response to neoadjuvant chemotherapy in early breast cancer

Author

Parkes, Eileen E., Savage, Kienan I., Lioe, Tong, Boyd, Clinton, Halliday, Sophia, Walker, Steven M., Lowry, Keith, Knight, Laura, Buckley, Niamh E., Grogan, Andrena, Logan, Gemma E., Clayton, Alison, Hurwitz, Jane, Kirk, Stephen J., Xu, Jiamei, Sidi, Fatima Abdullahi, Humphries, Matthew P., Bingham, Victoria, James, Jaqueline A., James, Colin R., Paul Harkin, D., Kennedy, Richard D., and McIntosh, Stuart A.

Published
2022
Full Text
View/download PDF

2. Male Breast Cancer

Author

Speirs, Valerie, Humphries, Matthew P., Shaaban, Abeer M., van Krieken, J. H. J. M., Series Editor, Sapino, Anna, editor, and Kulka, Janina, editor

Published
2020
Full Text
View/download PDF

4. Topographic analysis of pancreatic cancer by TMA and digital spatial profiling reveals biological complexity with potential therapeutic implications.

Author

Bingham, Victoria, Harewood, Louise, McQuaid, Stephen, Craig, Stephanie G., Revolta, Julia F., Kim, Chang S., Srivastava, Shambhavi, Quezada-Marín, Javier, Humphries, Matthew P., and Salto-Tellez, Manuel

Subjects
NUCLEOTIDE sequencing, PANCREATIC cancer, GENE expression, PANCREATIC duct, TUMOR markers, INTROGRESSION (Genetics)
Abstract

Pancreatic ductal adenocarcinoma (PDAC) remains one of the most lethal human malignancies. Tissue microarrays (TMA) are an established method of high throughput biomarker interrogation in tissues but may not capture histological features of cancer with potential biological relevance. Topographic TMAs (T-TMAs) representing pathophysiological hallmarks of cancer were constructed from representative, retrospective PDAC diagnostic material, including 72 individual core tissue samples. The T-TMA was interrogated with tissue hybridization-based experiments to confirm the accuracy of the topographic sampling, expression of pro-tumourigenic and immune mediators of cancer, totalling more than 750 individual biomarker analyses. A custom designed Next Generation Sequencing (NGS) panel and a spatial distribution-specific transcriptomic evaluation were also employed. The morphological choice of the pathophysiological hallmarks of cancer was confirmed by protein-specific expression. Quantitative analysis identified topography-specific patterns of expression in the IDO/TGF-β axis; with a heterogeneous relationship of inflammation and desmoplasia across hallmark areas and a general but variable protein and gene expression of c-MET. NGS results highlighted underlying genetic heterogeneity within samples, which may have a confounding influence on the expression of a particular biomarker. T-TMAs, integrated with quantitative biomarker digital scoring, are useful tools to identify hallmark specific expression of biomarkers in pancreatic cancer. [ABSTRACT FROM AUTHOR]

Published
2024
Full Text
View/download PDF

7. Whole-genome sequencing uncovers the genomic determinants of therapeutic resistance to immune checkpoint blockade

Author

Litchfield, Kevin, primary, Simpson, Benjamin, additional, Cha, Hongui, additional, Castro, Andrea, additional, Bentham, Robert, additional, Ryan, Lucy, additional, Dietzen, Michelle, additional, Thol, Kerstin, additional, Kinnersley, Ben, additional, Martin, Alice, additional, Chubb, Daniel, additional, Cornish, Alex, additional, Coulton, Alex, additional, Thakkar, Krupa, additional, Bailey, Chris, additional, Jennings, Charlotte, additional, Kaye, Danny, additional, Bansal, Daljeet, additional, Humphries, Matthew, additional, Wright, Alexander, additional, Colquhoun, Catherine, additional, Stankeviciute, Gaby, additional, Helliwell, Jacob, additional, Arumugam, Prabhu, additional, Treanor, Darren, additional, McGranahan, Nicholas, additional, Larkin, James, additional, Turajlic, Samra, additional, Swanton, Charles, additional, Greenig, Juliane, additional, Hiley, Crispin, additional, and Consortium, GEL Genomics England Research, additional

Published
2023
Full Text
View/download PDF

8. Immune status is prognostic for poor survival in colorectal cancer patients and is associated with tumour hypoxia

Author

Craig, Stephanie G., Humphries, Matthew P., Alderdice, Matthew, Bingham, Victoria, Richman, Susan D., Loughrey, Maurice B., Coleman, Helen G., Viratham-Pulsawatdi, Amelie, McCombe, Kris, Murray, Graeme I., Blake, Andrew, Domingo, Enric, Robineau, James, Brown, Louise, Fisher, David, Seymour, Matthew T., Quirke, Phil, Bankhead, Peter, McQuaid, Stephen, Lawler, Mark, McArt, Darragh G., Maughan, Tim S., James, Jacqueline A., and Salto-Tellez, Manuel

Published
2020
Full Text
View/download PDF

12. NAD(P)H Quinone Oxidoreductase 1 (NQO1) and NRH Quinone Oxidoreductase 2 (NQO2) : their inhibition by triazoloacridinones and imidazoacridinones

Author

Humphries, Matthew Philip and Stratford, Ian

Subjects
615.1, NQO2
Abstract

The human enzymes NQO1 and NQO2 are cytosoloic flavoproteins that catalyze the two electron reduction of a broad range of quinone substrates. NQO1 and 2 are over-expressed in several types of tumours, consequently making them attractive targets for drug development. Inhibition of NQO1 and NQO2 has been shown to reduce the development of some cancers. However current agents demonstrate off target effects and therefore more pharmacologically applicable compounds are needed. Initially a computational screen of the NCI database identified NSC 645827, a triazoleacridin-6-one (TA) with an IC50 of 0.7 µM. From this, a range of TAs were synthesised and evaluated for their ability to inhibit NQO1 and NQO2. From these data we identified several TAs which were the most potent inhibitors of NQO2 reported. The most potent compound being 10a (98 ± 10 nM), an N-oxide with low cellular toxicity and no DNA interaction. Taking the main pharmocaphore of the TA, a substructure search of the NCI database identified the imidazoacridin-6-one (IA) C1311, a known DNA binding agent and inhibitor of FLT3 kinase. Quantities of several IAs were obtained from the NCI and were investigated as potential NQO1 and NQO2 inhibitors. NSC 660841 was identified as the most potent inhibitor of NQO2 yet reported (6 ± 3 nM). Compounds were further investigated for potential off target effects.Representative compounds from both series were evaluated for their ability to modulate the cytotoxic effect of doxorubicin (DOX). There was no obvious relationship between the compound structures and the toxicity of DOX. Although no clear relationship could be determined between the compounds, a novel association between DOX, NQO1 and NQO2 was established. Compound A6B1 demonstrated the ability to increase the toxicity of DOX. It is hypothesised that a combination treatment of NQO2 inhibitors and DOX could lead to a greater therapeutic response as apposed to DOX alone. In summary, the results identify TAs and IAs to have the ability to inhibit both NQO1 and NQO2. The low cellular toxicity and high inhibitor potency of the N-oxide compounds makes them a suitable tool to study the enzymes without off target effects. Also these data provide a direction for future compound synthesis

Published
2012

13. Data from Metastasis and Immune Evasion from Extracellular cGAMP Hydrolysis

Author

Li, Jun, primary, Duran, Mercedes A., primary, Dhanota, Ninjit, primary, Chatila, Walid K., primary, Bettigole, Sarah E., primary, Kwon, John, primary, Sriram, Roshan K., primary, Humphries, Matthew P., primary, Salto-Tellez, Manuel, primary, James, Jacqueline A., primary, Hanna, Matthew G., primary, Melms, Johannes C., primary, Vallabhaneni, Sreeram, primary, Litchfield, Kevin, primary, Usaite, Ieva, primary, Biswas, Dhruva, primary, Bareja, Rohan, primary, Li, Hao Wei, primary, Martin, Maria Laura, primary, Dorsaint, Princesca, primary, Cavallo, Julie-Ann, primary, Li, Peng, primary, Pauli, Chantal, primary, Gottesdiener, Lee, primary, DiPardo, Benjamin J., primary, Hollmann, Travis J., primary, Merghoub, Taha, primary, Wen, Hannah Y., primary, Reis-Filho, Jorge S., primary, Riaz, Nadeem, primary, Su, Shin-San Michael, primary, Kalbasi, Anusha, primary, Vasan, Neil, primary, Powell, Simon N., primary, Wolchok, Jedd D., primary, Elemento, Olivier, primary, Swanton, Charles, primary, Shoushtari, Alexander N., primary, Parkes, Eileen E., primary, Izar, Benjamin, primary, and Bakhoum, Samuel F., primary

Published
2023
Full Text
View/download PDF

14. Supplementary Data PDF from Metastasis and Immune Evasion from Extracellular cGAMP Hydrolysis

Author

Li, Jun, primary, Duran, Mercedes A., primary, Dhanota, Ninjit, primary, Chatila, Walid K., primary, Bettigole, Sarah E., primary, Kwon, John, primary, Sriram, Roshan K., primary, Humphries, Matthew P., primary, Salto-Tellez, Manuel, primary, James, Jacqueline A., primary, Hanna, Matthew G., primary, Melms, Johannes C., primary, Vallabhaneni, Sreeram, primary, Litchfield, Kevin, primary, Usaite, Ieva, primary, Biswas, Dhruva, primary, Bareja, Rohan, primary, Li, Hao Wei, primary, Martin, Maria Laura, primary, Dorsaint, Princesca, primary, Cavallo, Julie-Ann, primary, Li, Peng, primary, Pauli, Chantal, primary, Gottesdiener, Lee, primary, DiPardo, Benjamin J., primary, Hollmann, Travis J., primary, Merghoub, Taha, primary, Wen, Hannah Y., primary, Reis-Filho, Jorge S., primary, Riaz, Nadeem, primary, Su, Shin-San Michael, primary, Kalbasi, Anusha, primary, Vasan, Neil, primary, Powell, Simon N., primary, Wolchok, Jedd D., primary, Elemento, Olivier, primary, Swanton, Charles, primary, Shoushtari, Alexander N., primary, Parkes, Eileen E., primary, Izar, Benjamin, primary, and Bakhoum, Samuel F., primary

Published
2023
Full Text
View/download PDF

15. supplementary figures, from In-depth Clinical and Biological Exploration of DNA Damage Immune Response as a Biomarker for Oxaliplatin Use in Colorectal Cancer

Author

Malla, Sudhir B., primary, Fisher, David J., primary, Domingo, Enric, primary, Blake, Andrew, primary, Hassanieh, Sylvana, primary, Redmond, Keara L., primary, Richman, Susan D., primary, Youdell, Michael, primary, Walker, Steven M., primary, Logan, Gemma E., primary, Chatzipli, Aikaterina, primary, Amirkhah, Raheleh, primary, Humphries, Matthew P., primary, Craig, Stephanie G., primary, McDermott, Ultan, primary, Seymour, Matthew T., primary, Morton, Dion G., primary, Quirke, Philip, primary, West, Nicholas P., primary, Salto-Tellez, Manuel, primary, Kennedy, Richard D., primary, Johnston, Patrick G., primary, Tomlinson, Ian, primary, Koelzer, Viktor H., primary, Campo, Letitia, primary, Kaplan, Richard S., primary, Longley, Daniel B., primary, Lawler, Mark, primary, Maughan, Timothy S., primary, Brown, Louise C., primary, and Dunne, Philip D., primary

Published
2023
Full Text
View/download PDF

16. Supplementary Results from In-depth Clinical and Biological Exploration of DNA Damage Immune Response as a Biomarker for Oxaliplatin Use in Colorectal Cancer

Author

Malla, Sudhir B., primary, Fisher, David J., primary, Domingo, Enric, primary, Blake, Andrew, primary, Hassanieh, Sylvana, primary, Redmond, Keara L., primary, Richman, Susan D., primary, Youdell, Michael, primary, Walker, Steven M., primary, Logan, Gemma E., primary, Chatzipli, Aikaterina, primary, Amirkhah, Raheleh, primary, Humphries, Matthew P., primary, Craig, Stephanie G., primary, McDermott, Ultan, primary, Seymour, Matthew T., primary, Morton, Dion G., primary, Quirke, Philip, primary, West, Nicholas P., primary, Salto-Tellez, Manuel, primary, Kennedy, Richard D., primary, Johnston, Patrick G., primary, Tomlinson, Ian, primary, Koelzer, Viktor H., primary, Campo, Letitia, primary, Kaplan, Richard S., primary, Longley, Daniel B., primary, Lawler, Mark, primary, Maughan, Timothy S., primary, Brown, Louise C., primary, and Dunne, Philip D., primary

Published
2023
Full Text
View/download PDF

17. Experimental workflow from A Case-Matched Gender Comparison Transcriptomic Screen Identifies eIF4E and eIF5 as Potential Prognostic Markers in Male Breast Cancer

Author

Humphries, Matthew P., primary, Sundara Rajan, Sreekumar, primary, Droop, Alastair, primary, Suleman, Charlotte A.B., primary, Carbone, Carmine, primary, Nilsson, Cecilia, primary, Honarpisheh, Hedieh, primary, Cserni, Gabor, primary, Dent, Jo, primary, Fulford, Laura, primary, Jordan, Lee B., primary, Jones, J. Louise, primary, Kanthan, Rani, primary, Litwiniuk, Maria, primary, Di Benedetto, Anna, primary, Mottolese, Marcella, primary, Provenzano, Elena, primary, Shousha, Sami, primary, Stephens, Mark, primary, Walker, Rosemary A., primary, Kulka, Janina, primary, Ellis, Ian O., primary, Jeffery, Margaret, primary, Thygesen, Helene H., primary, Cappelletti, Vera, primary, Daidone, Maria G., primary, Hedenfalk, Ingrid A., primary, Fjällskog, Marie-Louise, primary, Melisi, Davide, primary, Stead, Lucy F., primary, Shaaban, Abeer M., primary, and Speirs, Valerie, primary

Published
2023
Full Text
View/download PDF

18. Cut-off determination and representative staining profiles for eIF proteins determined by immunohistochemistry from A Case-Matched Gender Comparison Transcriptomic Screen Identifies eIF4E and eIF5 as Potential Prognostic Markers in Male Breast Cancer

Author

Humphries, Matthew P., primary, Sundara Rajan, Sreekumar, primary, Droop, Alastair, primary, Suleman, Charlotte A.B., primary, Carbone, Carmine, primary, Nilsson, Cecilia, primary, Honarpisheh, Hedieh, primary, Cserni, Gabor, primary, Dent, Jo, primary, Fulford, Laura, primary, Jordan, Lee B., primary, Jones, J. Louise, primary, Kanthan, Rani, primary, Litwiniuk, Maria, primary, Di Benedetto, Anna, primary, Mottolese, Marcella, primary, Provenzano, Elena, primary, Shousha, Sami, primary, Stephens, Mark, primary, Walker, Rosemary A., primary, Kulka, Janina, primary, Ellis, Ian O., primary, Jeffery, Margaret, primary, Thygesen, Helene H., primary, Cappelletti, Vera, primary, Daidone, Maria G., primary, Hedenfalk, Ingrid A., primary, Fjällskog, Marie-Louise, primary, Melisi, Davide, primary, Stead, Lucy F., primary, Shaaban, Abeer M., primary, and Speirs, Valerie, primary

Published
2023
Full Text
View/download PDF

19. Interrogation of Oncomine{trade mark, serif} from A Case-Matched Gender Comparison Transcriptomic Screen Identifies eIF4E and eIF5 as Potential Prognostic Markers in Male Breast Cancer

Author

Humphries, Matthew P., primary, Sundara Rajan, Sreekumar, primary, Droop, Alastair, primary, Suleman, Charlotte A.B., primary, Carbone, Carmine, primary, Nilsson, Cecilia, primary, Honarpisheh, Hedieh, primary, Cserni, Gabor, primary, Dent, Jo, primary, Fulford, Laura, primary, Jordan, Lee B., primary, Jones, J. Louise, primary, Kanthan, Rani, primary, Litwiniuk, Maria, primary, Di Benedetto, Anna, primary, Mottolese, Marcella, primary, Provenzano, Elena, primary, Shousha, Sami, primary, Stephens, Mark, primary, Walker, Rosemary A., primary, Kulka, Janina, primary, Ellis, Ian O., primary, Jeffery, Margaret, primary, Thygesen, Helene H., primary, Cappelletti, Vera, primary, Daidone, Maria G., primary, Hedenfalk, Ingrid A., primary, Fjällskog, Marie-Louise, primary, Melisi, Davide, primary, Stead, Lucy F., primary, Shaaban, Abeer M., primary, and Speirs, Valerie, primary

Published
2023
Full Text
View/download PDF

20. Supplementary Data from In-depth Clinical and Biological Exploration of DNA Damage Immune Response as a Biomarker for Oxaliplatin Use in Colorectal Cancer

Author

Malla, Sudhir B., primary, Fisher, David J., primary, Domingo, Enric, primary, Blake, Andrew, primary, Hassanieh, Sylvana, primary, Redmond, Keara L., primary, Richman, Susan D., primary, Youdell, Michael, primary, Walker, Steven M., primary, Logan, Gemma E., primary, Chatzipli, Aikaterina, primary, Amirkhah, Raheleh, primary, Humphries, Matthew P., primary, Craig, Stephanie G., primary, McDermott, Ultan, primary, Seymour, Matthew T., primary, Morton, Dion G., primary, Quirke, Philip, primary, West, Nicholas P., primary, Salto-Tellez, Manuel, primary, Kennedy, Richard D., primary, Johnston, Patrick G., primary, Tomlinson, Ian, primary, Koelzer, Viktor H., primary, Campo, Letitia, primary, Kaplan, Richard S., primary, Longley, Daniel B., primary, Lawler, Mark, primary, Maughan, Timothy S., primary, Brown, Louise C., primary, and Dunne, Philip D., primary

Published
2023
Full Text
View/download PDF

21. Subcellular Epithelial HMGB1 Expression Is Associated with Colorectal Neoplastic Progression, Male Sex, Mismatch Repair Protein Expression, Lymph Node Positivity, and an ‘Immune Cold’ Phenotype Associated with Poor Survival

Author

Porter, Ross J., primary, Murray, Graeme I., additional, Hapca, Sandra, additional, Hay, Andrew, additional, Craig, Stephanie G., additional, Humphries, Matthew P., additional, James, Jacqueline A., additional, Salto-Tellez, Manuel, additional, Brice, Daniel P., additional, Berry, Susan H., additional, and McLean, Mairi H., additional

Published
2023
Full Text
View/download PDF

24. Technical note on the exploration of COVID-19 in autopsy material

Author

Humphries, Matthew Phillip, primary, Bingham, Victoria, additional, Abdullah Sidi, Fatima, additional, Craig, Stephanie, additional, Lara, Beatrize, additional, El-daly, Hesham, additional, O'Doherty, Nicole, additional, Maxwell, Perry, additional, Lewis, Claire, additional, McQuaid, Stephen, additional, Lyness, James, additional, James, Jacqueline, additional, Snead, David R J, additional, and Salto-Tellez, Manuel, additional

Published
2023
Full Text
View/download PDF

26. ICOSeg: Real-Time ICOS Protein Expression Segmentation from Immunohistochemistry Slides Using a Lightweight Conv-Transformer Network

Author

Singh, Vivek Kumar, primary, Sarker, Md. Mostafa Kamal, additional, Makhlouf, Yasmine, additional, Craig, Stephanie G., additional, Humphries, Matthew P., additional, Loughrey, Maurice B., additional, James, Jacqueline A., additional, Salto-Tellez, Manuel, additional, O’Reilly, Paul, additional, and Maxwell, Perry, additional

Published
2022
Full Text
View/download PDF

28. Activation of a cGAS-STING-mediated immune response predicts response to neoadjuvant chemotherapy in early breast cancer

Author

Parkes, Eileen E, Savage, Kienan I, Lioe, Tong, Boyd, Clinton, Halliday, Sophia, Walker, Steven M, Lowry, Keith, Knight, Laura, Buckley, Niamh E, Grogan, Andrena, Logan, Gemma E, Clayton, Alison, Hurwitz, Jane, Kirk, Stephen J, Xu, Jiamei, Sidi, Fatima Abdullahi, Humphries, Matthew P, Bingham, Victoria, Neo-DDIR Investigators, James, Jaqueline A, James, Colin R, Paul Harkin, D, Kennedy, Richard D, and McIntosh, Stuart A

Abstract

BACKGROUND: The DNA-damage immune-response (DDIR) signature is an immune-driven gene expression signature retrospectively validated as predicting response to anthracycline-based therapy. This feasibility study prospectively evaluates the use of this assay to predict neoadjuvant chemotherapy response in early breast cancer. METHODS: This feasibility study assessed the integration of a novel biomarker into clinical workflows. Tumour samples were collected from patients receiving standard of care neoadjuvant chemotherapy (FEC + /-taxane and anti-HER2 therapy as appropriate) at baseline, mid- and post-chemotherapy. Baseline DDIR signature scores were correlated with pathological treatment response. RNA sequencing was used to assess chemotherapy/response-related changes in biologically linked gene signatures. RESULTS: DDIR signature reports were available within 14 days for 97.8% of 46 patients (13 TNBC, 16 HER2 + ve, 27 ER + HER2-ve). Positive scores predicted response to treatment (odds ratio 4.67 for RCB 0-1 disease (95% CI 1.13-15.09, P = 0.032)). DDIR positivity correlated with immune infiltration and upregulated immune-checkpoint gene expression. CONCLUSIONS: This study validates the DDIR signature as predictive of response to neoadjuvant chemotherapy which can be integrated into clinical workflows, potentially identifying a subgroup with high sensitivity to anthracycline chemotherapy. Transcriptomic data suggest induction with anthracycline-containing regimens in immune restricted, "cold" tumours may be effective for immune priming. TRIAL REGISTRATION: Not applicable (non-interventional study). CRUK Internal Database Number 14232.

Published
2021

30. Orthogonal MET analysis in a population‐representative stage II–III colon cancer cohort: prognostic and potential therapeutic implications

Author

Craig, Stephanie G., primary, Mende, Svenja, additional, Humphries, Matthew P., additional, Bingham, Victoria, additional, Viratham Pulsawatdi, Amélie, additional, Loughrey, Maurice B., additional, Coleman, Helen G., additional, McQuaid, Stephen, additional, Wilson, Richard H., additional, Van Schaeybroeck, Sandra, additional, James, Jacqueline A., additional, and Salto‐Tellez, Manuel, additional

Published
2021
Full Text
View/download PDF

31. The Potential of Digital Image Analysis to Determine Tumor Cell Content in Biobanked Formalin-Fixed, Paraffin-Embedded Tissue Samples

Author

Greene, Christine, primary, O'Doherty, Edwina, additional, Abdullahi Sidi, Fatima, additional, Bingham, Victoria, additional, Fisher, Natalie C., additional, Humphries, Matthew P., additional, Craig, Stephanie G., additional, Harewood, Louise, additional, McQuaid, Stephen, additional, Lewis, Claire, additional, and James, Jacqueline, additional

Published
2021
Full Text
View/download PDF

33. HistoClean: Open-source Software for Histological Image Pre-processing and Augmentation to Improve Development of Robust Convolutional Neural Networks

Author

McCombe, Kris D., primary, Craig, Stephanie G., additional, Pulsawatdi, Amélie Viratham, additional, Quezada-Marín, Javier I., additional, Hagan, Matthew, additional, Rajendran, Simon, additional, Humphries, Matthew P., additional, Bingham, Victoria, additional, Salto-Tellez, Manuel, additional, Gault, Richard, additional, and James, Jacqueline A., additional

Published
2021
Full Text
View/download PDF

34. Colonic epithelial cathelicidin (LL‐37) expression intensity is associated with progression of colorectal cancer and presence of CD8+ T cell infiltrate

Author

Porter, Ross J, primary, Murray, Graeme I, additional, Alnabulsi, Abdo, additional, Humphries, Matthew P, additional, James, Jacqueline A, additional, Salto‐Tellez, Manuel, additional, Craig, Stephanie G, additional, Wang, Ji M, additional, Yoshimura, Teizo, additional, and McLean, Mairi H, additional

Published
2021
Full Text
View/download PDF

35. Evolutionary genetic algorithm identifies IL2RB as a potential predictive biomarker for immune-checkpoint therapy in colorectal cancer

Author

Alderdice, Matthew, primary, Craig, Stephanie G, additional, Humphries, Matthew P, additional, Gilmore, Alan, additional, Johnston, Nicole, additional, Bingham, Victoria, additional, Coyle, Vicky, additional, Senevirathne, Seedevi, additional, Longley, Daniel B, additional, Loughrey, Maurice B, additional, McQuaid, Stephen, additional, James, Jacqueline A, additional, Salto-Tellez, Manuel, additional, Lawler, Mark, additional, and McArt, Darragh G, additional

Published
2021
Full Text
View/download PDF

36. In-depth Clinical and Biological Exploration of DNA Damage Immune Response as a Biomarker for Oxaliplatin Use in Colorectal Cancer

Author

Malla, Sudhir B., primary, Fisher, David J., additional, Domingo, Enric, additional, Blake, Andrew, additional, Hassanieh, Sylvana, additional, Redmond, Keara L., additional, Richman, Susan D., additional, Youdell, Michael, additional, Walker, Steven M., additional, Logan, Gemma E., additional, Chatzipli, Aikaterina, additional, Amirkhah, Raheleh, additional, Humphries, Matthew P., additional, Craig, Stephanie G., additional, McDermott, Ultan, additional, Seymour, Matthew T., additional, Morton, Dion G., additional, Quirke, Philip, additional, West, Nicholas P., additional, Salto-Tellez, Manuel, additional, Kennedy, Richard D., additional, Johnston, Patrick G., additional, Tomlinson, Ian, additional, Koelzer, Viktor H., additional, Campo, Letitia, additional, Kaplan, Richard S., additional, Longley, Daniel B., additional, Lawler, Mark, additional, Maughan, Timothy S., additional, Brown, Louise C., additional, and Dunne, Philip D., additional

Published
2021
Full Text
View/download PDF

37. Metastasis and Immune Evasion from Extracellular cGAMP Hydrolysis

Author

Li, Jun, primary, Duran, Mercedes A., additional, Dhanota, Ninjit, additional, Chatila, Walid K., additional, Bettigole, Sarah E., additional, Kwon, John, additional, Sriram, Roshan K., additional, Humphries, Matthew P., additional, Salto-Tellez, Manuel, additional, James, Jacqueline A., additional, Hanna, Matthew G., additional, Melms, Johannes C., additional, Vallabhaneni, Sreeram, additional, Litchfield, Kevin, additional, Usaite, Ieva, additional, Biswas, Dhruva, additional, Bareja, Rohan, additional, Li, Hao Wei, additional, Martin, Maria Laura, additional, Dorsaint, Princesca, additional, Cavallo, Julie-Ann, additional, Li, Peng, additional, Pauli, Chantal, additional, Gottesdiener, Lee, additional, DiPardo, Benjamin J., additional, Hollmann, Travis J., additional, Merghoub, Taha, additional, Wen, Hannah Y., additional, Reis-Filho, Jorge S., additional, Riaz, Nadeem, additional, Su, Shin-San Michael, additional, Kalbasi, Anusha, additional, Vasan, Neil, additional, Powell, Simon N., additional, Wolchok, Jedd D., additional, Elemento, Olivier, additional, Swanton, Charles, additional, Shoushtari, Alexander N., additional, Parkes, Eileen E., additional, Izar, Benjamin, additional, and Bakhoum, Samuel F., additional

Published
2020
Full Text
View/download PDF

39. Automated tumour recognition and digital pathology scoring unravels new role for PD-L1 in predicting good outcome in ER-/HER2+ breast cancer

Author

Humphries, Matthew P., Hynes, Sean, Bingham, Victoria, Cougot, Delphine, James, Jacqueline, Patel-Socha, Farah, Parkes, Eileen E., Blayney, Jaine K., O'Rorke, Michael A., Irwin, Gareth W., McArt, Darragh G., Kennedy, Richard D., Mullan, Paul B., McQuaid, Stephen, Salto-Tellez, Manuel, and Buckley, Niamh E.

Subjects
SDG 3 - Good Health and Well-being, Article Subject, lcsh:Neoplasms. Tumors. Oncology. Including cancer and carcinogens, lcsh:RC254-282, Research Article
Abstract

The role of PD-L1 as a prognostic and predictive biomarker is an area of great interest. However, there is a lack of consensus on how to deliver PD-L1 as a clinical biomarker. At the heart of this conundrum is the subjective scoring of PD-L1 IHC in most studies to date. Current standard scoring systems involve separation of epithelial and inflammatory cells and find clinical significance in different percentages of expression, e.g., above or below 1%. Clearly, an objective, reproducible and accurate approach to PD-L1 scoring would bring a degree of necessary consistency to this landscape. Using a systematic comparison of technologies and the application of QuPath, a digital pathology platform, we show that high PD-L1 expression is associated with improved clinical outcome in Triple Negative breast cancer in the context of standard of care (SoC) chemotherapy, consistent with previous findings. In addition, we demonstrate for the first time that high PD-L1 expression is also associated with better outcome in ER- disease as a whole including HER2+ breast cancer. We demonstrate the influence of antibody choice on quantification and clinical impact with the Ventana antibody (SP142) providing the most robust assay in our hands. Through sampling different regions of the tumour, we show that tumour rich regions display the greatest range of PD-L1 expression and this has the most clinical significance compared to stroma and lymphoid rich areas. Furthermore, we observe that both inflammatory and epithelial PD-L1 expression are associated with improved survival in the context of chemotherapy. Moreover, as seen with PD-L1 inhibitor studies, a low threshold of PD-L1 expression stratifies patient outcome. This emphasises the importance of using digital pathology and precise biomarker quantitation to achieve accurate and reproducible scores that can discriminate low PD-L1 expression.

Published
2020

40. Additional file 2 of The adaptive immune and immune checkpoint landscape of neoadjuvant treated esophageal adenocarcinoma using digital pathology quantitation

Author

Humphries, Matthew P., Craig, Stephanie G., Kacprzyk, Rafal, Fisher, Natalie C., Bingham, Victoria, McQuaid, Stephen, Murray, Graeme I., McManus, Damian, Turkington, Richard C., James, Jacqueline, and Salto-Tellez, Manuel

Subjects
Data_FILES
Abstract

Additional file 2: Table S2. R.O.C Cut Offs.

Published
2020
Full Text
View/download PDF

41. Additional file 4 of The adaptive immune and immune checkpoint landscape of neoadjuvant treated esophageal adenocarcinoma using digital pathology quantitation

Author

Humphries, Matthew P., Craig, Stephanie G., Kacprzyk, Rafal, Fisher, Natalie C., Bingham, Victoria, McQuaid, Stephen, Murray, Graeme I., McManus, Damian, Turkington, Richard C., James, Jacqueline, and Salto-Tellez, Manuel

Subjects
ComputingMethodologies_PATTERNRECOGNITION
Abstract

Additional file 4: Figure S1. Robust digital pathology workflow. Flow diagram demonstrates conceptually the process of biomarker quantification, strict quality control and data validation steps.

Published
2020
Full Text
View/download PDF

42. Additional file 3 of The adaptive immune and immune checkpoint landscape of neoadjuvant treated esophageal adenocarcinoma using digital pathology quantitation

Author

Humphries, Matthew P., Craig, Stephanie G., Kacprzyk, Rafal, Fisher, Natalie C., Bingham, Victoria, McQuaid, Stephen, Murray, Graeme I., McManus, Damian, Turkington, Richard C., James, Jacqueline, and Salto-Tellez, Manuel

Abstract

Additional file 3: Table S3. Discovery Cohort Multivariate Analysis Excluding TRG 1 and 2 cases.

Published
2020
Full Text
View/download PDF

44. Identifying mismatch repair‐deficient colon cancer: near‐perfect concordance between immunohistochemistry and microsatellite instability testing in a large, population‐based series

Author

Loughrey, Maurice B, primary, McGrath, Jason, additional, Coleman, Helen G, additional, Bankhead, Peter, additional, Maxwell, Perry, additional, McGready, Claire, additional, Bingham, Victoria, additional, Humphries, Matthew P, additional, Craig, Stephanie G, additional, McQuaid, Stephen, additional, Salto‐Tellez, Manuel, additional, and James, Jacqueline A, additional

Published
2020
Full Text
View/download PDF

46. A robust multiplex immunofluorescence and digital pathology workflow for the characterisation of the tumour immune microenvironment

Author

Viratham Pulsawatdi, Amélie, primary, Craig, Stephanie G., additional, Bingham, Victoria, additional, McCombe, Kris, additional, Humphries, Matthew P., additional, Senevirathne, Seedevi, additional, Richman, Susan D., additional, Quirke, Phil, additional, Campo, Leticia, additional, Domingo, Enric, additional, Maughan, Timothy S., additional, James, Jacqueline A., additional, and Salto‐Tellez, Manuel, additional

Published
2020
Full Text
View/download PDF

47. The zebrafish reference genome sequence and its relationship to the human genome

Author

Howe, Kerstin, Clark, Matthew D., Torroja, Carlos F., Torrance, James, Berthelot, Camille, Muffato, Matthieu, Collins, John E., Humphray, Sean, McLaren, Karen, Matthews, Lucy, McLaren, Stuart, Sealy, Ian, Caccamo, Mario, Churcher, Carol, Scott, Carol, Barrett, Jeffrey C., Koch, Romke, Rauch, Gerd-Jörg, White, Simon, Chow, William, Kilian, Britt, Quintais, Leonor T., Guerra-Assunção, José A., Zhou, Yi, Gu, Yong, Yen, Jennifer, Vogel, Jan-Hinnerk, Eyre, Tina, Redmond, Seth, Banerjee, Ruby, Chi, Jianxiang, Fu, Beiyuan, Langley, Elizabeth, Maguire, Sean F., Laird, Gavin K., Lloyd, David, Kenyon, Emma, Donaldson, Sarah, Sehra, Harminder, Almeida-King, Jeff, Loveland, Jane, Trevanion, Stephen, Jones, Matt, Quail, Mike, Willey, Dave, Hunt, Adrienne, Burton, John, Sims, Sarah, McLay, Kirsten, Plumb, Bob, Davis, Joy, Clee, Chris, Oliver, Karen, Clark, Richard, Riddle, Clare, Eliott, David, Threadgold, Glen, Harden, Glenn, Ware, Darren, Mortimer, Beverly, Kerry, Giselle, Heath, Paul, Phillimore, Benjamin, Tracey, Alan, Corby, Nicole, Dunn, Matthew, Johnson, Christopher, Wood, Jonathan, Clark, Susan, Pelan, Sarah, Griffiths, Guy, Smith, Michelle, Glithero, Rebecca, Howden, Philip, Barker, Nicholas, Stevens, Christopher, Harley, Joanna, Holt, Karen, Panagiotidis, Georgios, Lovell, Jamieson, Beasley, Helen, Henderson, Carl, Gordon, Daria, Auger, Katherine, Wright, Deborah, Collins, Joanna, Raisen, Claire, Dyer, Lauren, Leung, Kenric, Robertson, Lauren, Ambridge, Kirsty, Leongamornlert, Daniel, McGuire, Sarah, Gilderthorp, Ruth, Griffiths, Coline, Manthravadi, Deepa, Nichol, Sarah, Barker, Gary, Whitehead, Siobhan, Kay, Michael, Brown, Jacqueline, Murnane, Clare, Gray, Emma, Humphries, Matthew, Sycamore, Neil, Barker, Darren, Saunders, David, Wallis, Justene, Babbage, Anne, Hammond, Sian, Mashreghi-Mohammadi, Maryam, Barr, Lucy, Martin, Sancha, Wray, Paul, Ellington, Andrew, Matthews, Nicholas, Ellwood, Matthew, Woodmansey, Rebecca, Clark, Graham, Cooper, James, Tromans, Anthony, Grafham, Darren, Skuce, Carl, Pandian, Richard, Andrews, Robert, Harrison, Elliot, Kimberley, Andrew, Garnett, Jane, Fosker, Nigel, Hall, Rebekah, Garner, Patrick, Kelly, Daniel, Bird, Christine, Palmer, Sophie, Gehring, Ines, Berger, Andrea, Dooley, Christopher M., Ersan-Ürün, Zübeyde, Eser, Cigdem, Geiger, Horst, Geisler, Maria, Karotki, Lena, Kirn, Anette, Konantz, Judith, Konantz, Martina, Oberländer, Martina, Rudolph-Geiger, Silke, Teucke, Mathias, Osoegawa, Kazutoyo, Zhu, Baoli, Rapp, Amanda, Widaa, Sara, Langford, Cordelia, Yang, Fengtang, Carter, Nigel P., Harrow, Jennifer, Ning, Zemin, Herrero, Javier, Searle, Steve M. J., Enright, Anton, Geisler, Robert, Plasterk, Ronald H. A., Lee, Charles, Westerfield, Monte, de Jong, Pieter J., Zon, Leonard I., Postlethwait, John H., Nüsslein-Volhard, Christiane, Hubbard, Tim J. P., Crollius, Hugues Roest, Rogers, Jane, and Stemple, Derek L.

Published
2013
Full Text
View/download PDF

Catalog

Books, media, physical & digital resources
See catalog results