Publications -

Publications

2023

Suzuki T, Kilbey A, Casa-Rodríguez N, Lawlor A, Georgakopoulou A, Hayman H, Yin Swe KL, Nordin A, Cantù C, Vantourout P, Ridgway RA, Byrne RM, Chen L, Verzi MP, Gay DM, Gil Vázquez E, Belnoue-Davis HL, Gilroy K, Køstner AH, Kersten C, Thuwajit C, Andersen DK, Wiesheu R, Jandke A, Blyth K, Roseweir AK, Leedham SJ, Dunne PD, Edwards J, Hayday A, Sansom OJ, Coffelt SB. β-Catenin Drives Butyrophilin-like Molecule Loss and γδ T-cell Exclusion in Colon Cancer. Cancer Immunol Res. 2023 Aug 3;11(8):1137-1155. doi: 10.1158/2326-6066.CIR-22-0644.

Egan H, Treacy O, Lynch K, Leonard NA, O’Malley G, Reidy E, O’Neill A, Corry SM, De Veirman K, Vanderkerken K, Egan LJ, Ritter T, Hogan AM, Redmond K, Peng L, Che J, Gatlin W, Jayaraman P, Sheehan M, Canney A, Hynes SO, Kerr EM, Dunne PD, O’Dwyer ME, Ryan AE. Targeting stromal cell sialylation reverses T cell-mediated immunosuppression in the tumor microenvironment . Cell Rep. 2023 May 30;42(5):112475. doi: 10.1016/j.celrep.2023.112475. Epub 2023 May 10.

R Amirkhah, K Gilroy, S B Malla, T RM Lannagan, R M Byrne, N C Fisher, S M Corry, N E Mohamed, H Naderi-Meshkin, M L Mills, A D Campbell, R A Ridgway, B Ahmaderaghi, R Murray, A Berenguer Llergo, R Sanz-Pamplona, A Villanueva, E Batlle, R Salazar, M Lawler, O J Sansom, PD Dunne. MmCMS: mouse models’ consensus molecular subtypes of colorectal cancer. Nature BJC. 2023 Jan 30. doi: 10.1038/s41416-023-02157-6.

2022

Dustin J. Flanagan, Raheleh Amirkhah, David F. Vincent, Nuray Gundaz, Pauline Gentaz, Patrizia Cammareri, Aoife J. McCooey, Amy M. B. McCorry, Natalie C. Fisher, et al. Epithelial TGFβ engages growth-factor signalling to circumvent apoptosis and drive intestinal tumourigenesis with aggressive features. Nat Commun. 2022 Dec 7;13(1):7551. doi: 10.1038/s41467-022-35134-3.

Henderson RH, French D, McFerran E, Adams R, Wasan H, Glynne-Jones R, Fisher D, Richman S, Dunne PD, Wilde L, Maughan TS, Sullivan R, Lawler M. Spend less to achieve more: Economic analysis of intermittent versus continuous cetuximab in KRAS wild-type patients with metastatic colorectal cancer. J Cancer Policy. 2022 Sep;33:100342. doi: 10.1016/j.jcpo.2022.100342.

Begum M, Lewison G, Wang X, Dunne PD, Maughan T, Sullivan R, Lawler M. Global colorectal cancer research, 2007-2021: Outputs and funding. Int J Cancer. 2022 Sep 8. doi: 10.1002/ijc.34279.

Vasquez EG, Nasreddin N, Valbuena GN, Mulholland EJ, Belnoue-Davis HL, Eggington HR, Schenck RO, Wouters VM, Wirapati P, Gilroy K, Lannagan TRM, Flanagan DJ, Najumudeen AK, Omwenga S, McCorry AMB, Easton A, Koelzer VH, East JE, Morton D, Trusolino L, Maughan T, Campbell AD, Loughrey MB, Dunne PD, Tsantoulis P, Huels DJ, Tejpar S, Sansom OJ, Leedham SJ. Dynamic and adaptive cancer stem cell population admixture in colorectal neoplasia. Cell Stem Cell. 2022 Aug 4;29(8):1213-1228.e8. doi: 10.1016/j.stem.2022.07.008.

NC. Fisher , RM. Byrne , H Leslie, C Wood, A Legrini, AJ. Cameron, B Ahmaderaghi, SM. Corry, SB. Malla, R Amirkhah, AJ. McCooey, E Rogan, KL. Redmond, S Sakhnevych, E Domingo, J, Jackson, MB. Loughrey, S Leedham, T Maughan, M Lawler, OJ. Sansom, F Lamrock, VH. Koelzer, NB. Jamieson, and PD. Dunne, et al. Biological misinterpretation of transcriptional signatures in tumour samples can unknowingly undermine mechanistic understanding and faithful alignment with preclinical data. Clin Cancer Res. 2022 Jul 6;ccr.22.1102. doi: 10.1158/1078-0432.CCR-22-1102.

SM Corry, AMB McCorry, TRM Lannagan, NA Leonard, NC Fisher, RM Byrne, P Tsantoulis, X Cortes-Lavaud, R Amirkhah, KL Redmond, AJ McCooey, SB Malla, E Rogan, S Sakhnevych, et al. Activation of innate-adaptive immune machinery by poly(I:C) exposes a therapeutic vulnerability to prevent relapse in stroma-rich colon cancer. Gut 2022;0:1–16. doi:10.1136/gutjnl-2021-326183

Baharak Ahmaderaghi, Raheleh Amirkhah, James Jackson, Tamsin R M Lannagan, Kathryn Gilroy, Sudhir B Malla, Keara L Redmond , Gerard Quinn, Simon S McDade, ACRCelerate Consortium, Tim Maughan, Simon Leedham , Andrew S D Campbell, Owen J Sansom, Mark Lawler, Philip D Dunne. Molecular Subtyping Resource: a user-friendly tool for rapid biological discovery from transcriptional data .
2022 Mar 1;15(3):dmm049257. doi:10.1242/dmm.049257.

2021

Lindner AU, Salvucci M, McDonough E, Cho S, Stachtea X, O’Connell EP, Corwin AD, Santamaria-Pang A, Carberry S, Fichtner M, Van Schaeybroeck S, Laurent-Puig P, Burke JP, McNamara DA, Lawler M, Sood A, Graf JF, Rehm M, Dunne PD, et al. An atlas of inter- and intra-tumor heterogeneity of apoptosis competency in colorectal cancer tissue at single-cell resolution. Cell Death Differ. 2021 Nov 9. doi: 10.1038/s41418-021-00895-9.
Graf J, Cho S, McDonough E, Corwin A, Sood A, Lindner A, Salvucci M, Stachtea X, Van Schaeybroeck S, Dunne PD, et al. FLINO-A new method for immunofluorescence bioimage normalization. Bioinformatics. 2021 Oct 2:btab686. doi: 10.1093/bioinformatics/btab686.
Fisher NC, Loughrey MB, Coleman HG, Gelbard MD, Bankhead P, Dunne PD. Development of a semi-automated method for tumour budding assessment in colorectal cancer and comparison with manual methods. Histopathology. 2021 Sep 28. doi: 10.1111/his.14574.
Crawford N, Stott KJ, Sessler T, McCann C, McDaid W, Lees A, Latimer C, Fox JP, Munck JM, Smyth T, Shah A, Martins V, Lawler M, Dunne PD, et al. Clinical Positioning of the IAP Antagonist Tolinapant (ASTX660) in Colorectal Cancer. Epub 2021 Aug 13. PMID: 34389694
Loughrey MB, Fisher NC, McCooey AJ, Dunne PD. Comment on “Identification of EMT-related high-risk stage II colorectal cancer and characterisation of metastasis-related genes”. Br J Cancer. 2021 Mar;124(6):1175-1176.

Arafath K. Najumudeen et al. The amino acid transporter SLC7A5 is required for efficient growth of KRAS-mutant colorectal cancer. Nat Genet. 2021 Jan.
Sudhir B. Malla et al. In-depth Clinical and Biological Exploration of DNA Damage Immune Response as a Biomarker for Oxaliplatin Use in Colorectal Cancer. Clinical Cancer Research. 2021 Jan.

2020

Korsuk Sirinukunwattana, Enric Domingo, Susan D Richman, Keara L Redmond, Andrew Blake, et al. Image-based consensus molecular subtype (imCMS) classification of colorectal cancer using deep learning. Gut. 2020 Jul.

Andrea Lees, Alexander J McIntyre, Nyree T Crawford, Fiammetta Falcone, Christopher McCann, Caitriona Holohan, et al. The pseudo-caspase FLIP (L) regulates cell fate following p53 activation. Proc Natl Acad Sci U S A. 2020 Jul;
R McBride, BM Hicks, HG Coleman, MB Loughrey, AT Gavin, PD Dunne, et al. Prognosis following surgical resection versus local excision of stage pT1 colorectal cancer: A population-based cohort study. Surgeon. 2020. Apr;18(2):65-74.
Adam P Harvey, Emma Robinson, Kevin S Edgar, Ross McMullan, Karla M O’Neill, Matthew Alderdice, et al. Downregulation of PPARα during Experimental Left Ventricular Hypertrophy is Critically Dependent on Nox2 NADPH Oxidase Signalling. Int J Mol Sci. 2020 Jun;21(12):4406

2019

Kleeman SO, Koelzer VH, Jones HJ, Vazquez EG, Davis H, East JE, et al. Exploiting differential Wnt target gene expression to generate a molecular biomarker for colorectal cancer stratification. Gut. 2019 Sep.

Beirne JP, McArt DG, Roddy A, McDermott C, Ferris J, Buckley NE, et al. Defining the molecular evolution of extrauterine high grade serous carcinoma. Gynecol Oncol. 2019 Nov;155(2):305–17.
Amirkhah R, Naderi-Meshkin H, Shah JS, Dunne PD, Schmitz U. The Intricate Interplay between Epigenetic Events, Alternative Splicing and Noncoding RNA Deregulation in Colorectal Cancer. Cells. 2019 Aug;8(8).

McBride R, Hicks BM, Coleman HG, Loughrey MB, Gavin AT, Dunne PD, et al. Prognosis following surgical resection versus local excision of stage pT1 colorectal cancer: A population-based cohort study. Surgeon. 2019 Aug;
Dutton LR, Hoare OP, McCorry AMB, Redmond KL, Adam NE, Canamara S, et al. Fibroblast-derived Gremlin1 localises to epithelial cells at the base of the intestinal crypt. Oncotarget. 2019 Jul;10(45):4630–9.
Gilmore AR, Alderdice M, Savage KI, O’Reilly PG, Roddy AC, Dunne PD, et al. ACE: A Workbench Using Evolutionary Genetic Algorithms for Analyzing Association in TCGA. Cancer Res. 2019 Apr;79(8):2072–5.
Loughrey MB, Dunne PD, Coleman HG, McQuaid S, James JA. Punctate MLH1 mismatch repair immunostaining in colorectal cancer. Vol. 74, Histopathology. England; 2019. p. 795–7.

2018

Stupnikov A, O’Reilly PG, McInerney CE, Roddy AC, Dunne PD, Gilmore A, et al. Impact of Variable RNA-Sequencing Depth on Gene Expression Signatures and Target Compound Robustness: Case Study Examining Brain Tumor (Glioma) Disease Progression. JCO Precis Oncol [Internet]. 2018 Aug;2(2):1–17. Available from: http://ascopubs.org/doi/10.1200/PO.18.00014
McCorry AM, Loughrey MB, Longley DB, Lawler M, Dunne PD. Epithelial-to-mesenchymal transition signature assessment in colorectal cancer quantifies tumour stromal content rather than true transition. J Pathol. 2018 Dec;246(4):422–6.
O’Malley G, Treacy O, Lynch K, Naicker SD, Leonard NA, Lohan P, et al. Stromal Cell PD-L1 Inhibits CD8(+) T-cell Antitumor Immune Responses and Promotes Colon Cancer. Cancer Immunol Res. 2018 Nov;6(11):1426–41.
Loughrey MB, Bankhead P, Coleman HG, Hagan RS, Craig S, McCorry AMB, et al. Validation of the systematic scoring of immunohistochemically stained tumour tissue microarrays using QuPath digital image analysis. Histopathology. 2018 Aug;73(2):327–38.
Dunne PD, Coleman HG, Bankhead P, Alderdice M, Gray RT, McQuaid S, et al. Bcl-xL as a poor prognostic biomarker and predictor of response to adjuvant chemotherapy specifically in BRAF-mutant stage II and III colon cancer. Oncotarget. 2018 Mar;9(17):13834–47.
Alderdice M, Richman SD, Gollins S, Stewart JP, Hurt C, Adams R, et al. Prospective patient stratification into robust cancer-cell intrinsic subtypes from colorectal cancer biopsies. J Pathol. 2018 May;245(1):19–28.

2017

Bankhead P, Loughrey MB, Fernandez JA, Dombrowski Y, McArt DG, Dunne PD, et al. QuPath: Open source software for digital pathology image analysis. Sci Rep. 2017 Dec;7(1):16878.
Hutchinson RA, Coleman HG, Gately K, Young V, Nicholson S, Cummins R, et al. IHC-based subcellular quantification provides new insights into prognostic relevance of FLIP and procaspase-8 in non-small-cell lung cancer. Cell death Discov. 2017;3:17050.
Oddo D, Siravegna G, Gloghini A, Vernieri C, Mussolin B, Morano F, et al. Emergence of MET hyper-amplification at progression to MET and BRAF inhibition in colorectal cancer. Br J Cancer. 2017 Jul;117(3):347–52.
Alderdice M, Dunne PD, Cole AJ, O’Reilly PG, McArt DG, Bingham V, et al. Natural killer-like signature observed post therapy in locally advanced rectal cancer is a determinant of pathological response and improved survival. Mod Pathol an Off J United States Can Acad Pathol Inc. 2017 Sep;30(9):1287–98.
Alvi MA, Loughrey MB, Dunne P, McQuaid S, Turkington R, Fuchs M-A, et al. Molecular profiling of signet ring cell colorectal cancer provides a strong rationale for genomic targeted and immune checkpoint inhibitor therapies. Br J Cancer. 2017 Jul;117(2):203–9.
Dunne PD, Alderdice M, O’Reilly PG, Roddy AC, McCorry AMB, Richman S, et al. Cancer-cell intrinsic gene expression signatures overcome intratumoural heterogeneity bias in colorectal cancer patient classification. Nat Commun. 2017 May;8:15657.
Stewart JP, Richman S, Maughan T, Lawler M, Dunne PD, Salto-Tellez M. Standardising RNA profiling based biomarker application in cancer-The need for robust control of technical variables. Biochim Biophys acta Rev cancer. 2017 Aug;1868(1):258–72.
Dunne PD, Lawler M. Intratumoural Epigenetic Heterogeneity in Early Invasive Colorectal Cancer: A Prognostic Imprint? Vol. 152, Gastroenterology. United States; 2017. p. 1622–3.
Hynes SO, Coleman HG, Kelly PJ, Dunne PD, Salto-Tellez M, Loughrey MB. Response to Park et al. reply to “Back to the future: routine morphological assessment of the tumour microenvironment is prognostic in stage II/III colon cancer in a large population-based study”. Vol. 71, Histopathology. England; 2017. p. 327–9.
McLaughlin D, Zhao Y, O’Neill KM, Edgar KS, Dunne PD, Kearney AM, et al. Signalling mechanisms underlying doxorubicin and Nox2 NADPH oxidase-induced cardiomyopathy: involvement of mitofusin-2. Br J Pharmacol. 2017 Nov;174(21):3677–95.
Hynes SO, Coleman HG, Kelly PJ, Irwin S, O’Neill RF, Gray RT, et al. Back to the future: routine morphological assessment of the tumour microenvironment is prognostic in stage II/III colon cancer in a large population-based study. Histopathology. 2017 Jul;71(1):12–26.
Church RH, Ali I, Tate M, Lavin D, Krishnakumar A, Kok HM, et al. Gremlin1 plays a key role in kidney development and renal fibrosis. Am J Physiol Renal Physiol. 2017 Jun;312(6):F1141–57.
Wen Q, Dunne PD, O’Reilly PG, Li G, Bjourson AJ, McArt DG, et al. KRAS mutant colorectal cancer gene signatures identified angiotensin II receptor blockers as potential therapies. Oncotarget. 2017 Jan;8(2):3206–25.

2016

Dunne PD, McArt DG, O’Reilly PG, Coleman HG, Allen WL, Loughrey M, et al. Immune-Derived PD-L1 Gene Expression Defines a Subgroup of Stage II/III Colorectal Cancer Patients with Favorable Prognosis Who May Be Harmed by Adjuvant Chemotherapy. Cancer Immunol Res. 2016 Jul;4(7):582–91.
Bradley CA, Dunne PD, Bingham V, McQuaid S, Khawaja H, Craig S, et al. Transcriptional upregulation of c-MET is associated with invasion and tumor budding in colorectal cancer. Oncotarget. 2016 Nov;7(48):78932–45.
Dunne PD, O’Reilly PG, Coleman HG, Gray RT, Longley DB, Johnston PG, et al. Stratified analysis reveals chemokine-like factor (CKLF) as a potential prognostic marker in the MSI-immune consensus molecular subtype CMS1 of colorectal cancer. Oncotarget. 2016 Jun;7(24):36632–44.
Dunne PD, McArt DG, Bradley CA, O’Reilly PG, Barrett HL, Cummins R, et al. Challenging the Cancer Molecular Stratification Dogma: Intratumoral Heterogeneity Undermines Consensus Molecular Subtypes and Potential Diagnostic Value in Colorectal Cancer. Clin Cancer Res. 2016 Aug;22(16):4095–104.
O’Reilly PG, Wen Q, Bankhead P, Dunne PD, McArt DG, McPherson S, et al. QUADrATiC: scalable gene expression connectivity mapping for repurposing FDA-approved therapeutics. BMC Bioinformatics. 2016 May;17(1):198.
Dunne PD, Dasgupta S, Blayney JK, McArt DG, Redmond KL, Weir J-A, et al. EphA2 Expression Is a Key Driver of Migration and Invasion and a Poor Prognostic Marker in Colorectal Cancer. Clin Cancer Res. 2016 Jan;22(1):230–42.

2015 and earlier

Ong CW, Chong PY, McArt DG, Chan JY, Tan HT, Kumar AP, et al. The prognostic value of the stem-like group in colorectal cancer using a panel of immunohistochemistry markers. Oncotarget. 2015 May;6(14):12763–73.
McArt DG, Blayney JK, Boyle DP, Irwin GW, Moran M, Hutchinson RA, et al. PICan: An integromics framework for dynamic cancer biomarker discovery. Mol Oncol. 2015 Jun;9(6):1234–40.
Van Schaeybroeck S, Kalimutho M, Dunne PD, Carson R, Allen W, Jithesh P V, et al. ADAM17-dependent c-MET-STAT3 signaling mediates resistance to MEK inhibitors in KRAS mutant colorectal cancer. Cell Rep. 2014 Jun;7(6):1940–55.
Dunne PD, McArt DG, Blayney JK, Kalimutho M, Greer S, Wang T, et al. AXL is a key regulator of inherent and chemotherapy-induced invasion and predicts a poor clinical outcome in early-stage colon cancer. Clin Cancer Res. 2014 Jan;20(1):164–75.
McArt DG, Bankhead P, Dunne PD, Salto-Tellez M, Hamilton P, Zhang S-D. cudaMap: a GPU accelerated program for gene expression connectivity mapping. BMC Bioinformatics. 2013 Oct;14:305.
McArt DG, Dunne PD, Blayney JK, Salto-Tellez M, Van Schaeybroeck S, Hamilton PW, et al. Connectivity Mapping for Candidate Therapeutics Identification Using Next Generation Sequencing RNA-Seq Data. PLoS One. 2013;8(6):e66902.
Allen WL, Turkington RC, Stevenson L, Carson G, Coyle VM, Hector S, et al. Pharmacogenomic profiling and pathway analyses identify MAPK-dependent migration as an acute response to SN38 in p53 null and p53-mutant colorectal cancer cells. Mol Cancer Ther. 2012 Aug;11(8):1724–34.