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Exploiting differential Wnt target gene expression to generate a molecular biomarker for colorectal cancer stratification.

Kleeman SO, Koelzer VH, Jones HJ, Vazquez EG, Davis H, East JE, Arnold R, Koppens MA, Blake A, Domingo E, Cunningham C, Beggs AD, Pestinger V, Loughrey MB, Wang LM, Lannagan TR, Woods SL, Worthley D, Consortium SC, Tomlinson I, Dunne PD, Maughan T, Leedham SJ.

Gut. 2019 Sep 28. pii: gutjnl-2019-319126. doi: 10.1136/gutjnl-2019-319126. [Epub ahead of print]


Defining the molecular evolution of extrauterine high grade serous carcinoma.

Beirne JP, McArt DG, Roddy A, McDermott C, Ferris J, Buckley NE, Coulter P, McCabe N, Eddie SL, Dunne PD, O'Reilly P, Gilmore A, Feeney L, Ewing DL, Drapkin RI, Salto-Tellez M, Kennedy RD, Harley IJG, McCluggage WG, Mullan PB.

Gynecol Oncol. 2019 Sep 4. pii: S0090-8258(19)31481-7. doi: 10.1016/j.ygyno.2019.08.029. [Epub ahead of print]


The Intricate Interplay between Epigenetic Events, Alternative Splicing and Noncoding RNA Deregulation in Colorectal Cancer.

Amirkhah R, Naderi-Meshkin H, Shah JS, Dunne PD, Schmitz U.

Cells. 2019 Aug 19;8(8). pii: E929. doi: 10.3390/cells8080929. Review.


Prognosis following surgical resection versus local excision of stage pT1 colorectal cancer: A population-based cohort study.

McBride R, Hicks BM, Coleman HG, Loughrey MB, Gavin AT, Dunne PD, Campbell WJ.

Surgeon. 2019 Aug 8. pii: S1479-666X(19)30084-8. doi: 10.1016/j.surge.2019.06.004. [Epub ahead of print]


Fibroblast-derived Gremlin1 localises to epithelial cells at the base of the intestinal crypt.

Dutton LR, Hoare OP, McCorry AMB, Redmond KL, Adam NE, Canamara S, Bingham V, Mullan PB, Lawler M, Dunne PD, Brazil DP.

Oncotarget. 2019 Jul 23;10(45):4630-4639. doi: 10.18632/oncotarget.27050. eCollection 2019 Jul 23.


ACE: A Workbench Using Evolutionary Genetic Algorithms for Analyzing Association in TCGA.

Gilmore AR, Alderdice M, Savage KI, O'Reilly PG, Roddy AC, Dunne PD, Lawler M, McDade SS, Waugh DJ, McArt DG.

Cancer Res. 2019 Apr 15;79(8):2072-2075. doi: 10.1158/0008-5472.CAN-18-1976. Epub 2019 Feb 13.


Punctate MLH1 mismatch repair immunostaining in colorectal cancer.

Loughrey MB, Dunne PD, Coleman HG, McQuaid S, James JA.

Histopathology. 2019 Apr;74(5):795-797. doi: 10.1111/his.13780. Epub 2019 Feb 17. No abstract available.


Impact of Variable RNA-Sequencing Depth on Gene Expression Signatures and Target Compound Robustness: Case Study Examining Brain Tumor (Glioma) Disease Progression.

Stupnikov A, O'Reilly PG, McInerney CE, Roddy AC, Dunne PD, Gilmore A, Ellis HP, Flannery T, Healy E, McIntosh SA, Savage K, Kurian KM, Emmert-Streib F, Prise KM, Salto-Tellez M, McArt DG.

JCO Precis Oncol. 2018 Sep 13;2. doi: 10.1200/PO.18.00014.


Stromal Cell PD-L1 Inhibits CD8+ T-cell Antitumor Immune Responses and Promotes Colon Cancer.

O'Malley G, Treacy O, Lynch K, Naicker SD, Leonard NA, Lohan P, Dunne PD, Ritter T, Egan LJ, Ryan AE.

Cancer Immunol Res. 2018 Nov;6(11):1426-1441. doi: 10.1158/2326-6066.CIR-17-0443. Epub 2018 Sep 18. Erratum in: Cancer Immunol Res. 2019 Jan;7(1):162.


Epithelial-to-mesenchymal transition signature assessment in colorectal cancer quantifies tumour stromal content rather than true transition.

McCorry AM, Loughrey MB, Longley DB, Lawler M, Dunne PD.

J Pathol. 2018 Dec;246(4):422-426. doi: 10.1002/path.5155.


Transcriptional subtyping and CD8 immunohistochemistry identifies poor prognosis stage II/III colorectal cancer patients who benefit from adjuvant chemotherapy.

Allen WL, Dunne PD, McDade S, Scanlon E, Loughrey M, Coleman H, McCann C, McLaughlin K, Nemeth Z, Syed N, Jithesh P, Arthur K, Wilson R, Coyle V, McArt D, Murray GI, Samuel L, Nuciforo P, Jimenez J, Argiles G, Dienstmann R, Tabernero J, Messerini L, Nobili S, Mini E, Sheahan K, Ryan E, Johnston PG, Van Schaeybroeck S, Lawler M, Longley DB.

JCO Precis Oncol. 2018 Jun 13;2018. doi: 10.1200/PO.17.00241.


Previous Use of Antithrombotic Agents Reduces Mortality and Length of Hospital Stay in Patients With High-risk Upper Gastrointestinal Bleeding.

Dunne PDJ, Laursen SB, Laine L, Dalton HR, Ngu JH, Schultz M, Rahman A, Anderloni A, Murray IA, Stanley AJ.

Clin Gastroenterol Hepatol. 2019 Feb;17(3):440-447.e2. doi: 10.1016/j.cgh.2018.04.046. Epub 2018 Apr 26.


Validation of the systematic scoring of immunohistochemically stained tumour tissue microarrays using QuPath digital image analysis.

Loughrey MB, Bankhead P, Coleman HG, Hagan RS, Craig S, McCorry AMB, Gray RT, McQuaid S, Dunne PD, Hamilton PW, James JA, Salto-Tellez M.

Histopathology. 2018 Aug;73(2):327-338. doi: 10.1111/his.13516. Epub 2018 May 21.


Bcl-xL as a poor prognostic biomarker and predictor of response to adjuvant chemotherapy specifically in BRAF-mutant stage II and III colon cancer.

Dunne PD, Coleman HG, Bankhead P, Alderdice M, Gray RT, McQuaid S, Bingham V, Loughrey MB, James JA, McCorry AMB, Gilmore A, Holohan C, Klingbiel D, Tejpar S, Johnston PG, McArt DG, Di Nicolantonio F, Longley DB, Lawler M.

Oncotarget. 2018 Feb 13;9(17):13834-13847. doi: 10.18632/oncotarget.24481. eCollection 2018 Mar 2.


Prospective patient stratification into robust cancer-cell intrinsic subtypes from colorectal cancer biopsies.

Alderdice M, Richman SD, Gollins S, Stewart JP, Hurt C, Adams R, McCorry AM, Roddy AC, Vimalachandran D, Isella C, Medico E, Maughan T, McArt DG, Lawler M, Dunne PD.

J Pathol. 2018 May;245(1):19-28. doi: 10.1002/path.5051. Epub 2018 Mar 25.


Editorial: getting bullish about portal hypertension-chronic treatment with oral taurine?

Dunne PDJ, Fallowfield JA.

Aliment Pharmacol Ther. 2018 Feb;47(4):533-534. doi: 10.1111/apt.14444. No abstract available.


QuPath: Open source software for digital pathology image analysis.

Bankhead P, Loughrey MB, Fernández JA, Dombrowski Y, McArt DG, Dunne PD, McQuaid S, Gray RT, Murray LJ, Coleman HG, James JA, Salto-Tellez M, Hamilton PW.

Sci Rep. 2017 Dec 4;7(1):16878. doi: 10.1038/s41598-017-17204-5.


IHC-based subcellular quantification provides new insights into prognostic relevance of FLIP and procaspase-8 in non-small-cell lung cancer.

Hutchinson RA, Coleman HG, Gately K, Young V, Nicholson S, Cummins R, Kay E, Hynes SO, Dunne PD, Senevirathne S, Hamilton PW, McArt DG, Longley DB.

Cell Death Discov. 2017 Aug 14;3:17050. doi: 10.1038/cddiscovery.2017.50. eCollection 2017.


Emergence of MET hyper-amplification at progression to MET and BRAF inhibition in colorectal cancer.

Oddo D, Siravegna G, Gloghini A, Vernieri C, Mussolin B, Morano F, Crisafulli G, Berenato R, Corti G, Volpi CC, Buscarino M, Niger M, Dunne PD, Rospo G, Valtorta E, Bartolini A, Fucà G, Lamba S, Martinetti A, Di Bartolomeo M, de Braud F, Bardelli A, Pietrantonio F, Di Nicolantonio F.

Br J Cancer. 2017 Jul 25;117(3):347-352. doi: 10.1038/bjc.2017.196. Epub 2017 Jun 27.


Natural killer-like signature observed post therapy in locally advanced rectal cancer is a determinant of pathological response and improved survival.

Alderdice M, Dunne PD, Cole AJ, O'Reilly PG, McArt DG, Bingham V, Fuchs MA, McQuaid S, Loughrey MB, Murray GI, Samuel LM, Lawler M, Wilson RH, Salto-Tellez M, Coyle VM.

Mod Pathol. 2017 Sep;30(9):1287-1298. doi: 10.1038/modpathol.2017.47. Epub 2017 Jun 16.


Cancer-cell intrinsic gene expression signatures overcome intratumoural heterogeneity bias in colorectal cancer patient classification.

Dunne PD, Alderdice M, O'Reilly PG, Roddy AC, McCorry AMB, Richman S, Maughan T, McDade SS, Johnston PG, Longley DB, Kay E, McArt DG, Lawler M.

Nat Commun. 2017 May 31;8:15657. doi: 10.1038/ncomms15657.


Standardising RNA profiling based biomarker application in cancer-The need for robust control of technical variables.

Stewart JP, Richman S, Maughan T, Lawler M, Dunne PD, Salto-Tellez M.

Biochim Biophys Acta Rev Cancer. 2017 Aug;1868(1):258-272. doi: 10.1016/j.bbcan.2017.05.005. Epub 2017 May 23. Review.


Review article: recent insights into clinical decision-making in severe alcoholic hepatitis.

Dunne PDJ, Forrest EH.

Aliment Pharmacol Ther. 2017 Aug;46(3):274-281. doi: 10.1111/apt.14144. Epub 2017 May 21. Review.


Intratumoural Epigenetic Heterogeneity in Early Invasive Colorectal Cancer: A Prognostic Imprint?

Dunne PD, Lawler M.

Gastroenterology. 2017 May;152(6):1622-1623. doi: 10.1053/j.gastro.2016.09.071. Epub 2017 Apr 3. No abstract available.


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'.

Hynes SO, Coleman HG, Kelly PJ, Dunne PD, Salto-Tellez M, Loughrey MB.

Histopathology. 2017 Aug;71(2):327-329. doi: 10.1111/his.13221. Epub 2017 May 19. No abstract available.


Signalling mechanisms underlying doxorubicin and Nox2 NADPH oxidase-induced cardiomyopathy: involvement of mitofusin-2.

McLaughlin D, Zhao Y, O'Neill KM, Edgar KS, Dunne PD, Kearney AM, Grieve DJ, McDermott BJ.

Br J Pharmacol. 2017 Nov;174(21):3677-3695. doi: 10.1111/bph.13773. Epub 2017 Apr 22.


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.

Hynes SO, Coleman HG, Kelly PJ, Irwin S, O'Neill RF, Gray RT, McGready C, Dunne PD, McQuaid S, James JA, Salto-Tellez M, Loughrey MB.

Histopathology. 2017 Jul;71(1):12-26. doi: 10.1111/his.13181. Epub 2017 Apr 3.


Gremlin1 plays a key role in kidney development and renal fibrosis.

Church RH, Ali I, Tate M, Lavin D, Krishnakumar A, Kok HM, Hombrebueno JR, Dunne PD, Bingham V, Goldschmeding R, Martin F, Brazil DP.

Am J Physiol Renal Physiol. 2017 Jun 1;312(6):F1141-F1157. doi: 10.1152/ajprenal.00344.2016. Epub 2017 Jan 18.


KRAS mutant colorectal cancer gene signatures identified angiotensin II receptor blockers as potential therapies.

Wen Q, Dunne PD, O'Reilly PG, Li G, Bjourson AJ, McArt DG, Hamilton PW, Zhang SD.

Oncotarget. 2017 Jan 10;8(2):3206-3225. doi: 10.18632/oncotarget.13884.


Transcriptional upregulation of c-MET is associated with invasion and tumor budding in colorectal cancer.

Bradley CA, Dunne PD, Bingham V, McQuaid S, Khawaja H, Craig S, James J, Moore WL, McArt DG, Lawler M, Dasgupta S, Johnston PG, Van Schaeybroeck S.

Oncotarget. 2016 Nov 29;7(48):78932-78945. doi: 10.18632/oncotarget.12933.


Embracing an integromic approach to tissue biomarker research in cancer: Perspectives and lessons learned.

Li G, Bankhead P, Dunne PD, O'Reilly PG, James JA, Salto-Tellez M, Hamilton PW, McArt DG.

Brief Bioinform. 2017 Jul 1;18(4):634-646. doi: 10.1093/bib/bbw044.


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.

Dunne PD, McArt DG, O'Reilly PG, Coleman HG, Allen WL, Loughrey M, Van Schaeybroeck S, McDade S, Salto-Tellez M, Longley DB, Lawler M, Johnston PG.

Cancer Immunol Res. 2016 Jul;4(7):582-91. doi: 10.1158/2326-6066.CIR-15-0302. Epub 2016 May 13.


Stratified analysis reveals chemokine-like factor (CKLF) as a potential prognostic marker in the MSI-immune consensus molecular subtype CMS1 of colorectal cancer.

Dunne PD, O'Reilly PG, Coleman HG, Gray RT, Longley DB, Johnston PG, Salto-Tellez M, Lawler M, McArt DG.

Oncotarget. 2016 Jun 14;7(24):36632-36644. doi: 10.18632/oncotarget.9126.


Challenging the Cancer Molecular Stratification Dogma: Intratumoral Heterogeneity Undermines Consensus Molecular Subtypes and Potential Diagnostic Value in Colorectal Cancer.

Dunne PD, McArt DG, Bradley CA, O'Reilly PG, Barrett HL, Cummins R, O'Grady T, Arthur K, Loughrey MB, Allen WL, McDade SS, Waugh DJ, Hamilton PW, Longley DB, Kay EW, Johnston PG, Lawler M, Salto-Tellez M, Van Schaeybroeck S.

Clin Cancer Res. 2016 Aug 15;22(16):4095-104. doi: 10.1158/1078-0432.CCR-16-0032. Epub 2016 May 5.


QUADrATiC: scalable gene expression connectivity mapping for repurposing FDA-approved therapeutics.

O'Reilly PG, Wen Q, Bankhead P, Dunne PD, McArt DG, McPherson S, Hamilton PW, Mills KI, Zhang SD.

BMC Bioinformatics. 2016 May 4;17(1):198. doi: 10.1186/s12859-016-1062-1.


Remarkably low affinity of CD4/peptide-major histocompatibility complex class II protein interactions.

Jönsson P, Southcombe JH, Santos AM, Huo J, Fernandes RA, McColl J, Lever M, Evans EJ, Hudson A, Chang VT, Hanke T, Godkin A, Dunne PD, Horrocks MH, Palayret M, Screaton GR, Petersen J, Rossjohn J, Fugger L, Dushek O, Xu XN, Davis SJ, Klenerman D.

Proc Natl Acad Sci U S A. 2016 May 17;113(20):5682-7. doi: 10.1073/pnas.1513918113. Epub 2016 Apr 25.


Connectivity mapping using a combined gene signature from multiple colorectal cancer datasets identified candidate drugs including existing chemotherapies.

Wen Q, O'Reilly P, Dunne PD, Lawler M, Van Schaeybroeck S, Salto-Tellez M, Hamilton P, Zhang SD.

BMC Syst Biol. 2015;9 Suppl 5:S4. doi: 10.1186/1752-0509-9-S5-S4. Epub 2015 Sep 1.


EphA2 Expression Is a Key Driver of Migration and Invasion and a Poor Prognostic Marker in Colorectal Cancer.

Dunne PD, Dasgupta S, Blayney JK, McArt DG, Redmond KL, Weir JA, Bradley CA, Sasazuki T, Shirasawa S, Wang T, Srivastava S, Ong CW, Arthur K, Salto-Tellez M, Wilson RH, Johnston PG, Van Schaeybroeck S.

Clin Cancer Res. 2016 Jan 1;22(1):230-242. doi: 10.1158/1078-0432.CCR-15-0603. Epub 2015 Aug 17.


The prognostic value of the stem-like group in colorectal cancer using a panel of immunohistochemistry markers.

Ong CW, Chong PY, McArt DG, Chan JY, Tan HT, Kumar AP, Chung MC, Clément MV, Soong R, Van Schaeybroeck S, Waugh DJ, Johnston PG, Dunne PD, Salto-Tellez M.

Oncotarget. 2015 May 20;6(14):12763-73.


PICan: An integromics framework for dynamic cancer biomarker discovery.

McArt DG, Blayney JK, Boyle DP, Irwin GW, Moran M, Hutchinson RA, Bankhead P, Kieran D, Wang Y, Dunne PD, Kennedy RD, Mullan PB, Harkin DP, Catherwood MA, James JA, Salto-Tellez M, Hamilton PW.

Mol Oncol. 2015 Jun;9(6):1234-40. doi: 10.1016/j.molonc.2015.02.002. Epub 2015 Mar 4.


ADAM17-dependent c-MET-STAT3 signaling mediates resistance to MEK inhibitors in KRAS mutant colorectal cancer.

Van Schaeybroeck S, Kalimutho M, Dunne PD, Carson R, Allen W, Jithesh PV, Redmond KL, Sasazuki T, Shirasawa S, Blayney J, Michieli P, Fenning C, Lenz HJ, Lawler M, Longley DB, Johnston PG.

Cell Rep. 2014 Jun 26;7(6):1940-55. doi: 10.1016/j.celrep.2014.05.032. Epub 2014 Jun 12.


Fibroblast growth factor receptor 4 (FGFR4): a targetable regulator of drug resistance in colorectal cancer.

Turkington RC, Longley DB, Allen WL, Stevenson L, McLaughlin K, Dunne PD, Blayney JK, Salto-Tellez M, Van Schaeybroeck S, Johnston PG.

Cell Death Dis. 2014 Feb 6;5:e1046. doi: 10.1038/cddis.2014.10.


AXL is a key regulator of inherent and chemotherapy-induced invasion and predicts a poor clinical outcome in early-stage colon cancer.

Dunne PD, McArt DG, Blayney JK, Kalimutho M, Greer S, Wang T, Srivastava S, Ong CW, Arthur K, Loughrey M, Redmond K, Longley DB, Salto-Tellez M, Johnston PG, Van Schaeybroeck S.

Clin Cancer Res. 2014 Jan 1;20(1):164-75. doi: 10.1158/1078-0432.CCR-13-1354. Epub 2013 Oct 29.


cudaMap: a GPU accelerated program for gene expression connectivity mapping.

McArt DG, Bankhead P, Dunne PD, Salto-Tellez M, Hamilton P, Zhang SD.

BMC Bioinformatics. 2013 Oct 11;14:305. doi: 10.1186/1471-2105-14-305.


Connectivity Mapping for Candidate Therapeutics Identification Using Next Generation Sequencing RNA-Seq Data.

McArt DG, Dunne PD, Blayney JK, Salto-Tellez M, Van Schaeybroeck S, Hamilton PW, Zhang SD.

PLoS One. 2013 Jun 26;8(6):e66902. doi: 10.1371/journal.pone.0066902. Print 2013.


Quantitative single-molecule microscopy reveals that CENP-A(Cnp1) deposition occurs during G2 in fission yeast.

Lando D, Endesfelder U, Berger H, Subramanian L, Dunne PD, McColl J, Klenerman D, Carr AM, Sauer M, Allshire RC, Heilemann M, Laue ED.

Open Biol. 2012 Jul;2(7):120078. doi: 10.1098/rsob.120078.


The T cell receptor triggering apparatus is composed of monovalent or monomeric proteins.

James JR, McColl J, Oliveira MI, Dunne PD, Huang E, Jansson A, Nilsson P, Sleep DL, Gonçalves CM, Morgan SH, Felce JH, Mahen R, Fernandes RA, Carmo AM, Klenerman D, Davis SJ.

J Biol Chem. 2011 Sep 16;286(37):31993-2001. doi: 10.1074/jbc.M111.219212. Epub 2011 Jul 13.


DNMT1 deficiency triggers mismatch repair defects in human cells through depletion of repair protein levels in a process involving the DNA damage response.

Loughery JE, Dunne PD, O'Neill KM, Meehan RR, McDaid JR, Walsh CP.

Hum Mol Genet. 2011 Aug 15;20(16):3241-55. doi: 10.1093/hmg/ddr236. Epub 2011 Jun 2.


Selective diffusion barriers separate membrane compartments.

Bruckbauer A, Dunne PD, James P, Howes E, Zhou D, Jones R, Klenerman D.

Biophys J. 2010 Jul 7;99(1):L1-3. doi: 10.1016/j.bpj.2010.03.067.


Tracking diffusion of GM1 gangliosides and zona pellucida binding molecules in sperm plasma membranes following cholesterol efflux.

Jones R, Howes E, Dunne PD, James P, Bruckbauer A, Klenerman D.

Dev Biol. 2010 Mar 15;339(2):398-406. doi: 10.1016/j.ydbio.2009.12.044. Epub 2010 Jan 7.

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