Ocular Oncology Biobank - Publications 

Genome-wide study on uveal melanoma patients finds association to DNA repair gene TDP1​
Thomsen H, Chattopadhyay S, Hoffmann P, Nöthen MM, Kalirai H, Coupland SE, Jonas JB, Hemminki K, Försti A. Genome-wide study on uveal melanoma patients finds association to DNA repair gene TDP1. Melanoma Res. 2020 Apr;30(2):166-172. 

Loss of BAP1 expression is associated with an immunosuppressive microenvironment in uveal melanoma, with implications for immunotherapy development.
Figueiredo CR, Kalirai H, Sacco JJ, Azevedo RA, Duckworth A, Slupsky JR, Coulson JM, Coupland SE.
​Journal of Pathology. 2020 Apr;250(4):420-439.doi: 10.1002/path.5384.

Targeted Next-Generation Sequencing of 117 Routine Clinical Samples Provides Further Insights into the Molecular Landscape of Uveal Melanoma 
Sophie Thornton, Sarah E. Coupland,  Lisa Olohan, Julie S. Sibbring, John G. Kenny, Christiane Hertz-Fowler, Xuan Liu, Sam Haldenby, Heinrich Heimann, Rumana Hussain, Natalie Kipling, Azzam Taktak, Helen Kalirai.

Inhibition of ATM Increases the Radiosensitivity of Uveal Melanoma Cells to Photons and Protons
Rumana N. Hussain, Sarah E. Coupland, Jakub Khzouz, Helen Kalirai, Jason L. Parsons
Cancers 2020
(This article belongs to the Special Issue Proton Therapy For Cancers)

Characterization of Uveal Melanoma Cell Lines and Primary Tumor Samples in 3D Culture
Aughton K, Shahidipour H, Djirackor L, Coupland SE, Kalirai H.
Trans Vis Sci Tech. 2020;9(7):39

Piloting a Deep Learning Model for Predicting Nuclear BAP1 Immunohistochemical Expression of Uveal Melanoma from Hematoxylin-and-Eosin Sections
Hongrun Zhang; Helen Kalirai; Amelia Acha-Sagredo; Xiaoyun Yang; Yalin Zheng; Sarah E. Coupland
Translational Vision Science & Technology September 2020, Vol.9, 50. doi:https://doi.org/10.1167/tvst.9.2.50
 
High Cysteinyl Leukotriene Receptor 1 Expression Correlates with Poor Survival of Uveal Melanoma Patients and Cognate Antagonist Drugs Modulate the Growth, Cancer Secretome, and Metabolism of Uveal Melanoma Cells.
by Kayleigh Slater 1,2, Aisling B. Heeran 3, Sandra Garcia-Mulero 4,5, Helen Kalirai 6, Rebeca Sanz-Pamplona 4, Arman Rahman 1, Nebras Al-Attar 1, Mays Helmi 7, Fiona O’Connell 3, Rosa Bosch 8, Anna Portela 8, Alberto Villanueva 8, William M. Gallagher 1, Lasse D. Jensen 7, Josep M. Piulats 9,10, Sarah E. Coupland 6,11, Jacintha O’Sullivan 3 and Breandán N. Kennedy 1,*PMID: 33066024 DOI: 10.3390/cancers12102950  

Transcriptome Profiling Reveals New Insights into the Immune Microenvironment and Upregulation of Novel Biomarkers in Metastatic Uveal Melanoma.
Krishna Y, Acha-Sagredo A, Sabat-Pośpiech D, Kipling N, Clarke K, Figueiredo CR, Kalirai H, Coupland SE.
Cancers (Basel). 2020 Sep 30;12(10):E2832. doi: 10.3390/cancers12102832.
PMID: 33008022
 
Nestin expression in primary and metastatic uveal melanoma - possible biomarker for high-risk uveal melanoma.
Djirackor L, Shakir D, Kalirai H, Petrovski G, Coupland SE.
Acta Ophthalmol. 2018 Jan 16. doi: 10.1111/aos.13645. 

Patterns of BAP1 protein expression provide insights into prognostic significance and the biology of uveal melanoma.
Farquhar N, Thornton S, Coupland SE, Coulson JM, Sacco JJ, Krishna Y, Heimann H, Taktak A, Cebulla CM, Abdel-Rahman MH, Kalirai H.
J Pathol Clin Res. 2017 Nov 13;4(1):26-38. doi: 10.1002/cjp2.86. eCollection 2018 Jan.

Adipophilin expression in primary and metastatic uveal melanoma: a pilot study.
Fiorentzis M, Kalirai H, Katopodis P, Coupland SE.
Graefes Arch Clin Exp Ophthalmol. 2017 May;255(5):1049-1051. doi: 10.1007/s00417-017-3630-0. Epub 2017 Mar 15.

RasGRP3 Mediates MAPK Pathway Activation in GNAQ Mutant Uveal Melanoma.
Chen X, Wu Q, Depeille P, Chen P, Thornton S, Kalirai H, Coupland SE, Roose JP, Bastian BC.
Cancer Cell. 2017 May 8;31(5):685-696.e6. doi: 10.1016/j.ccell.2017.04.002.

Cell infiltrates in advanced metastatic uveal melanoma.
Krishna Y, McCarthy C, Kalirai H, Coupland SE.
Hum Pathol. 2017 Jun 24. pii: S0046-8177(17)30224-1. doi: 10.1016/j.humpath.2017.06.005. 

Integrative Analysis Identifies Four Molecular and Clinical Subsets in Uveal Melanoma.
Robertson AG, Shih J, Yau C, Gibb EA, Oba J, Mungall KL, Hess JM, Uzunangelov V, Walter V, Danilova L, Lichtenberg TM, Kucherlapati M, Kimes PK, Tang M, Penson A, Babur O, Akbani R, Bristow CA, Hoadley KA, Iype L, Chang MT; TCGA Research Network, Cherniack AD, Benz C, Mills GB, Verhaak RGW, Griewank KG, Felau I, Zenklusen JC, Gershenwald JE, Schoenfield L, Lazar AJ, Abdel-Rahman MH, Roman-Roman S, Stern MH, Cebulla CM, Williams MD, Jager MJ, Coupland SE, Esmaeli B, Kandoth C, Woodman SE.
Cancer Cell. 2017 Aug 14;32(2):204-220.e15. doi: 10.1016/j.ccell.2017.07.003.

Kinome-wide transcriptional profiling of uveal melanoma reveals new vulnerabilities to targeted therapeutics.
Bailey FP, Clarke K, Kalirai H, Kenyani J, Shahidipour H, Falciani F, Coulson JM, Sacco JJ, Coupland SE, Eyers PA.
Pigment Cell Melanoma Res. 2017 Oct 3. doi: 10.1111/pcmr.12650. 

Insights into genetic alterations of liver metastases from uveal melanoma.
McCarthy C, Kalirai H, Lake SL, Dodson A, Damato BE, Coupland SE.
Pigment Cell Melanoma Res. 2016 Jan;29(1):60-7. doi: 10.1111/pcmr.12433.

Lack of BAP1 protein expression in uveal melanoma is associated with increased metastatic risk and has utility in routine prognostic testing.
Kalirai H, Dodson A, Faqir S, Damato BE, Coupland SE.
Br J Cancer. 2014 Sep 23;111(7):1373-80. doi: 10.1038/bjc.2014.417.

Single Nucleotide Polymorphism Array Analysis of Uveal Melanomas Reveals That Amplification of CNKSR3 Is Correlated With Improved Patient Survival.
Lake SL, Damato BE, Kalirai H, Dodson AR, Taktak AF, Lloyd BH, Coupland SE.
Am J Pathol. 2013 Jan 25.