Leeds Melanoma Cohort (LMC) gene expression study

Array-based profiling (whole genome DASL HT12.4, Illumina Inc) in over 700 FFPE tumour blocks from the population-based Leeds Melanoma cohort recruited in the North of England, with a long follow up. Data used in tumour immune micro-environment investigation (Nsengimana et al 2018, J Clin Invest doi: 10.1172/JCI95351).

Type: Other
Archiver: European Genome-Phenome Archive (EGA)

2 Datasets 22 Publications

Click on a Dataset ID in the table below to learn more, and to find out who to contact about access to these data

Dataset ID	Description	Technology	Samples
EGAD00010001561	Quantile-normalised and batch corrected	Illumina HT12.4	703
EGAD00010001562	WG mRNA profiling in FFPE primary melanoma	Illumina HT12.4	703

Publications	Citations
β-Catenin-mediated immune evasion pathway frequently operates in primary cutaneous melanomas. Nsengimana J, Laye J, Filia A, O'Shea S, Muralidhar S, Poźniak J, Droop A, Chan M, Walker C, Parkinson L, Gascoyne J, Mell T, Polso M, Jewell R, Randerson-Moor J, Cook GP, Bishop DT, Newton-Bishop J. J Clin Invest 128: 2018 2048-2063	61
Genetic and Environmental Determinants of Immune Response to Cutaneous Melanoma. Poźniak J, Nsengimana J, Laye JP, O'Shea SJ, Diaz JMS, Droop AP, Filia A, Harland M, Davies JR, Mell T, Randerson-Moor JA, Muralidhar S, Hogan SA, Freiberger SN, Levesque MP, Cook GP, Bishop DT, Newton-Bishop J. Cancer Res 79: 2019 2684-2696	29
Transcriptomic Analysis Reveals Prognostic Molecular Signatures of Stage I Melanoma. Thakur R, Laye JP, Lauss M, Diaz JMS, O'Shea SJ, Poźniak J, Filia A, Harland M, Gascoyne J, Randerson-Moor JA, Chan M, Mell T, Jönsson G, Bishop DT, Newton-Bishop J, Barrett JH, Nsengimana J. Clin Cancer Res 25: 2019 7424-7435	22
MX 2 is a novel regulator of cell cycle in melanoma cells. Juraleviciute M, Pozniak J, Nsengimana J, Harland M, Randerson-Moor J, Wernhoff P, Bassarova A, Øy GF, Trøen G, Flørenes VA, Bishop DT, Herlyn M, Newton-Bishop J, Slipicevic A. Pigment Cell Melanoma Res 33: 2020 446-457	9
Gain-of-Function Genetic Alterations of G9a Drive Oncogenesis. Kato S, Weng QY, Insco ML, Chen KY, Muralidhar S, Pozniak J, Diaz JMS, Drier Y, Nguyen N, Lo JA, van Rooijen E, Kemeny LV, Zhan Y, Feng Y, Silkworth W, Powell CT, Liau BB, Xiong Y, Jin J, Newton-Bishop J, Zon LI, Bernstein BE, Fisher DE. Cancer Discov 10: 2020 980-997	35
PRL3-DDX21 Transcriptional Control of Endolysosomal Genes Restricts Melanocyte Stem Cell Differentiation. Johansson JA, Marie KL, Lu Y, Brombin A, Santoriello C, Zeng Z, Zich J, Gautier P, von Kriegsheim A, Brunsdon H, Wheeler AP, Dreger M, Houston DR, Dooley CM, Sims AH, Busch-Nentwich EM, Zon LI, Illingworth RS, Patton EE. Dev Cell 54: 2020 317-332.e9	27
Study of the Female Sex Survival Advantage in Melanoma-A Focus on X-Linked Epigenetic Regulators and Immune Responses in Two Cohorts. Emran AA, Nsengimana J, Punnia-Moorthy G, Schmitz U, Gallagher SJ, Newton-Bishop J, Tiffen JC, Hersey P. Cancers (Basel) 12: 2020 E2082	13
Gene co-expression and histone modification signatures are associated with melanoma progression, epithelial-to-mesenchymal transition, and metastasis. Azevedo H, Pessoa GC, de Luna Vitorino FN, Nsengimana J, Newton-Bishop J, Reis EM, da Cunha JPC, Jasiulionis MG. Clin Epigenetics 12: 2020 127	13
MX2 mediates establishment of interferon response profile, regulates XAF1, and can sensitize melanoma cells to targeted therapy. Juraleviciute M, Nsengimana J, Newton-Bishop J, Hendriks GJ, Slipicevic A. Cancer Med 10: 2021 2840-2854	4
Transcriptional signatures underlying dynamic phenotypic switching and novel disease biomarkers in a linear cellular model of melanoma progression. Pessoa DO, Rius FE, Papaiz DD, Ayub ALP, Morais AS, de Souza CF, da Paixão VF, Setubal JC, Newton-Bishop J, Nsengimana J, Azevedo H, Reis EM, Jasiulionis MG. Neoplasia 23: 2021 439-455	5
Loss of Ambra1 promotes melanoma growth and invasion. Di Leo L, Bodemeyer V, Bosisio FM, Claps G, Carretta M, Rizza S, Faienza F, Frias A, Khan S, Bordi M, Pacheco MP, Di Martino J, Bravo-Cordero JJ, Daniel CJ, Sears RC, Donia M, Madsen DH, Guldberg P, Filomeni G, Sauter T, Robert C, De Zio D, Cecconi F. Nat Commun 12: 2021 2550	35
Inherited duplications of PPP2R3B predispose to nevi and melanoma via a C21orf91-driven proliferative phenotype. Polubothu S, Zecchin D, Al-Olabi L, Lionarons DA, Harland M, Horswell S, Thomas AC, Hunt L, Wlodarchak N, Aguilera P, Brand S, Bryant D, Carrera C, Chen H, Elgar G, Harwood CA, Howell M, Larue L, Loughlin S, MacDonald J, Malvehy J, Barberan SM, da Silva VM, Molina M, Morrogh D, Moulding D, Nsengimana J, Pittman A, Puig-Butillé JA, Parmar K, Sebire NJ, Scherer S, Stadnik P, Stanier P, Tell G, Waelchli R, Zarrei M, Puig S, Bataille V, Xing Y, Healy E, Moore GE, Di WL, Newton-Bishop J, Downward J, Kinsler VA. Genet Med 23: 2021 1636-1647	1
SFPQ promotes an oncogenic transcriptomic state in melanoma. Bi O, Anene CA, Nsengimana J, Shelton M, Roberts W, Newton-Bishop J, Boyne JR. Oncogene 40: 2021 5192-5203	18
Cooperation between melanoma cell states promotes metastasis through heterotypic cluster formation. Campbell NR, Rao A, Hunter MV, Sznurkowska MK, Briker L, Zhang M, Baron M, Heilmann S, Deforet M, Kenny C, Ferretti LP, Huang TH, Perlee S, Garg M, Nsengimana J, Saini M, Montal E, Tagore M, Newton-Bishop J, Middleton MR, Corrie P, Adams DJ, Rabbie R, Aceto N, Levesque MP, Cornell RA, Yanai I, Xavier JB, White RM. Dev Cell 56: 2021 2808-2825.e10	35
Road to Metastasis: The TWEAK Pathway as a Discriminant between Metastasizing and Non-Metastasizing Thick Melanomas. Güvenç C, Antoranz A, Szumera-Ciećkiewicz A, Teterycz PP, Rutkowski PR, Rawson RV, Scolyer RA, Thompson JF, Newton-Bishop J, Stas M, Boecxstaens V, Bechter O, Vercauteren J, Garmyn M, van den Oord J, Bosisio FM. Int J Mol Sci 22: 2021 10568	3
ROR2 has a protective role in melanoma by inhibiting Akt activity, cell-cycle progression, and proliferation. Castro MV, Barbero GA, Villanueva MB, Grumolato L, Nsengimana J, Newton-Bishop J, Illescas E, Quezada MJ, Lopez-Bergami P. J Biomed Sci 28: 2021 76	9
Genes regulated by DNA methylation are involved in distinct phenotypes during melanoma progression and are prognostic factors for patients. Papaiz DD, Rius FE, Ayub ALP, Origassa CS, Gujar H, Pessoa DO, Reis EM, Nsengimana J, Newton-Bishop J, Mason CE, Weisenberger DJ, Liang G, Jasiulionis MG. Mol Oncol 16: 2022 1913-1930	3
Comprehensive Gene Expression Analysis to Identify Differences and Similarities between Sex- and Stage-Stratified Melanoma Samples. Chrysanthou E, Sehovic E, Ostano P, Chiorino G. Cells 11: 2022 1099	2
Genome-wide promoter methylation profiling in a cellular model of melanoma progression reveals markers of malignancy and metastasis that predict melanoma survival. Rius FE, Papaiz DD, Azevedo HFZ, Ayub ALP, Pessoa DO, Oliveira TF, Loureiro APM, Andrade F, Fujita A, Reis EM, Mason CE, Jasiulionis MG. Clin Epigenetics 14: 2022 68	5
Identifying the Transcriptional Drivers of Metastasis Embedded within Localized Melanoma. Suresh S, Rabbie R, Garg M, Lumaquin D, Huang TH, Montal E, Ma Y, Cruz NM, Tang X, Nsengimana J, Newton-Bishop J, Hunter MV, Zhu Y, Chen K, de Stanchina E, Adams DJ, White RM. Cancer Discov 13: 2023 194-215	5
N6-methyladenosine RNA Methylation Correlates with Immune Microenvironment and Immunotherapy Response of Melanoma. Wang G, Zeng D, Sweren E, Miao Y, Chen R, Chen J, Wang J, Liao W, Hu Z, Kang S, Garza LA. J Invest Dermatol 143: 2023 1579-1590.e5	4
Tumour-intrinsic endomembrane trafficking by ARF6 shapes an immunosuppressive microenvironment that drives melanomagenesis and response to checkpoint blockade therapy. Wee Y, Wang J, Wilson EC, Rich CP, Rogers A, Tong Z, DeGroot E, Gopal YNV, Davies MA, Ekiz HA, Tay JKH, Stubben C, Boucher KM, Oviedo JM, Fairfax KC, Williams MA, Holmen SL, Wolff RK, Grossmann AH. Nat Commun 15: 2024 6613	0