Brain Cancer @ Leeds

Dr Lucy Stead – Group Leader

Contact Information
Research
Resume
Grants Awarded
Publications
PhD Studentship Opportunites

Contact Information

Dr Lucy Stead
UKRI Future Leaders Fellow
Leeds Institute of Medical Research
Wellcome Trust Brenner Building
St James’s University Hospital
LS9 7TF, Leeds
United Kingdom

tel: +44 (0) 113 3438410
email: l.f.stead@leeds.ac.uk
twitter: @LucyFStead

Research

I am interested in investigating intratumour heterogeneity in GBM; specifically I wish to test whether treatment-resistant subclones emerge in recurrent tumours, and characterise them in clinically relevant ways in multiple patients. I am a trained computational biologist with expertise in next-generation sequencing data analysis.

Resume

Grants Awarded

Publications

Anna Golebiewska, Ann-Christin Hau, Anais Oudin, Daniel Stieber, Yahaya A. Yabo, Virginie Baus, Vanessa Barthelemy, Eliane Klein, Sebastien Bougnaud, Olivier Keunen, May Wantz, Alessandro Michelucci, Virginie Neirinckx, Arnaud Muller, Tony Kaoma, Petr V. Nazarov, Francisco Azuaje, Alfonso De Falco, Ben Flies, Lorraine Richart, Suresh Poovathingal, Thais Arns, Kamil Grzyb, Andreas Mock, Christel Herold-Mende, Anne Steino, Dennis Brown, Patrick May, Hrvoje Miletic, Tathiane M. Malta, Houtan Noushmehr, Yong-Jun Kwon, Winnie Jahn, Barbara Klink, Georgette Tanner, Lucy F. Stead, Michel Mittelbronn, Alexander Skupin, Frank Hertel, Rolf Bjerkvig, Simone P. Niclou (2020)
Primary and recurrent glioma patient-derived orthotopic xenografts (PDOX) represent relevant patient avatars for precision medicine
[bioRXiv]

Struve N, Binder ZA, Stead LF, Brend T, Bagley SJ, Faulkner C, Ott L, Müller-Goebel J, Weik AS, Hoffer K, Krug L, Rieckmann T, Bußmann L, Henze M, Morrissette JJD, Kurian KM, Schüller U, Petersen C, Rothkamm K, O Rourke DM, Short SC, Kriegs M. (2020)
EGFRvIII upregulates DNA mismatch repair resulting in increased temozolomide sensitivity of MGMT promoter methylated glioblastoma.
Oncogene [Pubmed]

Waleed S Al Amri, Lisa M Allinson, Diana E Baxter, Sandra M Bell, Andrew M. Hanby, Stacey J Jones, Abeer M Shaaban, Lucy F Stead, Eldo T Verghese and Thomas A Hughes (2020)
Genomic and expression analyses define MUC17 and PCNX1 as predictors of chemotherapy response in breast cancer
Molecular Cancer Therapeutics [Pubmed]

Floris P. Barthel, Kevin C. Johnson, Frederick S. Varn, Anzhela D. Moskalik, Georgette Tanner, Emre Kocakavuk, Kevin J. Anderson, Olajide Abiola, Kenneth Aldape, Kristin D. Alfaro, Donat Alpar, Samirkumar B. Amin, David M. Ashley, Pratiti Bandopadhayay, Jill S. Barnholtz-Sloan, Rameen Beroukhim, Christoph Bock, Priscilla K. Brastianos, Daniel J. Brat, Andrew R. Brodbelt, Alexander F. Bruns, Ketan R. Bulsara, Aruna Chakrabarty, Arnab Chakravarti, Jeffrey H. Chuang, Elizabeth B. Claus, Elizabeth J. Cochran, Jennifer Connelly, Joseph F. Costello, Gaetano Finocchiaro, Michael N. Fletcher, Pim J. French, Hui K. Gan, Mark R. Gilbert, Peter V. Gould, Matthew R. Grimmer, Antonio Iavarone, Azzam Ismail, Michael D. Jenkinson, Mustafa Khasraw, Hoon Kim, Mathilde C. M. Kouwenhoven, Peter S. LaViolette, Meihong Li, Peter Lichter, Keith L. Ligon, Allison K. Lowman, Tathiane M. Malta, Tali Mazor, Kerrie L. McDonald, Annette M. Molinaro, Do-Hyun Nam, Naema Nayyar, Ho Keung Ng, Chew Yee Ngan, Simone P. Niclou, Johanna M. Niers, Houtan Noushmehr, Javad Noorbakhsh, D. Ryan Ormond, Chul-Kee Park, Laila M. Poisson, Raul Rabadan, Bernhard Radlwimmer, Ganesh Rao, Guido Reifenberger, Jason K. Sa, Michael Schuster, Brian L. Shaw, Susan C. Short, Peter A. Sillevis Smitt, Andrew E. Sloan, Marion Smits, Hiromichi Suzuki, Ghazaleh Tabatabai, Erwin G. Van Meir, Colin Watts, Michael Weller, Pieter Wesseling, Bart A. Westerman, Georg Widhalm, Adelheid Woehrer, W. K. Alfred Yung, Gelareh Zadeh, Jason T. Huse, John F. De Groot, Lucy F. Stead and Roel G. W. Verhaak (2019)
Longitudinal molecular trajectories of diffuse glioma in adults
Nature

H. J. Close, L. F. Stead, J. Nsengimana, K. A. Reilly, A. Droop, H. Wurdak, R. K. Mathew, R. Corns, J. Newton‐Bishop, A. A. Melcher, S. C. Short, G. P. Cook and E. B. Wilson (2019)
Expression profiling of single cells and patient cohorts identifies multiple immunosuppressive pathways and an altered NK cell phenotype in glioblastoma
Clin Exp Immunol.Nov 30.
[Pubmed]

Rippaus, N.,Francisco-Bruns, A., Tanner, G., Taylor, C., Droop, A., Brüning-Richardson, A., Care, M.A., Wilkinson, J., Jenkinson, M.D., Brodbelt, A., Chakrabarty, A., Ismail, A., Short, S., and Stead, L.F (2019)
JARID2 facilitates transcriptional reprogramming in glioblastoma in response to standard treatment
[bioRXiv]

Stead, L.F and Verhaak, R.G.W. (2019)
Doomed from the TERT? A Two-Stage Model of Tumorigenesis in IDH-Wild-Type Glioblastoma
Cancer Cell. 34(4):542-544

Tanner, G., Westhead, D.R., Droop, A. and Stead, L.F. (2019)
Simulation of Heterogeneous Tumour Genomes with HeteroGenesis and In Silico Whole Exome Sequencing.
Bioinformatics. Aug 15;35(16):2850-2852
[Pubmed]

The GLASS Consortium members (2018)
Glioma Through the Looking GLASS: Molecular Evolution of Diffuse Gliomas and the Glioma Longitudinal AnalySiS Consortium
Neuro-Oncology
[Accepted Manuscript]

Samson A, Scott K, Taggart D†, West E, Wilson E, Nuovo G, Thomson S, Corns R, Mathew R, Fuller M, Kottke T, Thompson J, Ilett E, Cockle J, Van Hille P, Sivakumar G, Polson E, Turnbull S, Appleton E, Migneco G, Rose A, Coffey M, Beirne D, Collinson F, Ralph C, Anthoney A, Twelves C, Furness A, Quezada S, Wurdak H, Errington-Mais F, Pandha H, Harrington K, Selby P, Vile R, Griffin S, Stead, L.F, Short S, Melcher A (2018)
Intravenous Delivery of Oncolytic Reovirus to Brain Tumor Patients Immunologically Primes for Subsequent Checkpoint Blockade
Science Translational Medicine. Jan;10(422). pii: eaam7577
[Pubmed]

Droop, A., Bruns, A.F., Tanner, G., Rippaus, N., Morton, R., Harrison, S., King, H., Ashton, K., Syed, K., Jenkinson, M.D., Brodbelt, A., Chakrabarty, A.,Ismail, A., Short, S. and Stead, L.F (2018)
How to Analyse The Spatiotemporal Tumour Samples Needed To Investigate Cancer Evolution: A Case Study using Paired Primary and Recurrent Glioblastoma
International Journal of Cancer. Apr;142(8):1620-1626
[Pubmed]

Hurst, C.D, Alder, O., Platt, F.M., Droop, A., Stead, L.F, Burns, J.E., Burghel, G.J., Jain, S., Klimczak, L.J., Lindsay, H., Roulson, J.A., Taylor, C.F., Thygesen, H., Cameron, A.J., Ridley, A.J., Mott, H.R., Gordenin, D.A., Knowles, M.A. (2017)
Genomic Subtypes of Non-Invasive Bladder Cancer with Distinct Metabolic Profile, Clinical Outcome and Female Gender Bias in KDM6A Mutation Frequency
Cancer Cell. Nov;32(5):701-715.
[Pubmed]

Webster, P., Littlejohns, A., Gaunt, H., Young, R., Rode, B., Ritchie, J., Stead, L.F., Harrison, S., Droop., A, Martin, H., Tomlinson, D., Hyman, A., Appleby, H., Boxall, S., Bruns, A., Li, J., Prasad, K., Lodge, J., Burke, D. and Beech, D. (2017)
Upregulated WEE1 protects endothelial cells of colorectal cancer liver metastases.
Oncotarget. Jun;8(26):42288-42299.
[Pubmed]

King, H.O., Payne, H.L., Wright, A., Brend, T., Patel, K., Egnuni, T., Stead, L.F., Patel, A., Wurdak, H., and Short, S.C. (2017)
Rad51 is a Selective DNA Repair Target to Radiosensitise Glioma Stem Cells.
Stem Cell Reports. Jan; 8(1):125-139.
[Pubmed]

Humphries, M.P, Rajan, S.S, Droop, A., Suleman, C., Carbone, C., Nilsson, C., Honarpisheh, H., Cserni, G., Dent, J., Fulford, L., Jordan,L.B., Jones, J.L., Kanthan, R., Litwiniuk, M., Di Benedetto, A., Mottolese, M., Provenzano, E., Shousha, S., Stephens, M., Walker, R.A., Kulka, J., Ellis, I.O, Jeffery, M., Thygesen, H.H., Cappelletti, V., Daidone, M.G., Hedenfalk, I.A, Fjällskog, M., Melisi, D., Stead, L.F., Shaaban, A. and Speirs, V. (2017)
A Case Matched Gender Comparison Transcriptomic Screen Identifies eIF4E and eIF5 as Potential Prognostic and Tractable Biomarkers in Male Breast Cancer.
Clin Cancer Res. May; 23(10):2575-2583
[Pubmed]

Town, J., Pais, H., Harrison, S., Stead, L.F., Bataille, C., Bonjobpol, W., Zhang, J., and Rabbitts, T.H. (2016)
Exploring the surfaceome of Ewing sarcoma identifies a new and unique therapeutic target.
PNAS. Mar; 113(13):3603-8
[Pubmed]

Conway, C., Graham, J.L., Chengot, P., Daly, C., Chalkley, R., Ross, L., Droop, A.,Rabbitts, P. and Stead, L.F. (2015)
Elucidating drivers of oral epithelial dysplasia formation and malignant transformation to cancer using RNAseq.
Oncotarget. Nov; 6 (37): 40186-40201
[Pubmed]

Wood H.M., Conway C., Daly C., Chalkley R., Berri S., Senguven B., Stead L.F., Ross L., Egan P., Chengot P., Graham J.L., Sethi N., Ong T.K., High A., MacLennan K. and Rabbitts P.(2015)
The clonal relationships between pre-cancer and cancer revealed by ultra-deep sequencing
The Journal of Pathology. Nov; 237(3):296-306
[Pubmed]

Smith, L., Baxter, E.W., Chambers, P.A., Green, C.A., Hanby, A.M., Hughes, T.A., Nash, C.E., Millican-Slater, R.A., Stead, L.F., Verghese, E.T. and Speirs, V. (2015)
Down-regulation of miR-92 in breast epithelial cells and in normal but not tumour fibroblasts contributes to breast carcinogenesis.
PLOS One. Oct; 10(10): e0139698
[Pubmed]

Samman M., Wood H.M., Conway C., Stead L.F.,  Daly C., Chalkley R., Berri S., Senguven B., Ross L., Egan P., Chengot P., Ong T.K., Pentenero M., Gandolfo S., Cassenti A., Cassoni P., Al Ajlan A., Samkari A., Barrett W., MacLennan K., High A. and Rabbitts P. (2015)
A novel genomic signature reclassifies an oral cancer subtype
International Journal of Cancer. Nov; 137(10):2364-73
[Pubmed]

Stead, L.F., Thygesen, H.,Westhead, D.R. and Rabbitts, P. (2015)
Using common variants to indicate cancer genes.
International Journal of Cancer. Jan;136(1):241-245
[Pubmed]

Stead L.F., Devery A., Conway C., Egan P., Daly C., Berri S., Wood H.M., Belvedere O., Papagiannopoulos K., Ryan A., Rabbitts P. (2013)
An Integrated Inspection of the Somatic Mutations in a Lung Squamous Cell Carcinoma using Next-Generation Sequencing.
PLOS one. Nov;8(11):e78823
[PLOS ONE LINK]

Stead LF, Sutton KM, Taylor GR, Quirke P and Rabbitts, P. (2013)
Accurately identifying low-allelic fraction variants in single samples with next-generation sequencing; applications in tumour subclone resolution.
Human Mutation. Oct;34(10):1432-8
[Pubmed]

Chambers PA*, Stead LF*, Morgan JE, Carr IM, Sutton KM, Watson CM, Crowe V, Dickinson H, Roberts P, Mulatero C, Seymour M, Markham AF, Waring PM, Quirke P, Taylor GR. (2013)
Mutation Detection by Clonal Sequencing of PCR Amplicons and Grouped Read Typing is Applicable to Clinical Diagnostics.
Human Mutation. Jan;34(1):248-54
* JOINT FIRST AUTHORS
[PubMed]

Stead L.F., Berri S., Wood H.M., Egan P., Conway C., Daly C., Papagiannopoulos K., Rabbitts P. (2012)
The transcriptional consequences of somatic amplifications, deletions, and rearrangements in a human lung squamous cell carcinoma.
Neoplasia. Nov;14(11):1075-86.
[PubMed]

Stead L.F., Wood I.C. and Westhead D.R. (2011)
KvSNP; Accurately Predicting the Effect of Genetic Variants in Voltage-Gated Potassium Channels
Bioinformatics: Aug 15;27(16):2181-6
[PubMed]

Abbas L, Hajihashemi S, Stead L.F., Cooper GJ, Ware TL, Munsey TS, Whitfield TT, White SJ. (2011)
Functional and developmental expression of a zebrafish Kir1.1 (ROMK) potassium channel homologue Kcnj1.
J Physiol. Mar;589(6):1489-503.
[PubMed]

Stead L.F., Wood I.C. and Westhead D.R. (2010)
KvDB; Mining and Mapping Sequence Variants in Voltage-Gated Potassium Channels
Human Mutation: Aug;31(8):908-17.
[PubMed]

PhD Studentship Opportunites

If you are interested in completing a PhD in Dr Stead’s group, please contact her directly. There are no funded studentships available at present but expressions of interest, or self-funded students, are always welcomed.

 

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