Using a range of experimental stem and cell type-specific systems in human and model organisms, York Biomedical Research Institute researchers study the processes of development, differentiation and regeneration.

These provide the basis not only for studying fundamental biological mechanisms, but also for identifying the means to intervene in chronic disease processes.

Research snapshots


Theme Leader: Professor Jennifer Southgate, Department of Biology

Professor Southgate is a cell/molecular biologist who studies human urothelium, the epithelium of the urinary bladder. Her strategy is to use in vitro systems to investigate the cell/tissue biology of normal human urothelial cells in health and disease, including infection, inflammation and cancer. 

MemberExpertiseSelected publications
Professor Jennifer Southgate (Theme Leader)

Urothelium; bladder cancer; TERM (tissue engineering and regenerative medicine); transcriptomics; differentiation.

Fishwick C, Higgins J, Percival-Alwyn L, Hustler A, Pearson J, Bastkowski S, Moxon S, Swarbreck D, Greenman CD & Southgate, J 2017, 'Heterarchy of Transcription Factors Driving Basal and Luminal Cell Phenotypes in Human Urothelium', Cell death and differentiation, vol. 24, pp. 809-818. 

Biton, A, Bernard-Pierrot, I, Lou, Y, Krucker, C, Chapeaublanc, E, Rubio-Pérez, C, López-Bigas, N, Kamoun, A, Neuzillet, Y, Gestraud, P, Grieco, L, Rebouissou, S, deReyniès, A, Benhamou, S, Lebret, T, Southgate, J, Barillot, E, Allory, Y, Zinovyev, A & Radvanyi, F 2014, 'Independent Component Analysis Uncovers the Landscape of the Bladder Tumor Transcriptome and Reveals Insights into Luminal and Basal Subtypes', Cell reports, vol. 9, no. 4, pp. 1235-1245.

Dr Gonzalo Blanco Myopathy; Z-disc mechanotransduction; Electroporation; Skeletal muscle hypertrophy; Atrophy.

Jokl, EJ, Hughes, GL, Cracknell, TR, Pownall, ME & Blanco, G 2018, 'Transcriptional up-regulation of BAG3, a Chaperone Assisted Selective Autophagy factor, in animal models of KY-deficient hereditary myopathy', Disease Models & Mechanisms, vol. 11, dmm033225.

Blanco, G 2018, 'A genetic modifier suggests that endurance exercise exacerbates Huntington's disease', Human Molecular Genetics, pp. 1-9.

Dr Will Brackenbury Brain tumours; Breast cancer; Ion channels; Metastasis; Microglia.

Nelson, M, Millican-Slater, R, Forrest, LC & Brackenbury, WJ 2014, 'The sodium channel β1 subunit mediates outgrowth of neurite-like processes on breast cancer cells and promotes tumour growth and metastasis', International Journal of Cancer, vol. 135, no. 10, pp. 2338-2351.

Nelson, M, Yang, M, Dowle, A, Thomas, J & Brackenbury, W 2015, 'The sodium channel-blocking antiepileptic drug phenytoin inhibits breast tumour growth and metastasis.', Molecular Cancer, vol. 14, 13. 
Professor Nia Bryant Diabetes (Type-2); Membrane traffic; SNARE proteins; Insulin action; Neutropenia.

Kioumourtzoglou, D, Pryor, PR, Gould, GW & Bryant, NJ 2015, 'Alternate routes to the cell surface underpin insulin-regulated membrane trafficking of GLUT4', Journal of Cell Science, vol. 128, pp. 2423-2429.

Kioumourtzoglou, D, Gould, GW & Bryant, NJ 2014, 'Insulin stimulates syntaxin4 SNARE complex assembly via a novel regulatory mechanism', Molecular and Cellular Biology, vol. 34, no. 7, pp. 1271-1279.

Professor Andrzej Marek Brzozowski Insulin; IGF1; IGF2; Insulin/IGF Receptor; Neurodegeneration.

Roed, NK, Viola, CM, Kristensen, O, Schluckebier, G, Norrman, M, Sajid, W, Wade, JD, Andersen, AS, Kristensen, C, Ganderton, TR, Turkenburg, JP, De Meyts, P & Brzozowski, AM 2018 ‘Structures of insect Imp-L2 suggest an alternative strategy for regulating the bioavailability of insulin-like hormones’, Nature Communications, vol. 9, 3860.

Viková, J, Collinsová, M, Kletvíková, E, Budšínský, M, Záková, L, Veverka, V, Hexnerová, R, Aviñó, RJT, Straková, J, Selicharová, I, Vank, V, Wright, DW, Watson, CJ, Turkenburg, JP, Brzozowski, AM & Jiráek, J 2016, 'Rational steering of insulin binding specificity by intra-chain chemical crosslinking', Scientific Reports, vol. 6, 19431.

Professor Dawn Coverley

Cell cycle; Nuclear architecture; Early detection of cancer; Technology transfer.

Ridings-Figueroa, R, Stewart, ER, Nesterova, TB, Coker, H, Pintacuda, G, Godwin, J, Wilson, R, Haslam, A, Lilley, F, Ruigrok, R, Bageghni, SA, Albadrani, G, Mansfield , W, Roulson, J-A, Brockdorff, N, Ainscough, JFX & Coverley, DA 2017, 'The nuclear matrix protein CIZ1 facilitates localization of Xist RNA to the inactive X-chromosome territory', Genes & development, vol. 31, no. 9, pp. 876-888.

Coverley, DA, Higgins, GS, West, D, Jackson, OT, Dowle, A, Haslam, A, Ainscough, E, Chalkley, R & White, J 2017, 'A quantitative immunoassay for lung cancer biomarker CIZ1b in patient plasma', Clinical Biochemistry, vol. 50, no. 6, 336-343.

Professor Gideon Davies

Glycobiology; Carbohydrate chemistry; Leishmania; Structural biology; Activity-based probes.

Larsbrink, J, Rogers, TE, Hemsworth, GR, McKee, LS, Tauzin, AS, Spadiut, O, Klinter, S, Pudlo, NA, Urs, K, Koropatkin, NM, Creagh, AL, Haynes, CA, Kelly, AG, Cederholm, SN, Davies, GJ, Martens, EC & Brumer, H 2014, 'A discrete genetic locus confers xyloglucan metabolism in select human gut Bacteroidetes', Nature, vol. 506, no. 7489, pp. 498-502.

Roth, C, Chan, OY, Offen, WA, Hemsworth, GR, Willems, LI, King, DT, Varghese, V, Britton, R, Vocadlo, DJ & Davies, GJ 2017, 'Structural and functional insight into human O-GlcNAcase', NATURE CHEMICAL BIOLOGY, vol. 13, pp. 610-612.

Dr Martin Fascione Chemical biology; Glycosylation; PTMs; Protein bioconjugation; Organic synthesis.

Spears, RJ, Brabham, RL, Budhadev, D, Keenan, T, McKenna, SE, Walton, J, Brannigan, JA, Brzozowski, AM, Wilkinson, AJ, Plevin, MJ & Fascione, MA 2018, 'Site-selective C-C modification of proteins at neutral pH using organocatalyst-mediated cross aldol ligations', Chemical Science.

Brabham, RL, Spears, RJ, Walton, J, Tyagi, S, Lemke, E & Fascione, MA 2018, 'Palladium-unleashed proteins: gentle aldehyde decaging for site-selective protein modification', Chemical Communications, vol. 54, pp. 1501-1504.

Professor Paul Genever Mesenchymal stem/stromal cells; Bone marrow; Skeletal biology; Regenerative medicine; Cell and molecular biology.

James, S, Fox, J, Afsari, F, Lee, J, Clough, S, Knight, C, Ashmore, J, Ashton, P, Preham, O, Hoogduijn, M, Ponzoni, RDAR, Hancock, Y, Coles, M & Genever, P 2015, 'Multiparameter Analysis of Human Bone Marrow Stromal Cells Identifies Distinct Immunomodulatory and Differentiation-Competent Subtypes', Stem Cell Reports, vol. 4, no. 6, pp. 1004-1015.

Pennock, R, Bray, E, Pryor, P, James, S, McKeegan, P, Sturmey, R & Genever, P 2015, 'Human cell dedifferentiation in mesenchymal condensates through controlled autophagy', Scientific Reports, vol. 5, 13113.

Dr Yvette Hancock  Label-free methods; Biomolecular stratification; Biomarkers; Clinical translation; Raman spectroscopy.

Howlett, R, Read, N, Varghese, AS, Kershaw, C, Hancock, Y & Smith, MCM 2018, 'Streptomyces coelicolor strains lacking polyprenol phosphate mannose synthase and protein O-mannosyl transferase are hyper-susceptible to multiple antibiotics', Microbiology, vol. 164, pp. 369-382.

James, S, Fox, J, Afsari, F, Lee, J, Clough, S, Knight, C, Ashmore, J, Ashton, P, Preham, O, Hoogduijn, M, Ponzoni, RDAR, Hancock, Y, Coles, M & Genever, P 2015, 'Multiparameter Analysis of Human Bone Marrow Stromal Cells Identifies Distinct Immunomodulatory and Differentiation-Competent Subtypes', Stem Cell Reports, vol. 4, no. 6, pp. 1004-1015.

Dr Andrew Holding

Cancer; Nuclear Receptors; Computational Biology; Single Cell Sequencing; Functional Genomics.

Holding, AN, Giorgi, FM, Donnelly, A, Cullen, AE, Selth, LA, Markowetz, F 2018 ‘VULCAN: Network Dynamics of ER-α activation reveals reprogramming of GRHL2’, Genome Biology, vol. 20, 19.

Holding, AN, Cullen, AE, Markowetz, F 2018 ‘Genome-wide Estrogen Receptor-alpha activation is sustained, not cyclical’, eLife, vol. 7, e40854.

Professor Neil Hunt

Ultrafast spectroscopy; Biomolecular interactions; Protein-drug binding; Biofluid analysis.

Fritzsch, R, Donaldson, PM, Greetham, GM, Towrie, M, Parker, AW, Baker, MJ & Hunt, NT2018, 'Rapid Screening of DNA-Ligand Complexes via 2D-IR Spectroscopy and ANOVA-PCA', Analytical Chemistry, vol. 90, no. 4, pp. 2732-2740.

Shaw, DJ, Hill, RE, Simpson, N, Husseini, FS, Robb, K, Greetham, GM, Towrie, M, Parker, AW, Robinson, D, Hirst, JD, Hoskisson, PA & Hunt, NT 2017, 'Examining the role of protein structural dynamics in drug resistance in Mycobacterium tuberculosis', Chemical Science, vol. 8, no. 12, pp. 8384-8399.

Dr Roland Kröger

Ex situ and In situ Transmission Electron Microscopy; Bone and Teeth Structure; Composition and Properties; Raman Spectroscopy.

Reznikov, N, Bilton, MW, Lari, L, Stevens, M & Kröger, R 2018, 'Fractal-like hierarchical organization of bone begins at the nanoscale', Science, vol. 360, no. 6388, eaao2189.

Chatzipanagis, K, Baumann, CG, Sandri, M, Sprio, S, Tampieri, A & Kröger, R 2016, 'In situ mechanical and molecular investigations of collagen/apatite biomimetic composites combining Raman spectroscopy and stress-strain analysis', Acta Biomaterialia, vol. 46, pp. 278-285.

Dr Chris MacDonald

Membrane trafficking; Cell surface membrane proteins; Yeast genetics;
Fluorescence microscopy; Biochemistry.

MacDonald, C & Piper, RC 2017, 'Genetic dissection of early endosomal recycling highlights a TORC1-independent role for Rag GTPases', Journal of Cell Biology, Vol. 216, no. 10, pp. 3275-3290.

MacDonald, C, Payne, JA, Aboian, M, Smith, W, Katzmann, DJ & Piper, RC 2015, 'A Family of Tetraspans Organizes Cargo for Sorting into Multivesicular Bodies', Developmental Cell, vol. 33, no. 3, pp. 328-342.

Dr Andrew Mason

Cancer; Bioinformatics; Functional Genomics; Endogenous Retroviruses

Baker, SC, Mason, AS & Southgate, J 2020, 'Pro-carcinogen activation and mutational signatures model the initiation of carcinogenesis in human urothelial tissues in vitro', European Urology, vol. 78, no. 2, pp. 143-147.

Mason, AS, Lund, AR, Hocking, PM, Fulton, JE & Burt, DW 2020, 'Identification and characterisation of endogenous Avian Leukosis Virus subgroup E (ALVE) insertions in chicken whole genome sequencing data', Mobile DNA, vol. 11, 22.

Dr Agnes Noy Molecular modelling; DNA supercoiling; DNA:protein recognition; 3D genomics; gene therapy.

Sutthibutpong, T, Matek, C, Benham, CJ, Slade, GG, Noy, A, Laughton, CA, Doye, JPK, Louis, AA & Harris, SA 2016, 'Long-range correlations in the mechanics of small DNA circles under topological stress revealed by multi-scale simulation', Nucleic Acids Research, vol. 44, no. 19, pp. 9121-9130.

Ivani, I, Dans, PD, Noy, A, Perez, A, Faustino, I, Hospital, A, Whalter, J, Andrio, P, Goni, R, Balaceanu, A, Portella, G, Battistini, F, Gelpi, JL, Gonzalez, C, Vendruscolo, M, Laughton, CA, Harris, SA, Case, DA & Orozco, M 2016, 'Parmbsc1: a refined force-field for DNA simulations', Nature Methods, vol. 13, no. 1, pp. 55–58.

Professor Jane Thomas-Oates Mass spectrometry; Interdisciplinary science; Protein glycosylation; Therapeutics production; Environmental contamination.

Skeene, K, Walker, MJ, Clarke, G, Bergström, E, Genever, P, Ungar, D & Thomas-Oates, J2017, 'One filter, one sample and the N- and O-glyco(proteo)me: towards a system to study disorders of protein glycosylation. Toward a System to Study Disorders of Protein Glycosylation', Analytical Chemistry, vol. 89, no. 11, pp. 5840-5849.

Witkos, TM, Chan, WL, Joensuu, M, Rhiel, M, Pallister, E, Thomas-Oates, JE, Mould, P, Mironov, AA, Biot, C, Guerardel, Y, Morelle, W, Ungar, D, Wieland, FT, Jokitalo, E, Tassabehji, M, Kornak, U & Lowe, M 2019, 'GORAB scaffolds COPI at the trans-Golgi for efficient enzyme recycling and correct protein glycosylation', Nature Communications, vol. 10, no. 127, pp. 1-18

Dr Betsy Pownall Developmental biology; Embryology; Cell signalling; Genetics; Animal models of disease.

Fellgett, SW, Maguire, RJ & Pownall, ME 2015, 'Sulf1 has ligand-dependent effects on canonical and non-canonical Wnt signalling', Journal of Cell Science, vol. 128, no. 7, pp. 1408-21.

Jokl, EJ, Hughes, GL, Cracknell, TR, Pownall, ME & Blanco, G 2018, 'Transcriptional up-regulation of BAG3, a Chaperone Assisted Selective Autophagy factor, in animal models of KY-deficient hereditary myopathy', Disease Models & Mechanisms, vol. 128, no. 7, pp. 1408-1421.

Dr Chris Spicer Biomaterials; Tissue engineering; Protein chemistry; Chemical biology.

Spicer, CD, Booth, MA, Mawad, D, Armgarth, A, Nielsen, CB & Stevens, MM 2017, 'Synthesis of Hetero-bifunctional, End-Capped Oligo-EDOT Derivatives', Chem, vol. 2, no. 1, pp. 125-138.

Guex, AG, Spicer, CD, Armgarth, A, Gelmi, A, Humphrey, EJ, Terracciano, CM, Harding, SE & Stevens, MM 2017, 'Electrospun aniline-tetramer-co-polycaprolactone fibers for conductive, biodegradable scaffolds', MRS Communications, vol. 7, no. 3, pp. 375-382.

Dr Lianne Willems Chemical biology; Glycobiology; Muscular dystrophy; Structural biology; Small molecule probes.

Willems, LI, Beenakker, TJM, Murray, BS, Scheij, S, Kallemeijn, WW, Boot, RG, Verhoek, M, Donker-Koopman, WE, Ferraz, MJ, Rijssel, ERV, Florea, BI, Codée, JDC, Van Der Marel, GA, Aerts, JMFG & Overkleeft, HS 2014, 'Potent and selective activity-based probes for GH27 human retaining α-galactosidases', Journal of the American Chemical Society, vol. 136, no. 33, pp. 11622-11625.

Marques, ARA, Willems, LI, Herrera Moro, D, Florea, BI, Scheij, S, Ottenhoff, R, van Roomen, CPAA, Verhoek, M, Nelson, JK, Kallemeijn, WW, Biela-Banas, A, Martin, OR, Cachón‐González , MB, Kim, NN, Cox, TM, Boot, RG, Overkleeft, HS & Aerts, JMFG 2017, 'A Specific Activity-Based Probe to Monitor Family GH59 Galactosylceramidase, the Enzyme Deficient in Krabbe Disease', Chembiochem, vol. 18, no. 4, pp. 402-412.