Bioinformatics and Data Science

Recent Publications

2023

Santi, A., Kay, E.J., Neilson, L.J., McGarry, L., Lilla, S., Mullin, M., Paul, N.R., Fercoq, F., Koulouras, G., Blanco, G.R., Athineos, D., Mason, S., Hughes, M., Kieffer, Y., Nixon, C., Blyth, K., Mechta-Grigoriou, F., Carlin, L.M., Zanivan, S., 2023. Cancer-associated fibroblasts produce matrix-bound vesicles that influence endothelial cell function. bioRxiv.

2022

Falcone, M., Uribe, A.H., Papalazarou, V., Newman, A.C., Athineos, D., Stevenson, K., Sauvé, C.G., Gao, Y., Kim, J.K., Del Latto, M., Kierstead, M., Wu, C., Smith, J.J., Romesser, P.B., Chalmers, A.J., Blyth, K., Maddocks, O.D.K., 2022. Sensitisation of cancer cells to radiotherapy by serine and glycine starvation. Br J Cancer 127, 1773–1786.

Kay, E.J., Paterson, K., Riero-Domingo, C., Sumpton, D., Däbritz, J.H.M., Tardito, S., Boldrini, C., Hernandez-Fernaud, J.R., Athineos, D., Dhayade, S., Stepanova, E., Gjerga, E., Neilson, L.J., Lilla, S., Hedley, A., Koulouras, G., McGregor, G., Jamieson, C., Johson, R.M., Park, M., Kirschner, K., Miller, C., Kamphorst, J.J., Loayza-Puch, F., Saez-Rodriguez, J., Mazzone, M., Blyth, K., Zagoni, M., Zanivan, S., 2022. Cancer-associated fibroblasts require proline synthesis by PYCR1 for the deposition of pro-tumorigenic extracellular matrix. Nature Metabolism 4(6), 693–710.

2021

Humpton, T.J., Nomura, K., Weber, J., Magnussen, H.M., Hock, A.K., Nixon, C., Dhayade, S., Stevenson, D., Huang, D.T., Strathdee, D., Blyth, K., Vousden, K.H., 2021. Differential requirements for MDM2 E3 activity during embryogenesis and in adult mice. Genes & development 35(1-2), 117–132.

Latif, A.L., Newcombe, A., Li, S., Gilroy, K., Robertson, N.A., Lei, X., Stewart, H.J.S., Cole, J., Terradas, M.T., Rishi, L., McGarry, L., McKeeve, C., Reid, C., Clark, W., Campos, J., Kirschner, K., Davis, A., Lopez, J., Sakamaki, J.I., Morton, J.P., et al., 2021. BRD4-mediated repression of p53 is a target for combination therapy in AML. Nat Commun 12, 241.

Nacke, M., Sandilands, E., Nikolatou, K., Román-Fernández, Á., Mason, S., Patel, R., Lilla, S., Yelland, T., Galbraith, L.C.A., Freckmann, E.C., McGarry, L., Morton, J.P., Shanks, E., Leung, H.Y., Markert, E., Ismail, S., Zanivan, S., Blyth, K., Bryant, D.M., 2021. An ARF GTPase module promoting invasion and metastasis through regulating phosphoinositide metabolism. Nat Commun 12, 1623.

Newman, A.C., Falcone, M., Huerta Uribe, A., Zhang, T., Athineos, D., Pietzke, M., Vazquez, A., Blyth, K., Maddocks, O.D.K., 2021. Immune-regulated IDO1-dependent tryptophan metabolism is source of one-carbon units for pancreatic cancer and stellate cells. Mol Cell 81, 2290–2302.

Tajan, M., Hennequart, M., Cheung, E.C., Zani, F., Hock, A.K., Legrave, N., Maddocks, O.D.K., Ridgway, R.A., Athineos, D., Suárez-Bonnet, A., Ludwig, R.L., Novellasdemunt, L., Angelis, N., Li, V.S.W., Vlachogiannis, G., Valeri, N., Mainolfi, N., Suri, V., Friedman, A., Manfredi, M., et al., 2021. Serine synthesis pathway inhibition cooperates with dietary serine and glycine limitation for cancer therapy. Nat Commun 12, 366.

2020

Blagih, J., Zani, F., Chakravarty, P., Hennequart, M., Pilley, S., Hobor, S., Hock, A.K., Walton, J.B., Morton, J.P., Gronroos, E., Mason, S., Yang, M., McNeish, I., Swanton, C., Blyth, K., Vousden, K.H., 2020. Cancer-Specific Loss of p53 Leads to a Modulation of Myeloid and T Cell Responses. Cell reports 30, 481–496.e486.

Campbell, K.J., Blyth, K., 2020. Somatic base editing to model oncogenic drivers in breast cancer. Lab Anim 49, 115–116.

Caraffini, V., Geiger, O., Rosenberger, A., Hatzl, S., Perfler, B., Berg, J.L., Lim, C., Strobl, H., Kashofer, K., Schauer, S., Beham-Schmid, C., Hoefler, G., Geissler, K., Quehenberger, F., Kolch, W., Athineos, D., Blyth, K., Wolfler, A., Sill, H., Zebisch, A., 2020. Loss of RAF kinase inhibitor protein is involved in myelomonocytic differentiation and aggravates RAS-driven myeloid leukemogenesis. Haematologica 105, 375–386.

Cheung, E.C., DeNicola, G.M., Nixon, C., Blyth, K., Labuschagne, C.F., Tuveson, D.A., Vousden, K.H., 2020. Dynamic ROS Control by TIGAR Regulates the Initiation and Progression of Pancreatic Cancer. Cancer cell 37, 168–182.

Dhayade, S., Pietzke, M., Wiesheu, R., Tait-Mulder, J., Athineos, D., Sumpton, D., Coffelt, S., Blyth, K., Vazquez, A., 2020. Impact of Formate Supplementation on Body Weight and Plasma Amino Acids. Nutrients 12(8), 2181.

Lie, A.L.M., Mevel, R., Patel, R., Blyth, K., Baena, E., Kouskoff, V., Lacaud, G., 2020. RUNX1 Dosage in Development and Cancer. Mol Cells 43, 126–128.

Loveridge, C.J., Slater, S., Campbell, K.J., Nam, N.A., Knight, J., Ahmad, I., Hedley, A., Lilla, S., Repiscak, P., Patel, R., Salji, M., Fleming, J., Mitchell, L., Nixon, C., Strathdee, D., Neilson, M., Ntala, C., Bryson, S., Zanivan, S., Edwards, J., Robson, C.N., Goodyear, C.S., Blyth, K., Leung, H.Y., 2020. BRF1 accelerates prostate tumourigenesis and perturbs immune infiltration. Oncogene 39, 1797–1806.

MacKenzie, D.J., Robertson, N.A., Rather, I., Reid, C., Sendzikaite, G., Cruickshanks, H., McBryan, T., Hodges, A., Pritchard, C., Blyth, K., Adams, P.D., 2020. DNMT3B Oncogenic Activity in Human Intestinal Cancer Is Not Linked to CIMP or BRAFV600E Mutation. iScience 23, 100838–100838.

Millar, R., Kilbey, A., Remak, S.J., Severson, T.M., Dhayade, S., Sandilands, E., Foster, K., Bryant, D.M., Blyth, K., Coffelt, S.B., 2020. The MSP-RON axis stimulates cancer cell growth in models of triple negative breast cancer. Molecular oncology 14, 1868–1880.

Oizel, K., Tait-Mulder, J., Fernandez-de-Cossio-Diaz, J., Pietzke, M., Brunton, H., Lilla, S., Dhayade, S., Athineos, D., Blanco, G.R., Sumpton, D., Mackay, G.M., Blyth, K., Zanivan, S.R., Meiser, J., Vazquez, A., 2020. Formate induces a metabolic switch in nucleotide and energy metabolism. Cell death & disease 11, 310.

Ran, R., Harrison, H., Syamimi Ariffin, N., Ayub, R., Pegg, H.J., Deng, W., Mastro, A., Ottewell, P.D., Mason, S.M., Blyth, K., Holen, I., Shore, P., 2020. A role for CBFbeta in maintaining the metastatic phenotype of breast cancer cells. Oncogene 39, 2624–2637.

Rooney, N., Mason, S.M., McDonald, L., Däbritz, J.H.M., Campbell, K.J., Hedley, A., Howard, S., Athineos, D., Nixon, C., Clark, W., Leach, J.D.G., Sansom, O.J., Edwards, J., Cameron, E.R., Blyth, K., 2020. RUNX1 is a driver of renal cell carcinoma correlating with clinical outcome. Cancer Res 80, 2325–2339.

Rudzka, D.A., Mason, S., Neilson, M., McGarry, L., Kalna, G., Hedley, A., Blyth, K., Olson, M.F., 2020. Selection of established tumour cells through narrow diameter micropores enriches for elevated Ras/Raf/MEK/ERK MAPK signalling and enhanced tumour growth. Small GTPases 12(4), 294–310.

Sweeney, K., Cameron, E.R., Blyth, K., 2020. Complex Interplay between the RUNX Transcription Factors and Wnt/β-Catenin Pathway in Cancer: A Tango in the Night. Molecules and cells 43, 188–197.

2019

Hassan, S., Purdie, K.J., Wang, J., Harwood, C.A., Proby, C.M., Pourreyron, C., Mladkova, N., Nagano, A., Dhayade, S., Athineos, D., Caley, M., Mannella, V., Blyth, K., Inman, G.J., Leigh, I.M., 2019. A Unique Panel of Patient-Derived Cutaneous Squamous Cell Carcinoma Cell Lines Provides a Preclinical Pathway for Therapeutic Testing. International journal of molecular sciences 20, 3428.

Johnson, S.A., Ormsby, M.J., McIntosh, A., Tait, S.W.G., Blyth, K., Wall, D.M., 2019. Increasing the bactofection capacity of a mammalian expression vector by removal of the f1 ori. Cancer Gene Ther 26, 183–194.

Liko, D., Mitchell, L., Campbell, K.J., Ridgway, R.A., Jones, C., Dudek, K., King, A., Bryson, S., Stevenson, D., Blyth, K., Strathdee, D., Morton, J.P., Bird, T.G., Knight, J.R.P., Willis, A.E., Sansom, O.J., 2019. Brf1 loss and not overexpression disrupts tissues homeostasis in the intestine, liver and pancreas. Cell Death Differ 26, 2535–2550.

Rudzka, D.A., Spennati, G., McGarry, D.J., Chim, Y.H., Neilson, M., Ptak, A., Munro, J., Kalna, G., Hedley, A., Moralli, D., Green, C., Mason, S., Blyth, K., Mullin, M., Yin, H., Olson, M.F., 2019. Migration through physical constraints is enabled by MAPK-induced cell softening via actin cytoskeleton re-organization. Journal of cell science 132, jcs224071.

Vande Voorde, J., Ackermann, T., Pfetzer, N., Sumpton, D., Mackay, G., Kalna, G., Nixon, C., Blyth, K., Gottlieb, E., Tardito, S., 2019. Improving the metabolic fidelity of cancer models with a physiological cell culture medium. Science Advances 5, eaau7314.

2018

Campbell, K.J., Dhayade, S., Ferrari, N., Sims, A.H., Johnson, E., Mason, S.M., Dickson, A., Ryan, K.M., Kalna, G., Edwards, J., Tait, S.W.G., Blyth, K., 2018. MCL-1 is a prognostic indicator and drug target in breast cancer. Cell Death Dis 9, 19.

McCarroll, C.S., He, W., Foote, K., Bradley, A., McGlynn, K., Vidler, F., Nixon, C., Nather, K., Fattah, C., Riddell, A., Bowman, P., Elliott, E.B., Bell, M., Hawksby, C., MacKenzie, S.M., et al., 2018. Runx1 Deficiency Protects Against Adverse Cardiac Remodeling After Myocardial Infarction. Circulation 137, 57–70.

Meiser, J., Schuster, A., Pietzke, M., Vande Voorde, J., Athineos, D., Oizel, K., Burgos-Barragan, G., Wit, N., Dhayade, S., Morton, J.P., Dornier, E., Sumpton, D., Mackay, G.M., Blyth, K., Patel, K.J., et al., 2018. Increased formate overflow is a hallmark of oxidative cancer. Nat Commun 9, 1368.

Novo, D., Heath, N., Mitchell, L., Caligiuri, G., MacFarlane, A., Reijmer, D., Charlton, L., Knight, J., Calka, M., McGhee, E., Dornier, E., Sumpton, D., Mason, S., Echard, A., Klinkert, K., et al., 2018. Mutant p53s generate pro-invasive niches by influencing exosome podocalyxin levels. Nat Commun 9, 5069.

2017

Bulusu, V., Tumanov, S., Michalopoulou, E., van den Broek, N.J., MacKay, G., Nixon, C., Dhayade, S., Schug, Z.T., Vande Voorde, J., Blyth, K., Gottlieb, E., Vazquez, A., Kamphorst, J.J., 2017. Acetate Recapturing by Nuclear Acetyl-CoA Synthetase 2 Prevents Loss of Histone Acetylation during Oxygen and Serum Limitation. Cell Rep 18, 647–58.

Dornier, E., Rabas, N., Mitchell, L., Novo, D., Dhayade, S., Marco, S., Mackay, G., Sumpton, D., Pallares, M., Nixon, C., Blyth, K., Macpherson, I., Rainero, E., Norman, J.C., 2017. Glutaminolysis drives membrane trafficking to promote cancer invasion. Nat Commun 8, 2255.

Giampazolias, E., Zunino, B., Dhayade, S., Bock, F., Cloix, C., Cao, K., Roca, A., Lopez, J., Ichim, G., Proics, E., Rubio-Patino, C., Fort, L., Yatim, N., Woodham, E., Orozco, S., Taraborrelli, L., Peltzer, N., Lecis, D., Machesky, L., Walczak, H., et al., 2017. Mitochondrial permeabilization engages NF-kappaB-dependent anti-tumour activity under caspase deficiency. Nat Cell Biol 19, 1116–29.

Hernandez-Fernaud, J.R., Ruengeler, E., Casazza, A., Neilson, L.J., Pulleine, E., Santi, A., Ismail, S., Lilla, S., Dhayade, S., MacPherson, I.R., McNeish, I., Ennis, D., Ali, H., Kugeratski, F.G., Al Khamici, H., van den Biggelaar, M., van den Berghe, P.V., Cloix, C., McDonald, L., Millan, D., et al., 2017. Secreted CLIC3 drives cancer progression through its glutathione-dependent oxidoreductase activity. Nat Commun 8, 14206.

Hock, A.K., Cheung, E.C., Humpton, T.J., Monteverde, T., Paulus-Hock, V., Lee, P., McGhee, E., Scopelliti, A., Murphy, D.J., Strathdee, D., Blyth, K., Vousden, K.H., 2017. Development of an inducible mouse model of iRFP713 to track recombinase activity and tumour development in vivo. Sci Rep 7, 1837.

Loveridge, C.J., Mui, E.J., Patel, R., Tan, E.H., Ahmad, I., Welsh, M., Galbraith, J., Hedley, A., Nixon, C., Blyth, K., Sansom, O., Leung, H.Y., 2017. Increased T-cell Infiltration Elicited by Erk5 Deletion in a Pten-Deficient Mouse Model of Prostate Carcinogenesis. Cancer Res 77, 3158–68.

Loveridge, C.J., van 't Hof, R.J., Charlesworth, G., King, A., Tan, E.H., Rose, L., Daroszewska, A., Prior, A., Ahmad, I., Welsh, M., Mui, E.J., Ford, C., Salji, M., Sansom, O., Blyth, K., Leung, H.Y., 2017. Analysis of Nkx3.1:Cre-driven Erk5 deletion reveals a profound spinal deformity which is linked to increased osteoclast activity. Sci Rep 7, 13241.

Maddocks, O.D.K., Athineos, D., Cheung, E.C., Lee, P., Zhang, T., van den Broek, N.J.F., Mackay, G.M., Labuschagne, C.F., Gay, D., Kruiswijk, F., Blagih, J., Vincent, D.F., Campbell, K.J., Ceteci, F., Sansom, O.J., Blyth, K., Vousden, K.H., 2017. Modulating the therapeutic response of tumours to dietary serine and glycine starvation. Nature 544, 372–6.

Reid, S.E., Kay, E.J., Neilson, L.J., Henze, A.T., Serneels, J., McGhee, E.J., Dhayade, S., Nixon, C., Mackey, J.B., Santi, A., Swaminathan, K., Athineos, D., Papalazarou, V., Patella, F., Roman-Fernandez, A., ElMaghloob, Y., Hernandez-Fernaud, J.R., Adams, R.H., Ismail, S., Bryant, D.M., et al., 2017. Tumor matrix stiffness promotes metastatic cancer cell interaction with the endothelium. EMBO J 36, 2373–89.

van Tuyn, J., Jaber-Hijazi, F., MacKenzie, D., Cole, J.J., Mann, E., Pawlikowski, J.S., Singh Rai, T., Nelson, D.M., McBryan, T., Ivanov, A., Blyth, K., Wu, H., Milling, S., Adams, P.D., 2017. Oncogene-Expressing Senescent Melanocytes Upregulate Mhc Class Ii, A Candidate Melanoma Suppressor Function. J Invest Dermatol 137, 2197–207.

Walton, J.B., Farquharson, M., Mason, S., Port, J., Kruspig, B., Dowson, S., Stevenson, D., Murphy, D., Matzuk, M., Kim, J., Coffelt, S., Blyth, K., McNeish, I.A., 2017. CRISPR/Cas9-derived models of ovarian high grade serous carcinoma targeting Brca1, Pten and Nf1, and correlation with platinum sensitivity. Sci Rep 7, 16827.

Weigert, M., Binks, A., Dowson, S., Leung, E.Y.L., Athineos, D., Yu, X., Mullin, M., Walton, J.B., Orange, C., Ennis, D., Blyth, K., Tait, S.W.G., McNeish, I.A., 2017. RIPK3 promotes adenovirus type 5 activity. Cell Death and Disease 8, 3206.

Holen, I., Speirs, V., Morrissey, B., Blyth, K., 2017. In vivo models in breast cancer research: progress, challenges and future directions. Dis Model Mech 10, 359–71.

Morrissey, B., Blyth, K., Carter, P., Chelala, C., Jones, L., Holen, I., Speirs, V., 2017. The Sharing Experimental Animal Resources, Coordinating Holdings (SEARCH) Framework: Encouraging Reduction, Replacement, and Refinement in Animal Research. PLoS Biol 15, e2000719.

Riggio, A.I., Blyth, K., 2017. The Enigmatic Role of RUNX1 in Female-Related Cancers: Current Knowledge & Future Perspectives. FEBS J 284, 2345–62.

Rooney, N., Riggio, A.I., Mendoza-Villanueva, D., Shore, P., Cameron, E.R., Blyth, K., 2017. Runx Genes in Breast Cancer and the Mammary Lineage. Adv Exp Med Biol 962, 353–68.

2016

Birch, J., Clarke, C.J., Campbell, A.D., Campbell, K., Mitchell, L., Liko, D., Kalna, G., Strathdee, D., Sansom, O.J., Neilson, M., Blyth, K., Norman, J.C., 2016. The initiator methionine tRNA drives cell migration and invasion leading to increased metastatic potential in melanoma. Biol Open 5, 1371–1379.

Blyth, K., Carter, P., Morrissey, B., Chelala, C., Jones, L., Holen, I., Speirs, V., 2016. SEARCHBreast: a new resource to locate and share surplus archival material from breast cancer animal models to help address the 3Rs. Breast Cancer Res Treat 56, 447–52.

Meiser, J., Tumanov, S., Maddocks, O., Labuschagne, C.F., Athineos, D., Van Den Broek, N., Mackay, G.M., Gottlieb, E., Blyth, K., Vousden, K., Kamphorst, J.J., Vazquez, A., 2016. Serine one-carbon catabolism with formate overflow. Science Advances 2, e1601273.

Morrissey, B., Blyth, K., Carter, P., Chelala, C., Jones, L., Holen, I., Speirs, V., 2016. SEARCHBreast: a new online resource to make surplus material from in vivo models of breast cancer visible and accessible to researchers. Breast Cancer Res 18, 59.