Proteomics

Introduction

 Zanivan head 2020 129

 Prof Sara Zanivan

Head of Proteomics Facility

sara.zanivan@glasgow.ac.uk

The Advanced Technology Proteomic Facility develops MS-based platforms and works together with researchers to provide a new level of understanding in tumour biology. We have developed pipelines for the analysis of a wide range of biological samples, from single proteins to the complete proteome of cells, organoids and tissues.

Our group has recently developed new methods to study cysteine oxidation (van der Reest, Lilla et al. Nature Communications 2018), cell secretomes (Hernandez-Fernaud, Ruengeler et al. Nature Communications 2017) and transmembrane receptor trafficking (Diaz-Vera et al. Journal Cell Science 2017).

We have three MS instruments, each coupled to an Easy-nLC system:

  • Orbitrap Fusion Lumos
  • Q-Exactive HF
  • LTQ Orbitrap Elite

We use a variety of methods for protein digestion:

  • filter-aided sample preparation (FASP)
  • in-gel
  • in-solution

for proteome and post-translational modifications analysis:

  • high-pH reversed-phase chromatography peptide fractionation
  • gel-based protein fractionation

to accurately measure proteins and peptides:

  • Label-free
  • TMT
  • SILAC
  • Dimethyl
  • Isotope-labelled IAA (for cysteine oxidation)

We analyse our MS data with

  • MaxQuant computational platform
  • Progenesis and Skyline for the analysis of pRM data
  • Mascot for single protein identification
  • Perseus and Scaffold for data compilation, analysis and dissemination.

 Sara Zanivan also leads the Tumour Microenvironment and Proteomics research group.

Recent Publications

2021

Ahmed SF, Buetow L, Gabrielsen M, Lilla S, Sibbet GJ, Sumpton D, Zanivan S, Hedley A, Clark W, Huang DT. E3 ligase-inactivation rewires CBL interactome to elicit oncogenesis by hijacking RTK-CBL-CIN85 axis. Oncogene. 2021;40:2149-2164.

Kugeratski FG, Hodge K, Lilla S, McAndrews KM, Zhou X, Hwang RF, Zanivan S, Kalluri R. Quantitative proteomics identifies the core proteome of exosomes with syntenin-1 as the highest abundant protein and a putative universal biomarker. Nat Cell Biol. 2021;23:631-641.

Martinez RS, Salji MJ, Rushworth L, Ntala C, Rodriguez Blanco G, Hedley A, Clark W, Peixoto P, Hervouet E, Renaude E, Kung SHY, Galbraith LCA, Nixon C, Lilla S, MacKay GM, Fazli L, Gaughan L, Sumpton D, Gleave ME, Zanivan S, Blomme A, Leung HY. SLFN5 Regulates LAT1-Mediated mTOR Activation in Castration-Resistant Prostate Cancer. Cancer Res. 2021;81:3664-3678.

2020

Blomme A, Ford CA, Mui E, Patel R, Ntala C, Jamieson LE, Planque M, McGregor GH, Peixoto P, Hervouet E, Nixon C, Salji M, Gaughan L, Markert E, Repiscak P, Sumpton D, Rodriguez Blanco G, Lilla S, Kamphorst JJ, Graham D, Faulds K, MacKay GM, Fendt S-M, Zanivan S, Leung HY. 2,4-dienoyl-CoA reductase regulates lipid homeostasis in treatment-resistant prostate cancer. Nat Commun. 2020; 11: 2508

Cao X, Lilla S, Cao Z, Pringle MA, Oka OBV, Robinson PJ, Szmaja T, van Lith M, Zanivan S, Bulleid NJ. The mammalian cytosolic thioredoxin reductase pathway acts via a membrane protein to reduce ER-localised proteins. Journal of cell science. 2020;10.1242/jcs.241976.

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

Taskinen ME, Närvä E, Conway JRW, Hinojosa LS, Lilla S, Mai A, De Franceschi N, Elo LL, Grosse R, Zanivan S, Norman JC, Ivaska J. MASTL promotes cell contractility and motility through kinase-independent signaling. J Cell Biol. 2020; 219.

2019

Ferraro DA, Patella F, Zanivan S, Donato C, Aceto N, Giannotta M, Dejana E, Diepenbruck M, Christofori G, Buess M. Endothelial cell-derived nidogen-1 inhibits migration of SK-BR-3 breast cancer cells. BMC Cancer. 2019; 19: 312.

Loveridge CJ, Slater S, Campbell KJ, Nam NA, 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 CN, Goodyear CS, Blyth K, Leung HY. BRF1 accelerates prostate tumourigenesis and perturbs immune infiltration. Oncogene. 2019; 39: 1797–1806

Kugeratski FG, Atkinson SJ, Neilson LJ, Lilla S, Knight JRP, Serneels J, Juin A, Ismail S, Bryant DM, Markert EK, Machesky LM, Mazzone M, Sansom OJ, Zanivan S. Hypoxic cancer-associated fibroblasts increase NCBP2-AS2/HIAR to promote endothelial sprouting through enhanced VEGF signaling. Science signaling 2019; 12: eaan8247.

Whitelaw JA, Lilla S, Paul NR, Fort L, Zanivan S, Machesky LM. CYRI/ Fam49 Proteins Represent a New Class of Rac1 Interactors. Communicative & integrative biology. 2019;12:112-118.

Wilczynska A, Gillen SL, Schmidt T, Meijer HA, Jukes-Jones R, Langlais C, Kopra K, Lu WT, Godfrey JD, Hawley BR, Hodge K, Zanivan S, Cain K, Le Quesne J, Bushell M. eIF4A2 drives repression of translation at initiation by Ccr4-Not through purine-rich motifs in the 5'UTR. Genome Biol. 2019; 20: 262.

2018

Dandoulaki M, Petsalaki E, Sumpton D, Zanivan S, Zachos G. Src activation by Chk1 promotes actin patch formation and prevents chromatin bridge breakage in cytokinesis. J Cell Biol 2018.217: 3071–3089

Fort L, Batista JM, Thomason PA, Spence HJ, Whitelaw JA, Tweedy L, Greaves J, Martin KJ, Anderson KI, Brown P, Lilla S, Neilson MP, Tafelmeyer P, Zanivan S, Ismail S, Bryant DM, Tomkinson NCO, Chamberlain LH, Mastick GS, Insall RH, Machesky LM. Fam49/CYRI interacts with Rac1 and locally suppresses protrusions. Nat Cell Biol. 2018; 20: 1159-71.

Port J, Muthalagu N, Raja M, Ceteci F, Monteverde T, Kruspig B, Hedley A, Kalna G, Lilla S, Neilson L, Brucoli M, Gyuraszova K, Tait-Mulder J, Mezna M, Svambaryte S, Bryson A, Sumpton D, McVie A, Nixon C, Drysdale M, Esumi H, Murray GI, Sansom OJ, Zanivan SR, Murphy DJ. Colorectal Tumors Require NUAK1 for Protection from Oxidative Stress. Cancer Discov. 2018 May; 8(5): 632-47.

Unbekandt M, Belshaw S, Bower J, Clarke M, Cordes J, Crighton D, Croft DR, Drysdale MJ, Garnett MJ, Gill K, Gray C, Greenhalgh DA, Hall JA, Konczal J, Lilla S, McArthur D, McConnell P, McDonald L, McGarry L, McKinnon H. Discovery of potent and selective MRCK inhibitors with therapeutic effect on skin cancer. Cancer Res. 2018;

van der Reest J, Lilla S, Zheng L, Zanivan S, Gottlieb E. Proteome-wide analysis of cysteine oxidation reveals metabolic sensitivity to redox stress. Nat Commun. 2018; 9: 1581

2017

Hernandez-Fernaud JR, Ruengeler E, Casazza A, Neilson LJ, Pulleine E, Santi A, Ismail S, Lilla S, Dhayade S, MacPherson IR, McNeish I, Ennis D, Ali H, Kugeratski FG, Al Khamici H, van den Biggelaar M, van den Berghe PV, Cloix C, McDonald L, Millan D, Hoyle A, Kuchnio A, Carmeliet P, Valenzuela SM, Blyth K, Yin H, Mazzone M, Norman JC, Zanivan S. Secreted CLIC3 drives cancer progression through its glutathione-dependent oxidoreductase activity. Nat Commun. 2017 Feb 15;8:14206

2016

Clarke CJ, Berg TJ, Birch J, Ennis D, Mitchell L, Cloix C, Campbell A, Sumpton D, Nixon C, Campbell K, Bridgeman VL, Vermeulen PB, Foo S, Kostaras E, Jones JL, Haywood L, Pulleine E, Yin H, Strathdee D, Sansom O, Blyth K, McNeish I, Zanivan S, Reynolds AR, Norman JC. The Initiator Methionine tRNA Drives Secretion of Type II Collagen from Stromal Fibroblasts to Promote Tumor Growth and Angiogenesis. Curr Biol. 2016 Mar 21;26(6):755-65

Frej AD, Clark J, Le Roy CI, Lilla S, Thomason PA, Otto GP, Churchill G, Insall RH, Claus SP, Hawkins P, Stephens L, Williams RS. The Inositol-3-Phosphate Synthase Biosynthetic Enzyme Has Distinct Catalytic and Metabolic Roles. Mol Cell Biol. 2016 May 2;36(10):1464-79

McGarry DJ, Shchepinova MM, Lilla S, Hartley RC, Olson MF. A Cell-Permeable Biscyclooctyne As a Novel Probe for the Identification of Protein Sulfenic Acids. ACS Chem Biol. 2016 Dec 16;11(12):3300-3304

Group Members

Proteomics lab 2020 125

Head

Sara Zanivan

Senior Scientific Officers

Kelly Hodge
Sergio Lilla

Bioinformatician

Grigorios Koulouras

 

Research

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Seminars

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