The Institute of Cancer Research, London
Research
We are interested in solving questions about the biology underlying health and disease by studying molecular processes and pathways. To do this we use a range of techniques including mass spectrometry, biochemistry, molecular biology and informatics, to study protein function, proteome composition and organisation.
The Proteomic mass spectrometry team complements the research programmes of the Sanger Institute to further understanding of the relationship between the genome and the proteome (expressed protein complement). Through our research and collaborations we explore protein-protein interactions, cell signalling and protein expression in a range of human, pathogen and model organisms.
Our research portfolio encompasses all levels of proteome complexity: from whole organism characterisation to subcellular organelles, from protein complexes to post-translation modifications.
Publications
1: Liess AKL, Kucerova A, Schweimer K, Yu L, Roumeliotis TI, Diebold M, Dybkov O,
Sotriffer C, Urlaub H, Choudhary JS, Mansfeld J, Lorenz S. Autoinhibition
Mechanism of the Ubiquitin-Conjugating Enzyme UBE2S by Autoubiquitination.
Structure. 2019 Aug 6;27(8):1195-1210.e7. doi: 10.1016/j.str.2019.05.008. Epub
2019 Jun 20. PubMed PMID: 31230944.
2: Gentzel M, Pardo M, Subramaniam S, Stewart AF, Choudhary JS. Proteomic
navigation using proximity-labeling. Methods. 2019 Jul 15;164-165:67-72. doi:
10.1016/j.ymeth.2019.03.028. Epub 2019 Apr 4. PubMed PMID: 30953756.
3: Hopkins EGD, Roumeliotis TI, Mullineaux-Sanders C, Choudhary JS, Frankel G.
Intestinal Epithelial Cells and the Microbiome Undergo Swift Reprogramming at the
Inception of Colonic Citrobacter rodentium Infection. MBio. 2019 Apr 2;10(2).
pii: e00062-19. doi: 10.1128/mBio.00062-19. PubMed PMID: 30940698; PubMed Central
PMCID: PMC6445932.
4: Roumeliotis TI, Weisser H, Choudhary JS. Evaluation of a Dual Isolation Width
Acquisition Method for Isobaric Labeling Ratio Decompression. J Proteome Res.
2019 Mar 1;18(3):1433-1440. doi: 10.1021/acs.jproteome.8b00870. Epub 2019 Jan 3.
PubMed PMID: 30576155; PubMed Central PMCID: PMC6399672.
5: Bakos G, Yu L, Gak IA, Roumeliotis TI, Liakopoulos D, Choudhary JS, Mansfeld
J. An E2-ubiquitin thioester-driven approach to identify substrates modified with
ubiquitin and ubiquitin-like molecules. Nat Commun. 2018 Nov 14;9(1):4776. doi:
10.1038/s41467-018-07251-5. PubMed PMID: 30429481; PubMed Central PMCID:
PMC6235928.
6: Berger CN, Crepin VF, Roumeliotis TI, Wright JC, Serafini N, Pevsner-Fischer
M, Yu L, Elinav E, Di Santo JP, Choudhary JS, Frankel G. The Citrobacter
rodentium type III secretion system effector EspO affects mucosal damage repair
and antimicrobial responses. PLoS Pathog. 2018 Oct 26;14(10):e1007406. doi:
10.1371/journal.ppat.1007406. eCollection 2018 Oct. PubMed PMID: 30365535; PubMed
Central PMCID: PMC6221368.
7: Schlaffner CN, Pirklbauer GJ, Bender A, Steen JAJ, Choudhary JS. A Fast and
Quantitative Method for Post-translational Modification and Variant Enabled
Mapping of Peptides to Genomes. J Vis Exp. 2018 May 22;(135). doi: 10.3791/57633.
PubMed PMID: 29889196; PubMed Central PMCID: PMC6101353.
8: Steinberg J, Brooks RA, Southam L, Bhatnagar S, Roumeliotis TI, Hatzikotoulas
K, Zengini E, Wilkinson JM, Choudhary JS, McCaskie AW, Zeggini E. Widespread
epigenomic, transcriptomic and proteomic differences between hip osteophytic and
articular chondrocytes in osteoarthritis. Rheumatology (Oxford). 2018 Aug
1;57(8):1481-1489. doi: 10.1093/rheumatology/key101. PubMed PMID: 29741735;
PubMed Central PMCID: PMC6055583.
9: Gozdecka M, Meduri E, Mazan M, Tzelepis K, Dudek M, Knights AJ, Pardo M, Yu L,
Choudhary JS, Metzakopian E, Iyer V, Yun H, Park N, Varela I, Bautista R, Collord
G, Dovey O, Garyfallos DA, De Braekeleer E, Kondo S, Cooper J, Göttgens B,
Bullinger L, Northcott PA, Adams D, Vassiliou GS, Huntly BJP. UTX-mediated
enhancer and chromatin remodeling suppresses myeloid leukemogenesis through
noncatalytic inverse regulation of ETS and GATA programs. Nat Genet. 2018
Jun;50(6):883-894. doi: 10.1038/s41588-018-0114-z. Epub 2018 May 7. PubMed PMID:
29736013; PubMed Central PMCID: PMC6029661.
10: Mayer L, Jasztal M, Pardo M, Aguera de Haro S, Collins J, Bariana TK,
Smethurst PA, Grassi L, Petersen R, Nurden P, Favier R, Yu L, Meacham S, Astle
WJ, Choudhary J, Yue WW, Ouwehand WH, Guerrero JA. Nbeal2 interacts with Dock7,
Sec16a, and Vac14. Blood. 2018 Mar 1;131(9):1000-1011. doi:
10.1182/blood-2017-08-800359. Epub 2017 Nov 29. PubMed PMID: 29187380; PubMed
Central PMCID: PMC5877783.
11: Gialitakis M, Tolaini M, Li Y, Pardo M, Yu L, Toribio A, Choudhary JS, Niakan
K, Papayannopoulos V, Stockinger B. Activation of the Aryl Hydrocarbon Receptor
Interferes with Early Embryonic Development. Stem Cell Reports. 2017 Nov
14;9(5):1377-1386. doi: 10.1016/j.stemcr.2017.09.025. Epub 2017 Oct 26. PubMed
PMID: 29107595; PubMed Central PMCID: PMC5831049.
12: Berger CN, Crepin VF, Roumeliotis TI, Wright JC, Carson D, Pevsner-Fischer M,
Furniss RCD, Dougan G, Dori-Bachash M, Yu L, Clements A, Collins JW, Elinav E,
Larrouy-Maumus GJ, Choudhary JS, Frankel G. Citrobacter rodentium Subverts ATP
Flux and Cholesterol Homeostasis in Intestinal Epithelial Cells In Vivo. Cell
Metab. 2017 Nov 7;26(5):738-752.e6. doi: 10.1016/j.cmet.2017.09.003. Epub 2017
Oct 5. PubMed PMID: 28988824; PubMed Central PMCID: PMC5695859.
13: Roumeliotis TI, Williams SP, Gonçalves E, Alsinet C, Del Castillo
Velasco-Herrera M, Aben N, Ghavidel FZ, Michaut M, Schubert M, Price S, Wright
JC, Yu L, Yang M, Dienstmann R, Guinney J, Beltrao P, Brazma A, Pardo M, Stegle
O, Adams DJ, Wessels L, Saez-Rodriguez J, McDermott U, Choudhary JS. Genomic
Determinants of Protein Abundance Variation in Colorectal Cancer Cells. Cell Rep.
2017 Aug 29;20(9):2201-2214. doi: 10.1016/j.celrep.2017.08.010. PubMed PMID:
28854368; PubMed Central PMCID: PMC5583477.
