Improvement of untargeted proteomics workflow for surfaceome profiling and its evaluation through the implementation of quality controls: Application to multiple myeloma
CIRM - Centre Interdisciplinaire de Recherche sur le Médicament - ULiège [BE]
Disciplines :
Pharmacy, pharmacology & toxicology
Author, co-author :
Gou, Marie-Jia ; Université de Liège - ULiège > Unités de recherche interfacultaires > Centre Interdisciplinaire de Recherche sur le Médicament (CIRM)
Charpentier, Julien ; Université de Liège - ULiège > Département de pharmacie > Pharmacie galénique
Cobraiville, Gaël ; Centre Hospitalier Universitaire de Liège - CHU > > Service de rhumatologie
Crommen, Jacques ; Université de Liège - ULiège > Département de pharmacie
Caers, Jo ; Centre Hospitalier Universitaire de Liège - CHU > > Service d'hématologie clinique
Fillet, Marianne ; Université de Liège - ULiège > Département de pharmacie > Analyse des médicaments
Language :
English
Title :
Improvement of untargeted proteomics workflow for surfaceome profiling and its evaluation through the implementation of quality controls: Application to multiple myeloma
Ackley, J., Ochoa, M.A., Ghoshal, D., Roy, K., Lonial, S., Boise, L.H., Keeping myeloma in check: the past, present and future of immunotherapy in multiple myeloma. Cancers (Basel) 13 (2021), 1–27, 10.3390/cancers13194787.
Laubach, J.P., Paba Prada, C.E., Richardson, P.G., Longo, D.L., Daratumumab, Elotuzumab, and the development of therapeutic monoclonal antibodies in multiple myeloma. Clin. Pharmacol. Ther. 101 (2017), 81–88, 10.1002/cpt.550.
Giuliani, N., Accardi, F., Marchica, V., Dalla Palma, B., Storti, P., Toscani, D., Vicario, E., Malavasi, F., Novel targets for the treatment of relapsing multiple myeloma. Expert Rev. Hematol. 12 (2019), 481–496, 10.1080/17474086.2019.1624158.
Soekojo, C.Y., Ooi, M., de Mel, S., Chng, W.J., Immunotherapy in multiple myeloma. Cells 9 (2020), 1–38, 10.3390/cells9030601.
Van De Donk, N.W.C.J., Usmani, S.Z., CD38 antibodies in multiple myeloma: mechanisms of action and modes of resistance. Front. Immunol., 9, 2018, 10.3389/fimmu.2018.02134.
Carrillo-Rodriguez, P., Selheim, F., Hernandez-Valladares, M., Mass spectrometry-based proteomics workflows in cancer research: the relevance of choosing the right steps. Cancers (Basel), 15, 2023, 555, 10.3390/cancers15020555.
Macklin, A., Khan, S., Kislinger, T., Recent advances in mass spectrometry based clinical proteomics: applications to cancer research. Clin. Proteonomics, 17, 2020, 10.1186/s12014-020-09283-w.
Ding, Z., Wang, N., Ji, N., Chen, Z.S., Proteomics technologies for cancer liquid biopsies. Mol. Cancer, 21, 2022, 10.1186/s12943-022-01526-8.
Nys, G., Cobraiville, G., Fillet, M., Multidimensional performance assessment of micro pillar array column chromatography combined to ion mobility-mass spectrometry for proteome research. Anal. Chim. Acta 1086 (2019), 1–13, 10.1016/j.aca.2019.08.068.
Nys, G., Nix, C., Cobraiville, G., Servais, A.C., Fillet, M., Enhancing protein discoverability by data independent acquisition assisted by ion mobility mass spectrometry. Talanta, 213, 2020, 10.1016/j.talanta.2020.120812.
Nix, C., Cobraiville, G., Gou, M.J., Fillet, M., Potential of single pulse and multiplexed drift-tube ion mobility spectrometry coupled to micropillar array column for proteomics studies. Int. J. Mol. Sci., 23, 2022, 10.3390/ijms23147497.
Pauwels, J., Fijałkowska, D., Eyckerman, S., Gevaert, K., Mass spectrometry and the cellular surfaceome. Mass Spectrom. Rev. 41 (2022), 804–841, 10.1002/mas.21690.
Li, Y., Qin, H., Ye, M., An overview on enrichment methods for cell surface proteome profiling. J. Separ. Sci. 43 (2020), 292–312, 10.1002/jssc.201900700.
Kuhlmann, L., Cummins, E., Samudio, I., Kislinger, T., Cell-surface proteomics for the identification of novel therapeutic targets in cancer. Expert Rev. Proteomics 15 (2018), 259–275, 10.1080/14789450.2018.1429924.
Rose, M., Cardon, T., Aboulouard, S., Hajjaji, N., Kobeissy, F., Duhamel, M., Fournier, I., Salzet, M., Surfaceome proteomic of glioblastoma revealed potential targets for immunotherapy. Front. Immunol., 12, 2021, 10.3389/fimmu.2021.746168.
Li, Y., Wang, Y., Mao, J., Yao, Y., Wang, K., Qiao, Q., Fang, Z., Ye, M., Sensitive profiling of cell surface proteome by using an optimized biotinylation method. J. Proteonomics 196 (2019), 33–41, 10.1016/j.jprot.2019.01.015.
Langó, T., Kuffa, K., Tóth, G., Turiák, L., Drahos, L., Tusnády, G.E., Comprehensive discovery of the accessible primary amino group-containing segments from cell surface proteins by fine-tuning a high-throughput biotinylation method. Int. J. Mol. Sci., 24, 2023, 10.3390/ijms24010273.
Ferguson, I.D., Patiño-Escobar, B., Tuomivaara, S.T., Lin, Y.H.T., Nix, M.A., Leung, K.K., Kasap, C., Ramos, E., Nieves Vasquez, W., Talbot, A., Hale, M., Naik, A., Kishishita, A., Choudhry, P., Lopez-Girona, A., Miao, W., Wong, S.W., Wolf, J.L., Martin, T.G., Shah, N., Vandenberg, S., Prakash, S., Besse, L., Driessen, C., Posey, A.D., Mullins, R.D., Eyquem, J., Wells, J.A., Wiita, A.P., The surfaceome of multiple myeloma cells suggests potential immunotherapeutic strategies and protein markers of drug resistance. Nat. Commun., 13, 2022, 10.1038/s41467-022-31810-6.
Oldham, R.A.A., Faber, M.L., Keppel, T.R., Buchberger, A.R., Waas, M., Hari, P., Gundry, R.L., Medin, J.A., Discovery and validation of surface N -glycoproteins in MM cell lines and patient samples uncovers immunotherapy targets. J. Immunother. Cancer, 8, 2020, 10.1136/jitc-2020-000915.
Anderson, G.S.F., Ballester-Beltran, J., Giotopoulos, G., Guerrero, J.A., Surget, S., Williamson, J.C., So, T., Bloxham, D., Aubareda, A., Asby, R., Walker, I., Jenkinson, L., Soilleux, E.J., Roy, J.P., Teod Osio, A., Ficken, C., Officer-Jones, L., Nasser, S., Skerget, S., Keats, J.J., Greaves, P., Tai, Y.-T., Anderson, K.C., Macfarlane, M., Thaventhiran, J.E., Huntly, B.J.P., Lehner, P.J., Chapman, M.A., Unbiased cell surface proteomics identifies SEMA4A as an effective immunotherapy target for myeloma. Blood 139 (2022), 2471–2482 http://ashpublications.org/blood/article-pdf/139/16/2471/1892596/bloodbld2021015161.pdf.
Lejeune, M., Kose, M.C., Jassin, M., Gou, M.-J., Herbet, A., Duray, E., Cobraiville, G., Foguenne, J., Boquet, D., Gothot, A., Beguin, Y., Fillet, M., Caers, J., Integrative analysis of proteomics and transcriptomics reveals Endothelin Receptor B as novel single target and identifies new combinatorial targets for multiple myeloma. Hemasphere, 7, 2023, 10.1097/HS9.0000000000000901.
Gou, M.J., Kose, M.C., Crommen, J., Nix, C., Cobraiville, G., Caers, J., Fillet, M., Contribution of capillary zone electrophoresis hyphenated with drift tube ion mobility mass spectrometry as a complementary tool to microfluidic reversed phase liquid chromatography for antigen discovery. Int. J. Mol. Sci., 23, 2022, 10.3390/ijms232113350.
Kyte, J., Doolittle, R.F., A simple method for displaying the hydropathic character of a protein. J. Mol. Biol. 157 (1982), 105–132, 10.1016/0022-2836(82)90515-0.
Cho, K.J., Roche, P.A., Monitoring MHC-II endocytosis and recycling using cell-surface protein biotinylation-based assays. Methods in Molecular Biology, 2019, Humana Press Inc, 271–277, 10.1007/978-1-4939-9450-2_19.
Li, M., Peng, F., Wang, G., Liang, X., Shao, M., Chen, Z., Chen, Y., Coupling of cell surface biotinylation and SILAC-based quantitative proteomics identified myoferlin as a potential therapeutic target for nasopharyngeal carcinoma metastasis. Front. Cell Dev. Biol., 9, 2021, 10.3389/fcell.2021.621810.
McNulty, J., Krishnamoorthy, V., Amoroso, D., Moser, M., Tris(3-hydroxypropyl)phosphine (THPP): a mild, air-stable reagent for the rapid, reductive cleavage of small-molecule disulfides. Bioorg. Med. Chem. Lett. 25 (2015), 4114–4117, 10.1016/j.bmcl.2015.08.027.
Siepen, J.A., Keevil, E.J., Knight, D., Hubbard, S.J., Prediction of missed cleavage sites in tryptic peptides aids protein identification in proteomics. J. Proteome Res. 6 (2007), 399–408, 10.1021/pr060507u.
Glatter, T., Ludwig, C., Ahrné, E., Aebersold, R., Heck, A.J.R., Schmidt, A., Large-scale quantitative assessment of different in-solution protein digestion protocols reveals superior cleavage efficiency of tandem Lys-C/trypsin proteolysis over trypsin digestion. J. Proteome Res. 11 (2012), 5145–5156, 10.1021/pr300273g.
Gussakovsky, D., Anderson, G., Spicer, V., Krokhin, O.V., Peptide separation selectivity in proteomics LC-MS experiments: comparison of formic and mixed formic/heptafluorobutyric acids ion-pairing modifiers. J. Separ. Sci. 43 (2020), 3830–3839, 10.1002/jssc.202000578.
Varnavides, G., Madern, M., Anrather, D., Hartl, N., Reiter, W., Hartl, M., In Search of a universal method: a comparative survey of bottom-up proteomics sample preparation methods. J. Proteome Res. 21 (2022), 2397–2411, 10.1021/acs.jproteome.2c00265.
Bittremieux, W., Tabb, D.L., Impens, F., Staes, A., Timmerman, E., Martens, L., Laukens, K., Quality control in mass spectrometry-based proteomics. Mass Spectrom. Rev. 37 (2018), 697–711, 10.1002/mas.21544.
Nakayasu, E.S., Gritsenko, M., Piehowski, P.D., Gao, Y., Orton, D.J., Schepmoes, A.A., Fillmore, T.L., Frohnert, B.I., Rewers, M., Krischer, J.P., Ansong, C., Suchy-Dicey, A.M., Evans-Molina, C., Qian, W.J., Webb-Robertson, B.J.M., Metz, T.O., Tutorial: best practices and considerations for mass-spectrometry-based protein biomarker discovery and validation. Nat. Protoc. 16 (2021), 3737–3760, 10.1038/s41596-021-00566-6.
Bittremieux, W., Valkenborg, D., Martens, L., Laukens, K., Computational quality control tools for mass spectrometry proteomics. Proteomics, 17, 2017, 10.1002/pmic.201600159.
Human Protein Atlas https://www.proteinatlas.org/(access date: 10/01/2023).
