Abstract
Systematic exploration of the dynamic human plasma proteome enables the discovery of novel protein biomarkers. Using state-of-the-art technologies holds the promise to facilitate a better diagnosis and risk prediction of diseases. Cardiovascular disease (CVD) pathophysiology is characterized for unbalancing of processes such as vascular inflammation, endothelial dysfunction, or lipid profiles among others. Such processes have a direct impact on the dynamic and complex composition of blood and hence the plasma proteome. Therefore, the study of the plasma proteome comprises an excellent exploratory source of biomarker research particularly for CVD. We describe the protocol for performing the discovery of protein biomarker candidates using the suspension bead array technology. The process does not require depletion steps to remove abundant proteins and consumes only a few microliters of sample from the body fluid of interest. The approach is scalable to measure many analytes as well as large numbers of samples. Moreover, we describe a bead-assisted antibody-labeling process that helps to develop quantitative assays for validation purposes and facilitate the translation of the identified candidates into clinical studies.
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References
Lyngbakken MN, Myhre PL, Røsjø H, Omland T (2019) Novel biomarkers of cardiovascular disease: applications in clinical practice. Crit Rev Clin Lab Sci 56(1):33–60. https://doi.org/10.1080/10408363.2018.1525335
Issaq HJ, Xiao Z, Ventra TD (2007) Serum and plasma proteomics. Chem Rev 107(8):3601–3620. https://doi.org/10.1021/cr068287r
Uhlén M, Karlsson MJ, Hober A, Svensson AS, Scheffel J, Kotol D, Zhong W, Tebani A, Strandberg L, Edfors F, Sjöstedt E, Mulder J, Mardinoglu A, Berling A, Ekblad S, Dannemeyer M, Kanje S, Rockberg J, Lundqvist M, Malm M, Volk AL, Nilsson P, Månberg A, Dodig-Crnkovic T, Pin E, Zwahlen M, Oksvold P, von Feilitzen K, Häussler RS, Hong MG, Lindskog C, Ponten F, Katona B, Vuu J, Lindström E, Nielsen J, Robinson J, Ayoglu B, Mahdessian D, Sullivan D, Thul P, Danielsson F, Stadler C, Lundberg E, Bergström G, Gummesson A, Voldborg BG, Tegel H, Hober S, Forsström B, Schwenk JM, Fagerberg L, Sivertsson Å (2019) The human secretome. Sci Signal 12(609):eaaz0274. https://doi.org/10.1126/scisignal.aaz0274
Ignjatovic V, Geyer PE, Palaniappan KK, Chaaban JE, Omenn GS, Baker MS, Deutsch EW, Schwenk JM (2019) Mass spectrometry-based plasma proteomics: considerations from sample collection to achieving translational data. J Proteome Res 18(12):4085–4097. https://doi.org/10.1021/acs.jproteome.9b00503
Hayashida K, Bartlett AH, Chen Y, Park PW (2010) Molecular and cellular mechanisms of ectodomain shedding. Anat Rec 293(6):925–937. https://doi.org/10.1002/ar.20757
Bowen RA, Remaley AT (2014) Interferences from blood collection tube components on clinical chemistry assays. Biochem Med 24(1):31–44. https://doi.org/10.11613/BM.2014.006
Byström S, Eklund M, Hong MG, Fredolini C, Eriksson M, Czene K, Hall P, Schwenk JM, Gabrielson M (2018) Affinity proteomic profiling of plasma for proteins associated to area-based mammographic breast density. Breast Cancer Res 20(1):14. https://doi.org/10.1186/s13058-018-0940-z
Lourido L, Ayoglu B, Fernández-Tajes J, Oreiro N, Henjes F, Hellström C, Schwenk JM, Ruiz-Romero C, Nilsson P, Blanco FJ (2017) Discovery of circulating proteins associated to knee radiographic osteoarthritis. Sci Rep 7(1):137. https://doi.org/10.1038/s41598-017-00195-8
Drobin K, Marczyk M, Halle M, Danielsson D, Papiez A, Sangsuwan T, Bendes A, Hong MG, Qundos U, Harms-Ringdahl M, Wersäll P, Polanska J, Schwenk JM, Haghdoost S (2020) Molecular profiling for predictors of radiosensitivity in patients with breast or head-and-neck cancer. Cancers 12(3):753. https://doi.org/10.3390/cancers12030753
Häggmark A, Hamsten C, Wiklundh E, Lindskog C, Mattsson C, Andersson E, Lundberg IE, Grönlund H, Schwenk JM, Eklund A, Grunewald J, Nilsson P (2015) Proteomic profiling reveals autoimmune targets in sarcoidosis. Am J Respir Crit Care Med 191(5):574–583. https://doi.org/10.1164/rccm.201407-1341OC
Bruzelius M, Iglesias MJ, Hong MG, Sanchez-Rivera L, Gyorgy B, Souto JC, Frånberg M, Fredolini C, Strawbridge RJ, Holmström M, Hamsten A, Uhlén M, Silveira A, Soria JM, Smadja DM, Butler LM, Schwenk JM, Morange PE, Trégouët DA, Odeberg J (2016) PDGFB, a new candidate plasma biomarker for venous thromboembolism: results from the VEREMA affinity proteomics study. Blood 128(23):e59–e66. https://doi.org/10.1182/blood-2016-05-711846
Matic LP, Jesus Iglesias M, Vesterlund M, Lengquist M, Hong MG, Saieed S, Sanchez-Rivera L, Berg M, Razuvaev A, Kronqvist M, Lund K, Caidahl K, Gillgren P, Pontén F, Uhlén M, Schwenk JM, Hansson GK, Paulsson-Berne G, Fagman E, Roy J, Hultgren R, Bergström G, Lehtiö J, Odeberg J, Hedin U (2018) Novel multiomics profiling of human carotid atherosclerotic plaques and plasma reveals biliverdin reductase B as a marker of intraplaque hemorrhage. JACC Basic Transl Sci 3(4):464–480. https://doi.org/10.1016/j.jacbts.2018.04.001
Drobin K, Nilsson P, Schwenk JM (2013) Highly multiplexed antibody suspension bead arrays for plasma protein profiling. Methods Mol Biol 1023:137–145. https://doi.org/10.1007/978-1-4614-7209-4_8
Schwenk JM, Nilsson P (2011) Assessment of antibody specificity using suspension bead arrays. Methods Mol Biol 785:183–189. https://doi.org/10.1007/978-1-61779-286-1_12
Fredolini C, Byström S, Sanchez-Rivera L, Ioannou M, Tamburro D, Pontén F, Branca RM, Nilsson P, Lehtiö J, Schwenk JM (2019) Systematic assessment of antibody selectivity in plasma based on a resource of enrichment profiles. Sci Rep 9(1):8324. https://doi.org/10.1038/s41598-019-43552-5
Edfors F, Hober A, Linderbäck K, Maddalo G, Azimi A, Sivertsson Å, Tegel H, Hober S, Szigyarto CA, Fagerberg L, von Feilitzen K, Oksvold P, Lindskog C, Forsström B, Uhlen M (2018) Enhanced validation of antibodies for research applications. Nat Commun 9(1):4130. https://doi.org/10.1038/s41467-018-06642-y
Häussler RS, Bendes A, Iglesias M, Sanchez-Rivera L, Dodig-Crnković T, Byström S, Fredolini C, Birgersson E, Dale M, Edfors F, Fagerberg L, Rockberg J, Tegel H, Uhlén M, Qundos U, Schwenk JM (2019) Systematic development of sandwich immunoassays for the plasma secretome. Proteomics 19(15):e1900008. https://doi.org/10.1002/pmic.201900008
Dezfouli M, Vickovic S, Iglesias MJ, Nilsson P, Schwenk JM, Ahmadian A (2014) Magnetic bead assisted labeling of antibodies at nanogram scale. Proteomics 14(1):14–18. https://doi.org/10.1002/pmic.201300283
Acknowledgments
We like to thank past and current plasma profiling facility members and Dr. Mahya Dezfouli for all the contributions to developing and setting up the protocols here described. The Affinity profiling and Human Protein Atlas groups are recognized for their contribution to the affinity reagents and laboratory instrumentation. The following organizations are acknowledged for financial support to our research: Stockholm County Council, Vinnova—Swedish Innovation Agency, KCAP founded by Erling-Persson Family Foundation, Swedish Heart Lung Foundation, Science for Life Laboratory, and Knut and Alice Wallenberg Foundation.
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Iglesias, M.J., Schwenk, J.M., Odeberg, J. (2021). Affinity Proteomics Assays for Cardiovascular and Atherosclerotic Disease Biomarkers. In: Barderas, R., LaBaer, J., Srivastava, S. (eds) Protein Microarrays for Disease Analysis. Methods in Molecular Biology, vol 2344. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1562-1_12
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DOI: https://doi.org/10.1007/978-1-0716-1562-1_12
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