Quantitative proteomics of small numbers of closely-related cells: Selection of the optimal method for a clinical setting

Kyra van der Pan, Sara Kassem, Indu Khatri, Arnoud H. de Ru, George M.C. Janssen, Rayman T.N. Tjokrodirijo, Fadi al Makindji, Eftychia Stavrakaki, Anniek L. de Jager, Brigitta A.E. Naber, Inge F. de Laat, Alesha Louis, Wouter B.L. van den Bossche, Lisette B. Vogelezang, Rutger K. Balvers, Martine L.M. Lamfers, Peter A. van Veelen, Alberto Orfao, Jacques J.M. van Dongen*, Cristina TeodosioPaula Díez

*Corresponding author for this work

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Abstract

Mass spectrometry (MS)-based proteomics profiling has undoubtedly increased the knowledge about cellular processes and functions. However, its applicability for paucicellular sample analyses is currently limited. Although new approaches have been developed for single-cell studies, most of them have not (yet) been standardized and/or require highly specific (often home-built) devices, thereby limiting their broad implementation, particularly in non-specialized settings. To select an optimal MS-oriented proteomics approach applicable in translational research and clinical settings, we assessed 10 different sample preparation procedures in paucicellular samples of closely-related cell types. Particularly, five cell lysis protocols using different chemistries and mechanical forces were combined with two sample clean-up techniques (C18 filter- and SP3-based), followed by tandem mass tag (TMT)-based protein quantification. The evaluation was structured in three phases: first, cell lines from hematopoietic (THP-1) and non-hematopoietic (HT-29) origins were used to test the approaches showing the combination of a urea-based lysis buffer with the SP3 bead-based clean-up system as the best performer. Parameters such as reproducibility, accessibility, spatial distribution, ease of use, processing time and cost were considered. In the second phase, the performance of the method was tested on maturation-related cell populations: three different monocyte subsets from peripheral blood and, for the first time, macrophages/microglia (MAC) from glioblastoma samples, together with T cells from both tissues. The analysis of 50,000 cells down to only 2,500 cells revealed different protein expression profiles associated with the distinct cell populations. Accordingly, a closer relationship was observed between non-classical monocytes and MAC, with the latter showing the co-expression of M1 and M2 macrophage markers, although pro-tumoral and anti-inflammatory proteins were more represented. In the third phase, the results were validated by high-end spectral flow cytometry on paired monocyte/MAC samples to further determine the sensitivity of the MS approach selected. Finally, the feasibility of the method was proven in 194 additional samples corresponding to 38 different cell types, including cells from different tissue origins, cellular lineages, maturation stages and stimuli. In summary, we selected a reproducible, easy-to-implement sample preparation method for MS-based proteomic characterization of paucicellular samples, also applicable in the setting of functionally closely-related cell populations.

Original languageEnglish
Article number997305
Number of pages20
JournalFrontiers in Medicine
Volume9
DOIs
Publication statusPublished - 27 Sep 2022

Bibliographical note

Funding Information:
The presented work was funded by the European Research Council under the European Union's Horizon 2020 Research and Innovation Programme with an ERC Advanced Grant (ERC-2015-AdG 695655, TiMaScan).

Publisher Copyright:
Copyright © 2022 van der Pan, Kassem, Khatri, de Ru, Janssen, Tjokrodirijo, al Makindji, Stavrakaki, de Jager, Naber, de Laat, Louis, van den Bossche, Vogelezang, Balvers, Lamfers, van Veelen, Orfao, van Dongen, Teodosio and Díez.

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