دورية أكاديمية
Quantitative proteomics of small numbers of closely-related cells: Selection of the optimal method for a clinical setting.
| العنوان: | Quantitative proteomics of small numbers of closely-related cells: Selection of the optimal method for a clinical setting. |
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| المؤلفون: | van der Pan K; Department of Immunology, Leiden University Medical Center (LUMC), Leiden, Netherlands., Kassem S; Department of Immunology, Leiden University Medical Center (LUMC), Leiden, Netherlands., Khatri I; Department of Immunology, Leiden University Medical Center (LUMC), Leiden, Netherlands.; Leiden Computational Biology Center, LUMC, Leiden, Netherlands., de Ru AH; Center for Proteomics and Metabolomics, LUMC, Leiden, Netherlands., Janssen GMC; Center for Proteomics and Metabolomics, LUMC, Leiden, Netherlands., Tjokrodirijo RTN; Center for Proteomics and Metabolomics, LUMC, Leiden, Netherlands., Al Makindji F; Department of Immunology, Leiden University Medical Center (LUMC), Leiden, Netherlands., Stavrakaki E; Department of Neurosurgery, Erasmus MC, Rotterdam, Netherlands., de Jager AL; Department of Immunology, Leiden University Medical Center (LUMC), Leiden, Netherlands., Naber BAE; Department of Immunology, Leiden University Medical Center (LUMC), Leiden, Netherlands., de Laat IF; Department of Immunology, Leiden University Medical Center (LUMC), Leiden, Netherlands., Louis A; Department of Immunology, Leiden University Medical Center (LUMC), Leiden, Netherlands., van den Bossche WBL; Department of Neurosurgery, Erasmus MC, Rotterdam, Netherlands., Vogelezang LB; Department of Neurosurgery, Erasmus MC, Rotterdam, Netherlands., Balvers RK; Department of Neurosurgery, Erasmus MC, Rotterdam, Netherlands., Lamfers MLM; Department of Neurosurgery, Erasmus MC, Rotterdam, Netherlands., van Veelen PA; Center for Proteomics and Metabolomics, LUMC, Leiden, Netherlands., Orfao A; Translational and Clinical Research Program, Cancer Research Center (IBMCC; University of Salamanca-CSIC), Salamanca, Spain.; Cytometry Service, NUCLEUS, Department of Medicine, University of Salamanca and Institute of Biomedical Research of Salamanca (IBSAL), Salamanca, Spain., van Dongen JJM; Department of Immunology, Leiden University Medical Center (LUMC), Leiden, Netherlands.; Translational and Clinical Research Program, Cancer Research Center (IBMCC; University of Salamanca-CSIC), Salamanca, Spain.; Cytometry Service, NUCLEUS, Department of Medicine, University of Salamanca and Institute of Biomedical Research of Salamanca (IBSAL), Salamanca, Spain., Teodosio C; Department of Immunology, Leiden University Medical Center (LUMC), Leiden, Netherlands.; Translational and Clinical Research Program, Cancer Research Center (IBMCC; University of Salamanca-CSIC), Salamanca, Spain.; Cytometry Service, NUCLEUS, Department of Medicine, University of Salamanca and Institute of Biomedical Research of Salamanca (IBSAL), Salamanca, Spain., Díez P; Department of Immunology, Leiden University Medical Center (LUMC), Leiden, Netherlands.; Translational and Clinical Research Program, Cancer Research Center (IBMCC; University of Salamanca-CSIC), Salamanca, Spain.; Cytometry Service, NUCLEUS, Department of Medicine, University of Salamanca and Institute of Biomedical Research of Salamanca (IBSAL), Salamanca, Spain. |
| المصدر: | Frontiers in medicine [Front Med (Lausanne)] 2022 Sep 27; Vol. 9, pp. 997305. Date of Electronic Publication: 2022 Sep 27 (Print Publication: 2022). |
| نوع المنشور: | Journal Article |
| اللغة: | English |
| بيانات الدورية: | Publisher: Frontiers Media S.A Country of Publication: Switzerland NLM ID: 101648047 Publication Model: eCollection Cited Medium: Print ISSN: 2296-858X (Print) Linking ISSN: 2296858X NLM ISO Abbreviation: Front Med (Lausanne) Subsets: PubMed not MEDLINE |
| أسماء مطبوعة: | Original Publication: Lausanne, Switzerland : Frontiers Media S.A., [2014]- |
| مستخلص: | 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. Competing Interests: Authors JD and AO are chairmen of the EuroFlow scientific foundation, which receives royalties from licensed patents, which are collectively owned by the participants of the EuroFlow foundation, to be exclusively used for the continuation of the EuroFlow collaboration and sustainability of the EuroFlow consortium, originally supported by the European Commission (EU-STREP Project LSHB-CT-2006-018708). Authors JD and AO report an Educational Services Agreement from BD Biosciences (San José, CA) and a Scientific Advisor Agreement with Cytognos; all related fees and honoraria are for the involved university departments at Leiden University Medical Center and University of Salamanca. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. (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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| فهرسة مساهمة: | Keywords: closely-related cells; low cell numbers; macrophage; monocyte; paucicellular clinical samples; proteome characterization |
| تواريخ الأحداث: | Date Created: 20221014 Latest Revision: 20221015 |
| رمز التحديث: | 20221213 |
| مُعرف محوري في PubMed: | PMC9553008 |
| DOI: | 10.3389/fmed.2022.997305 |
| PMID: | 36237552 |
| قاعدة البيانات: | MEDLINE |
Full Text Finder | تدمد: | 2296-858X |
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| DOI: | 10.3389/fmed.2022.997305 |