Automation of single‐cell proteomic sample preparation

Alexovič, Michal; Sabó, Ján; Longuespée, Rémi

doi:10.1002/pmic.202100198

Cited by 17 publications

(15 citation statements)

References 43 publications

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“…In such context, proteins with significantly altered abundancies between healthy and disease samples, can be used as biomarker candidates helping for diagnosis, prognosis, monitoring and eventually therapy in personalized medicine [1–3]. Recent advances in protein sample preparation and analysis provided powerful platforms that enabled deep proteome coverages and selection of disease‐related biomarker candidates [4–7].…”

Section: Introductionmentioning

confidence: 99%

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Human peripheral blood mononuclear cells: A review of recent proteomic applications

et al. 2022

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Human peripheral blood mononuclear cells (PBMCs) represent a sentinel blood sample which reacts to different pathophysiological stimuli in the form of immunological responses/immunophenotypic changes. The study of molecular content of PBMCs can provide better understanding of immune processes giving the possibility of monitoring the health conditions of the host organism. Proteomic analysis of PBMCs can achieve mentioned goal as important immune-related biomarkers are easily accessible for analysis. PBMCs have been gaining attention in different research areas including preclinical or clinical investigations. In this review, recent applications of proteomic analysis of PBMCs are described and discussed. Approaches are divided based on different proteomic workflows such as in-gel, in-solution and on-filter modes. The effect of various diseases such as autoimmune, cancer, neurodegenerative, viral, metabolic, and various immune stimulations such as radiation, vaccine, corticosteroids over PBMCs proteome, are described with emphasis on promising protein biomarker candidates.

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Section: Introductionmentioning

confidence: 99%

“…powerful platforms that enabled deep proteome coverages and selection of disease-related biomarker candidates [4][5][6][7].…”

mentioning

confidence: 99%

Human peripheral blood mononuclear cells: A review of recent proteomic applications

et al. 2022

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“…For instance, serotonin (MW 176), expressed during the cleavage stage, is involved in the determination of the left-right axis [13]; retinoic acid (MW 300) and adrenaline (MW 183), expressed from gastrula to neurula, are required for posteriorization [14,15]; and γ-aminobutyric acid (GABA) (MW 103), expressed after neurula, has a role in embryonic elongation [16]. Research on metabolic activities via metabolomics in the embryo holds great potential to raise our understanding of the developmental processes that control cell-type specification by combining with the other omics data obtained by previous studies [17][18][19]. It is also significant to find dorsoventral-specific secreted molecules, generally contained in the supernatant of cultured cells, and small molecules that determine cell-autonomous differentiation inside cells.…”

Section: Introductionmentioning

confidence: 99%

Comparative Metabolomics of Small Molecules Specifically Expressed in the Dorsal or Ventral Marginal Zones in Vertebrate Gastrula

et al. 2022

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Many previous studies have reported the various proteins specifically secreted as inducers in the dorsal or ventral regions in vertebrate gastrula. However, little is known about the effect on cell fate of small molecules below 1000 Da. We therefore tried to identify small molecules specifically expressed in the dorsal marginal zone (DMZ) or ventral marginal zone (VMZ) in vertebrate gastrula. Small intracellular and secreted molecules were detected using explants and supernatant samples. Hydrophilic metabolites were analyzed by capillary ion chromatography–mass spectrometry and liquid chromatography–mass spectrometry, and lipids were analyzed by supercritical fluid chromatography–tandem mass spectrometry. In total, 190 hydrophilic metabolites and 396 lipids were identified. The DMZ was found to have high amounts of glycolysis- and glutathione metabolism-related metabolites in explants, and the VMZ was richer in purine metabolism-related metabolites. We also discovered some hydrophilic metabolites and lipids differentially contained in the DMZ or VMZ. Our research would contribute to a deeper understanding of the cellular physiology that regulates early embryogenesis.

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“…Research on biomarkers for early cancer diagnosis is growing [6]. Because microRNAs (miRNAs) are small and well preserved in formalin, researchers are searching for miRNA biomarkers and the corresponding target genes indicative of transitions from SH/CH-nonA to EC over a long-term follow-up, miRNAs are evolutionarily conserved, non-coding RNAs that are usually between 21 and 25 nucleotides in length; they function by binding to the 3 untranslated regions of mRNAs, where they repress protein translation or promote mRNA degradation [7].…”

Section: Introductionmentioning

confidence: 99%

MicroRNAs as Predictors of Future Uterine Malignancy in Endometrial Hyperplasia without Atypia

Lin

Yang

et al. 2022

JPM

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The histological criteria for classifying endometrial hyperplasia (EH) are based on architectural crowding and nuclear atypia; however, diagnostic agreement among pathologists is poor. We investigated molecular biomarkers of endometrial cancer (EC) risk in women with simple hyperplasia or complex hyperplasia without atypia (SH/CH-nonA). Forty-nine patients with EC preceded by SH/CH-nonA were identified, of which 23 were excluded (15 with complex atypical hyperplasia (CAH), six not consenting, one with a diagnosis <6 months prior, and one lost to follow-up). The EH tissues of these patients were compared with those of patients with SH/CH-nonA that did not progress to EC (control) through microRNA (miRNA) array analysis, and the results were verified in an expanded cohort through reverse transcription-quantitative polymerase chain reaction (RT-qPCR). MiRNA arrays analyses revealed 20 miRNAs that differed significantly (p < 0.05, fold change >4) between the control (n = 12) and case (n = 6) patients. Multiplex RT-qPCR for the 20 miRNAs in the expanded cohort (94 control and 25 case patients) led to the validation of miR-30a-3p (p = 0.0009), miR-141 (p < 0.0001), miR-200a (p < 0.0001), and miR-200b (p < 0.0001) as relevant biomarkers, among which miR-141, miR-200a, and miR-200b regulate the expression of phosphatase and tensin homolog (PTEN). For the prediction of EC, the area under the curve for miR-30a-3p, miR-141, miR-200a, and miR-200b was 0.623, 0.754, 0.783, and 0.704, respectively. The percentage of complete PTEN loss was significantly higher in the case group than in the control group (24% vs. 0%, p < 0.001, Fisher’s exact test). A combination of complete PTEN loss and miR-200a provided optimal prediction performance (sensitivity = 0.760; specificity = 1.000; positive predictive value = 1.000; negative predictive value = 0.937; accuracy = 0.947). MiR-30a-3p, miR-141, miR-200a, miR-200b, and complete PTEN loss may be useful tissue biomarkers for predicting EC risk among patients with SH/CH-nonA.

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Automation of single‐cell proteomic sample preparation

Cited by 17 publications

References 43 publications

Human peripheral blood mononuclear cells: A review of recent proteomic applications

Human peripheral blood mononuclear cells: A review of recent proteomic applications

Comparative Metabolomics of Small Molecules Specifically Expressed in the Dorsal or Ventral Marginal Zones in Vertebrate Gastrula

MicroRNAs as Predictors of Future Uterine Malignancy in Endometrial Hyperplasia without Atypia

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