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To overcome the limitations of traditional bulk proteomics analysis, Creative Biolabs offers single cell proteomics analysis services. We offer single cell tumor signaling profiling service to discover the functional cell phenotype at the single cell level, which enables us to have a deeper understanding of the biological activities and heterogeneity of tumor cells.

Introduction

At present, single-cell intracellular proteome solution is known as a new standard in single-cell functional biology. The single-cell intracellular proteome solution measures cellular protein to protein interactions and adaptive resistance pathways. It can provide comprehensive functional profiling of each cell type across a large panels. Please send your sample to us. We will run an entire highly-multiplexed proteomics workflow, and send fully analyzed data to you within several weeks.

  • Technology workflow
  • The chip captures single cells in each microchamber, and detects the full range of phosphoproteins, enabling predictive intracellular discoveries.

    • Unique Single-Cell Intracellular Proteome solution.
    • Single-Cell Intracellular Proteome workflow.Figure 1. Single-Cell Intracellular Proteome workflow.

    • Data can be generated same day and is automatically analyzed for instant analysis and publication-ready data visualizations.
    • Data visualization analysis.Figure 2. Data visualization analysis.

    • Unique single-cell proteomics technology enablesmapping of proteomic pathways at the single cell level.
    • Microchambers capture single cells. Unique proteomicbarcode captures the full range of phosphoproteins, enabling predictive intracellular discoveries.
    • Unique proteomicbarcode captures.Figure 3. Unique proteomicbarcode captures.

    • Push-button informatics suite. Revealing true functional biology to accelerate research and medicine with Single-Cell Proteomics.

Data analysis.Figure 4. Data analysis.

  • Panel Menu
    • Human Tumor Signaling
    • P-PRAS40, P-IkBα, P-NF-kβ p65, P-Met, P-p44/42 MAPK, P-S6 Ribosomal, P-Rb, P-p90RSK, P-STAT3, P-MEK1/2, P-Stat1, P-Stat5, P-eIF4E, Cleaved PARP, Alpha Tubulin.

    • Human Adaptive Immune
    • P-Akt, P-p53, P-PD1, P-LCK, P-CD3 zeta, P-Zap70, P-CCR7, P-CD28, P-41BB, P-MEK 1/2, P-P44/42 MAPK (ERK1/2), P-Jak1, P-Jak2, P-AMPK, P-PI3K, P-mTOR, P-P21, P-LAT, P-NF-kB p65, Alpha Tubulin.

  • Advantage of Single-Cell Intracellular Proteome
  • The breakthrough Single-Cell Intracellular Proteome Solution allows users to analyze signaling cascades of many phosphoproteins directly from each single cell, across thousands of single cells in parallel, for the first time. The leap over existing technologies like western blot, mass spectrometry, and flow cytometry, is the Single-Cell Intracellular Proteome solution’s ability to quantify and highly multiplex 15+ intracellular analytes simultaneously from each cell, and thus detect critical protein to protein interactions and signaling networks in rare cells and cell subsets.

    • Highly Multiplexed Analysis
    • Highly multiplexed phosphoprotein analysis at single-cell resolution.

    • Functional Phenotyping
    • Functional Phenotyping targeting 500-1500 single cells per chip.

    • Fully Automated
    • Fully automated, quick, and cost-efficient workflow.

Applications of Single-Cell Intracellular Proteome

  • Predicting and Overcoming Resistance Using Single-Cell Intracellular Proteomic and Metabolomic Analysis Tools

    At present, Cancer cells have been characterized at the genetic and genomic levels. The functional mechanisms impacting protein-driven functional behaviors and activities can only be revealed through single-cell proteomics. Single-cell proteomics has helped researchers overcome resistance to targeted inhibitors, leading to better strategies and combination therapies.

    1. Single-cell intracellular proteomics and single-cell metabolomics combine to characterize drug resistance in melanoma cells.
    2. Proteomic analysis is instrumental in filling the knowledge gap left by genomics, especially at the single-cell level.
    3. Using our proteomic barcoding technology, researchers characterized cellular heterogeneity within cell populations at different timepoints.
Paper Title Multi-omic single-cell snapshots reveal multiple independent trajectories to drug tolerance in a melanoma cell line
Journal Nature Communications
IF 14.919
Published 2020
Abstract This paper integrate experiments and theory to determine the trajectories that single BRAFV600Emutant melanoma cancer cells take between drug-naive and drug-tolerant states. Although single-cell omics tools can yield snapshots of the cell-state landscape, the determination of individual cell trajectories through that space can be confounded by stochastic cell-state switching. Assayed for a panel of signaling, phenotypic, and metabolic regulators at points across 5 days of drug treatment to uncover a cell-state landscape with two paths connecting drug-naive and drug-tolerant states.
Sample Patient-derived melanoma cell line, M397
Methods Quantification of single-cell trace and Single-cell clustering
Result

Single-cell integrated proteomic and metabolic analysis, when viewed at the level of individual analytes, provides evidence of initial drug response at D1, a drug-induced cell-state change at D3, and emerging drug tolerance at D5, prior to an increase in cell proliferation (full drug resistance), which has been shown to occur a few weeks later.

Single-cell proteomic and metabolic analysis of early drug response in M397 cells (Su et al., 2020).Figure 5. Single-cell proteomic and metabolic analysis of early drug response in M397 cells (Su et al., 2020).

  • p53 as an Immune System Modulator in Cancer

    p53 is arguably most well-known as a cell cycle regulator and an initiator of apoptosis and senescence. p53 dysfunction often leads to cancer, and it’s the most frequently mutated gene in human cancer cells.

Paper Title p53 increases MHC class I expression by upregulating the endoplasmic reticulum aminopeptidase ERAP1
Journal Nature Communications
IF 14.919
Published 2020
Abstract The tumour cell line HCT116, which lacks p53 exhibits significantly lower major histocompatibility complex I expression than its wild-type counterpart. Using a combination of chromatin immunoprecipitation sequencing and gene expression analysis, we demonstrate that p53 upregulates expression of endoplasmic reticulum aminopeptidase 1 by binding to its cognate response element in the ERAP1 gene. Silencing of p53 decreases endoplasmic reticulum aminopeptidase 1 protein levels and therefore major histocompatibility complex I expression. We further show that this mechanism operates in A549 cells infected with H1N1 influenza virus, in which H1N1 activates p53, leading to endoplasmic reticulum aminopepti-dase 1 upregulation and a corresponding increase in major histocompatibility complex I expression.
Result

Nutlin 3 treatment caused a marked increase in ERAP1 protein in HCT116 (p53+/+) cells, with concomitant p53 protein accumulation and p21 induction, while in HCT116 (p53-/-) cells, there was no change in ERAP1 protein level. Nutlin 3-treated HCT116 (p53+/+) and HCT116 (p53-/-) cells were then subjected to flow cytometric analysis of MHC class I surface expression after 24 and 48h incubation. Increased MHC I expression was evident in p53+/+ HCT116 cells at both time points, while no increase was seen in p53-/- cells. HCT116 (p53-/-and p53+/+) cells after 48 h of Nutlin 3 treatment were also labelled with antibodies against MHC I for fluorescence microscopic analysis, further demonstrating the p53-dependent increase in MHC class I expression. Genotoxic drugs also induce p53 expression, and treatment of the isogenic HCT116 cell lines with 5-fluorouracil (5-FU) accordingly increased ERAP1 mRNA expression with concomitant MHC class I upregulation in p53+/+ HCT116 cells.

Nutlin 3 and 5-FU treatment increases MHC class I expression in a p53-dependent manner (Wang, Niu, Lai, & Ren, 2013).Figure 6. Nutlin 3 and 5-FU treatment increases MHC class I expression in a p53-dependent manner (Wang, Niu, Lai, & Ren, 2013).

Paper Title Human NK Cells Are Alerted to Induction of p53 in Cancer Cells by Upregulation of the NKG2D Ligands ULBP1 and ULBP2
Journal Cancer Research
IF 12.701
Published 2011
Abstract This paper report that induction of wild-type p53, but not mutant p53, strongly upregulated mRNA and cell surface expression of ULBP1 and -2, whereas expression of other NK cell ligands was not affected. Defined intronic p53-responsive elements in these two novel p53 target genes. Coculture of wild-type p53-induced human tumor cells with primary human NK cells enhanced NKG2D-dependent degranulation and IFN-γ production by NK cells. Accordingly, treatment of certain wild-type p53-expressing tumor cell lines with the p53-reactivating small molecular compound RITA resulted in upregulation of ULBP2 mRNA and cell surface protein expression.
Result

The cloned intronic sequences of the ULBP1 and -2 genes and the p53RE deletion constructs. Luciferase reporter analyses showed that luciferase activity was strongly increased upon transfection with a p53 containing plasmid in a dose-dependent manner when the luciferase constructs containing the 530 bp long fragments of the first introns of the ULBP1 and -2 genes were present. Deletion of all potential p53REs (ULBP1/2_∆p53RE1/2) from these constructs resulted in a reduction of luciferase activity to the levels of the empty vector control.

One intronic p53RE in the ULBP1 and ULBP2 geness are sufficient to induce expression of a luciferase reporter gene (Textor et al., 2011)Figure 7. One intronic p53RE in the ULBP1 and ULBP2 geness are sufficient to induce expression of a luciferase reporter gene (Textor et al., 2011)

References

  1. Su, Y., Ko, M. E., Cheng, H., Zhu, R., Xue, M., Wang, J., Heath, J. R. (2020). Multi-omic single-cell snapshots reveal multiple independent trajectories to drug tolerance in a melanoma cell line. Nat Commun, 11(1), 2345.
  2. Textor, S., Fiegler, N., Arnold, A., Porgador, A., Hofmann, T. G., & Cerwenka, A. (2011). Human NK cells are alerted to induction of p53 in cancer cells by upregulation of the NKG2D ligands ULBP1 and ULBP2. Cancer Res, 71(18), 5998-6009.
  3. Wang, B., Niu, D., Lai, L., & Ren, E. C. (2013). p53 increases MHC class I expression by upregulating the endoplasmic reticulum aminopeptidase ERAP1. Nat Commun, 4, 2359.
! ! For Research Use Only. Not for diagnostic or therapeutic purposes.

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