Abig challenge in the field is that cancer cells develop resistance to targeted therapies, and researchers are striving to understand and characterize how these cancer cells are adapting in response to these therapies. However, the inherent functional heterogeneity in cancer cells makes this challenging. This heterogeneity complicates translating data from genetic profiles or responses into associated functional behaviors or phenotypes. Although 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 singlecell proteomics. IsoPlexis' single-cell proteomics has helped researchers overcome resistance to targeted inhibitors, leading to better strategies and combination therapies.

Single-cell intracellular proteomics and single-cell metabolomics combine to characterize drug resistance in melanoma cells

The constant adaptation of cancer cells poses a great challenge for developing drug-based treatments, as cells that initially respond can quickly adopt drug-resistant states. IsoPlexis’ single-cell proteomics and multiomic...

In a recent Nature Communications article, James Heath's team from the California Institute of Technology described using predictive single-cell intracellular proteomics and metabolomics to identify how a cancer cell line transitions to a final drug-resistant state via two distinct trajectories.1 When BRAFV600E mutant melanoma cells are treated with BRAF inhibitors, they quickly become drug tolerant. To analyze what was happening within these cells to create a drug resistant state, Heath's team treated these mutant cells with the BRAF inhibitor vemurafenib for varying durations and analyzed them using integrated single-cell intracellular proteomics and metabolomics.

Using IsoPlexis' proteomic barcoding technology, the researchers characterized cellular heterogeneity within cell populations at different timepoints and quantitatively connected multiple timepoints to characterize dynamic heterogeneity on an individual cell level. Cellular state changes became prominent around day 3, as most probed analytes exhibited a sharp but transitory increase in variance. Indeed, all of the metabolic enzymes and signaling phosphoproteins, all metabolic regulators except for one, and all resistant state markers and regulators except for one displayed this phenomenon. This information showed Heath's team that cancer cell responses to a common stimulus may entail multiple divergent functional pathways while still resulting in the same genomic phenotype. Understanding these functional adaptations allowed the team to predict and develop an effective therapeutic combination to overcome this adaptive resistance.

Revealing true function with the IsoLight proteomic hub

Proteomic analysis is instrumental in filling the knowledge gap left by genomics, especially at the single-cell level. The IsoLight system from IsoPlexis enables researchers to ascertain true cellular functional phenotypes. Going beyond the limited information provided by cell surface marker expression, IsoCode single-cell intracellular proteomic chips provide information on protein-protein interactions and pathway activation or deactivation, emphasizing changes in protein expression and alterations in phosphorylation profiles.

The IsoPlexis single-cell proteomics platform, the IsoLight, functions as a proteomic hub that uncovers the true function from cancer and immune cells. IsoPlexis' proteomics hub functionally phenotypes adaptive and innate immune cell populations and examines cell populations that shape the tumor microenvironment by looking at the secretome, intracellular proteome, and metabolome. The platform is capable of identifying up to 32 different cytokines and intracellular proteins in a multiplexed manner at the singlecell level. This is all combined with IsoPlexis’ fully automated plug-and-play IsoSpeak software suite. This powerful software analyzes data same day with intuitive and publication-ready advanced visualizations to help researchers further accelerate their therapies.

Visit IsoPlexis.com for more information on IsoPlexis’ intracellular proteome and metabolome technologies.


  1. Y. Su et al., “Multi-omic single-cell snapshots reveal multiple independent trajectories to drug tolerance in a melanoma cell line,” Nat Commun, 11:2345, 2020.

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