Imaging Mass Cytometry & Triple Negative Breast Cancer

As I mentioned in the ΔTissue page, one of the program's goals was to combine various profiling techniques to capture comprehensive data across different scales and modalities. One of these modalities was Imaging Mass Cytometry (IMC). Using Triple-Negative Breast Cancer (TNBC) tissue samples provided by Maddy Parsons (KCL), we developed our pipeline and constructed predictive models.
Before diving into the image analysis pipeline, I will briefly explain what IMC is and why we focused on TNBC.

Imaging Mass Cytometry

Imaging Mass Cytometry is a cutting-edge technique that combines mass spectrometry with imaging to provide high-dimensional spatial information about tissues at the cellular level. It allows researchers to visualize and analyse the expression of multiple proteins, DNA, RNA, and other biomolecules in tissue samples simultaneously.

How IMC works?

  • Sample Preparation: Tissue sections or cell smears are fixed onto a slide. Antibodies conjugated to metal isotopes (instead of fluorescent dyes) are applied to the sample. Each antibody is specific to a particular biomolecule of interest.
  • Laser Ablation: A laser scans the sample, ablating tiny regions (usually 1 µm in diameter) one at a time, releasing the bound metal isotopes.
  • Mass Spectrometry: The ablated material is transported to a time-of-flight mass spectrometer, where the metal isotopes are detected and quantified. Each isotope corresponds to a specific biomolecule, allowing for multiplexed detection.
  • Image Reconstruction: The spatial distribution of the detected isotopes is mapped back to the tissue sample, creating high-dimensional images where each pixel contains data about multiple biomolecules.

​Key Advantages of IMC

IMC generates high-dimensional spatial images that provide a comprehensive view of biomolecule distributions in tissues. These images are powerful tools for studying complex biological systems, offering insights into cellular behaviours, tissue organization, and disease mechanisms. Some of the key advantages of IMC over other modalities are:
  • Ability to analyse dozens of markers simultaneously in a spatially resolved manner.
  • No spectral overlap issues, unlike fluorescence-based imaging.
  • Provides both spatial and quantitative insights, enhancing understanding of tissue architecture and function.

What type of images does IMC generate?

Since my work was not only focused on analysing the images but also on improving image analysis techniques, I would like to provide a detailed explanation of the types of images generated by IMC.
IMC produces multi-channel, high-dimensional spatial images that show the localization and abundance of various biomolecules within a tissue sample. Some characteristics of the IMC Images are:
  • Multi-channel Images: Each channel corresponds to a specific biomolecule (e.g., a protein, RNA, or marker of interest). IMC can analyse 30-40 markers or more simultaneously in a single scan.
  • High Spatial Resolution: IMC generates images with a resolution of ~1 µm per pixel, which is sufficient to study individual cells and their subcellular compartments.
  • Quantitative Data: Unlike traditional fluorescence imaging, IMC provides quantitative information about the abundance of each biomolecule by measuring the signal intensity of the corresponding metal isotope.​
Picture
Example of an IMC image. Taken from: https://store.standardbio.com
  • Tissue Context: IMC retains the spatial organization of the sample, making it possible to study the relationships between cells, their microenvironment, and tissue structure.
  • False-Colour Representation: Since IMC data spans multiple dimensions, images are often displayed in false colour, where different markers are assigned specific colours for visualization. Researchers can overlay channels to observe co-localization or relationships between markers.

Triple Negative Breast Cancer

TNBC is a subtype of breast cancer that accounts for 15-20% of all breast cancers and is characterized by loss of progesterone receptor, oestrogen receptor, and epidermal growth factor receptor (HER2). Patients diagnosed with TNBC have the highest risk of metastasis of any breast cancer and have a 40-80% risk of recurrence after therapy.

TNBCs are highly heterogeneous, with significant variability in molecular profiles, immune cell infiltration, and tumour microenvironment composition, and evidence suggests this heterogeneity contributes to resistance to chemotherapy and relapse.

Development of resistance to chemotherapy appears to occur through epigenetic changes that modify the activity of key regulators of cell state and produce “persister” cells that can survive prolonged treatment with chemotherapy.

This complexity makes imaging approaches like Imaging Mass Cytometry crucial, as they can reveal the spatial organization and abundance of key cell populations driving these processes, providing valuable insights for therapeutic strategies.
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