Seeing cancer in context

Cancer doesn’t develop in isolation – it evolves within a dynamic and often hostile environment, shaped by immune cells, stromal components, and molecular signals. Understanding this tumor microenvironment (TME) is key to improving how we diagnose, treat, and monitor cancer¹.

Spatial proteomics and spatial transcriptomics are helping researchers to do that. These technologies keep the tissue samples intact, allowing scientists to map proteins and gene expression in situ². Instead of averaging signals across a sample, spatial methods reveal how different cell types interact and how these interactions influence disease progression.

Moving beyond mass spectrometry

For years, mass spectrometry has been the go-to method for proteomic analysis. While powerful, it’s not always practical for large-scale translational research. That’s where high-plex, antibody-based approaches come in.

Dr. Arutha Kulasinghe, Associate Professor and Principal Research Fellow, Clinical-oMx Lab, University of Queensland, explains:

“Mass spec isn’t scalable for large sample numbers. We’re now using high-plex proteomics – antibody-based methods with molecular barcodes – to get a multi-omic view across multiple pathways.”

This shift has opened the door to new tools that deliver scale, specificity, and spatial detail in one package. Among them is the 580-plex Immuno-Oncology Proteome Atlas (IPA), launched in 2023 through a collaboration between Abcam and NanoString/Bruker. The panel uses 100% Abcam antibodies and was designed to help researchers explore the hallmarks of cancer with greater depth and breadth³.

A new scale of discovery

The 580-plex panel enables researchers to profile hundreds of proteins from a single tissue section. When combined with tissue microarrays, the scale becomes even more powerful.

“We’re now profiling 100 patients on a single slide with 500 antibodies or more,” says Kulasinghe. “That’s really powerful. It’s broad enough to cast a wide net.”

This approach was put to the test in a recent study focused on head and neck squamous cell carcinoma (HNSCC)⁴. The team used the 580-plex panel to analyze tumor and stromal regions from a tissue microarray, separating pan-cytokeratin-positive and -negative cells. They then compared protein expression between patients with long-term survival and those with poorer outcomes.

The results revealed distinct proteomic signatures linked to survival. These findings were further integrated with spatial transcriptomics data, creating a multi-layered view of the TME. It was a compelling proof-of-concept that demonstrated the potential of high-plex spatial proteomics to uncover clinically relevant insights.

From discovery to validation

One of the strengths of high-plex panels is their ability to support both discovery and validation. Researchers can start with a broad screen, hundreds or even thousands of proteins, and then narrow down to a smaller set of biomarkers for further study.

“Plex is king,” says Kulasinghe. “You might start with 1,000 proteins, but eventually you’ll narrow it down to a handful that really matter.”

This flexibility is especially valuable in cancer research, where the biology is complex and context-dependent. The ability to explore multiple pathways simultaneously helps researchers identify patterns that might be missed with lower-plex or bulk approaches.

What’s next for spatial technologies?

The field of spatial biology is evolving rapidly, and new platforms are expanding the possibilities for high-plex analysis. These technologies allow faster workflows, higher resolution, and more accessible data integration⁵.

But with more data comes new challenges. Interpreting high-plex results requires robust bioinformatics tools and careful validation. As Kulasinghe notes,

“These assays need to be validated. You might find a signature, but you have to prove it works.”

That’s where collaboration and standardization will play a key role. Integrating spatial proteomics with other data types, such as genomics, transcriptomics, and clinical outcomes, will help researchers build more comprehensive disease models.

A new era of cancer research

Spatial proteomics is already changing how we tackle cancer research. These tools show us exactly how cells behave where they naturally live, meaning we can spot new biomarkers, figure out why treatments stop working, and build therapies that hit the right targets.

The 580-plex panel fits right into this shift. It gives you a practical and accessible way to explore cancer's complexity. As more studies embrace spatial approaches, we're seeing insights that get richer every day.

At Abcam, we're excited to be part of your spatial biology journey; whether you're just getting started or scaling up your spatial proteomics work, we're here with the tools, resources, and support to keep you moving forward.

References

1.    Khosravi GR, et al. Immunologic tumor microenvironment modulators for turning cold tumors hot.  Cancer Commun. (Lond.)   44, 521–553 (2024).

2.    Robles-Remacho A, et al. Spatial Transcriptomics: Emerging Technologies in Tissue Gene Expression Profiling.  Anal. Chem.   95, 15450–15460 (2023).

3.    NanoString launches the most comprehensive spatial proteomics panel ever offered. Available at: https://www.abcam.com/en-us/press-releases/nanostring-launches-spatial-proteomics-panel (Accessed: 16 June 2025).

4.    Tan CW, Berrell N, Donovan ML, et al. The development of a high-plex spatial proteomic methodology for the characterisation of the head and neck tumour microenvironment.  Preprint at Research Square  https://doi.org/10.21203/rs.3.rs-5272207/v1 (2024).

5.    Bressan D, et al. The dawn of spatial omics.  Science   381, eabq4964 (2023).