Welcome to part 1 of our AACR 2024 recap series. In this series, we highlight the great science and spatial biology technologies showcased at the event. In this first installment below, we cover a poster demonstrating the potential of the PhenoCycler-Fusion 2.0 platform for multiomics research.
Novel multiomic approaches are needed to fully understand the complexity of tumors, tumor microenvironments (TMEs), and the body’s response to therapeutic intervention. To that end, a team of scientists from the University of Queensland and Akoya Biosciences recently collaborated on a project that made use of spatial phenotyping in conjunction with targeted spatial RNA detection. They aimed to uncover the molecular mechanisms underlying the response to immune checkpoint inhibitors (ICIs) in head and neck squamous cell cancer (HNSCC).
Findings from this work were shared in a poster presentation at the 2024 American Association for Cancer Research (AACR) annual meeting in San Diego.
Watch Video
Watch Akoya Senior Technical Application Scientist Avik Mukherjee, PhD, present the poster, Ultrahigh-plex Multiomic Spatial Phenotyping of Head and Neck Cancer Tissue Uncovers Protein and RNA Signatures of Immunotherapy Response.
Research Focus: Bringing Spatial Context to Biomarker of Patient Response
The use of immunotherapies in cancer treatment, particularly for head and neck cancers, has revolutionized the therapeutic landscape. In recent years, targeted immune checkpoint inhibitors, particularly those targeting the PD-1/PD-L1 pathway, have shown promising results in treating mucosal HNSCC. These therapies offer hope for durable treatment, providing long-term benefits to patients. Despite their potential, the challenge remains that methods of identifying biomarkers to predict the effectiveness of these targeted ICI therapies still need to be developed and improved.
Exploring the spatial context of tumor biomarkers and the TME’s composition, context, and cellular architecture is critical to understanding the molecular mechanisms of patient response to immunotherapy. Using a multiomic approach to characterizing biomarker signatures, differentiating between responsive and unresponsive HNSCC phenotypes may be possible.
In this study led by Dr. Arutha Kulasinghe from the University of Queensland, the team used tissue from an HNSCC patient with a partial response to Pembrolizumab/Nivolumab treatment. The tissue sample was pathologically annotated with H&E staining as containing a large tumor mass, a regionally intact tonsil, an esophageal submucosal gland, lymphatic ducts, and normal squamous epithelium. This diverse tissue sample was used to establish a new method of characterizing the TME with ultrahigh-plex spatial phenotyping and targeted RNA spatial detection.
Technology Spotlight: Multiomic Spatial Phenotyping
To characterize the abundance of various markers related to both tumor characteristics and immunobiology, the research team used four pre-designed Akoya PhenoCode Discovery Panel Modules along with a custom 56-plex panel. This 101-plex antibody panel enabled labeling markers for immune cell lineages, checkpoints, metabolism, and cell stress to comprehensively characterize the HNSCC tissue sample. Additionally, the team developed and tested two different 4-plex ViewRNA panels; one focused on lymphocytic activation and recruitment and the other with genes that function in immune activation and response. They used the novel ViewRNA panel on the HNSCC tissue to detect cytokine and chemokine molecules that may modulate lymphocyte activation and immune activation in the TME.
Both the protein and RNA assays were performed on PhenoCycler-Fusion 2.0. This advanced system facilitated rapid labeling combined with molecular barcoding chemistry and single-cell resolution imaging of whole-slide tissue sections containing millions of cells. Through this work, the authors demonstrated that the PhenoCycler workflow, in addition to enabling ultrahigh-plex protein spatial phenotyping, can detect RNA targets using the ViewRNA tissue assay.
Key Findings: Distinct Signature Across Tumor Regions
- The ultrahigh-plex antibody panel removed numerous limitations of individual core panels by allowing the team to visualize markers of immune function, stress, and metabolic signatures concurrently.
- By capturing whole-slide images, the authors uncovered intra-tumoral heterogeneity. Specifically, spatial phenotyping revealed that mature tertiary lymphoid structure (TLS) was observed exclusively in one region of the tumor (Tumor 4). At the same time, intra-tumoral heterogeneity in metabolic and stress profiles occurred between tumor regions 3 and 4.
- A targeted study of the TLS was used to establish the ViewRNA panel design by determining what RNA markers were differentially regulated in the TLS compared to the germinal cells.
- Targeted spatial RNA analysis revealed distinct patterns of lymphocyte activation, recruitment, and immune response dynamics in tumor 3 vs tumor
Download the full poster in PDF format for a closer look.
Conclusions: Multiomic Spatial Phenotyping Provides New Insights into Immunotherapy Response
In this first-of-its-kind study combining ultrahigh-plex spatial phenotyping and targeted spatial RNA analysis on the PhenoCycler-Fusion 2.0 plaftorm, the research team resolved key markers and identified anatomical structures in an HNSCC tissue sample. This multiomic approach elucidated distinct spatial domains and substantial intra-tumoral heterogeneity in immune, stress, and metabolic signatures. Furthermore, they obtained single-cell resolution of key protein determinants and signaling pathways among the tumor and the TME underlying the partial immune therapy response observed in the patient.
These data demonstrate that spatial organization and interactions within the TME are pivotal in how patients respond to ICI therapy. This work provides a new methodology for understanding the mechanisms governing response to immune checkpoint inhibitor therapies and ultimately predicting patient response.
For more information:
- See how the PhenoCycler-Fusion 2.0 solution is helping provide insights into complex biological systems and gain a better understanding of cellular microenvironments.
- Watch the on-demand recording of our AACR Spotlight Theater presentation, “Spatial Biology 2.0: Spatial Insights & Precision Medicine at Unprecedented Scale”.
- Reach out if you’d like to discuss how Akoya’s spatial biology solutions can help you advance your research.
