The Path to Clinical Relevance: Moving from Spatial Transcriptomics to Protein Profiling
Spatial biology is a rapidly evolving discipline that advances human health by leveraging imaging technologies. It encompasses research activities ranging from whole-transcriptome profiling to clinically impactful single-protein biomarker tests.
Translational researchers aiming to derive clinically useful protein profiling panels from whole transcriptome insights face unique challenges: deciding which biomarkers to include in the panel, validating the reagents for reliable results, then testing large numbers of clinical samples for statistically powered results tied to clinical outcomes.
Translational spatial biology studies involve quantification of tissue microenvironments at scale, unlocking mechanistic, prognostic, and predictive insights to improve patient care. In this context, protein-level analysis remains the gold standard for understanding disease mechanisms and evaluating therapeutic responses. The central challenge for researchers is clear: How can you design a clinically relevant biomarker panel that captures sufficient biological complexity to assess efficacy, while maintaining the throughput required for large preclinical studies and clinical trials?
Non-Small Cell Lung Cancer. Tumor microenvironment profiling measuring infiltration of tumor (yellow) by macrophages and T cells. Lines are dilation zones to capture the density of immune cells near the tumor.
From Discovery to Clinical Value
Over the past decade, discovery activities using spatial transcriptomics technologies have led to an explosion of candidate microenvironment biomarkers with potential clinical value. Translational activities are then required to determine their clinical relevance. These activities involve first validating RNA leads at the protein level, as cellular phenotype and function are dictated by protein expression, followed by microenvironment analysis tied to clinical outcomes at the statistically-powered large-cohort study level.
The typical workflow for moving from spatial transcriptomics results to multiplex IF panel testing involves these steps:
- Identify RNA leads with spatial transcriptomics to identify a short list of RNA leads within the tissue
- Validate RNA leads at the protein level using immunohistochemistry (IHC)
- Combine validated protein markers with established markers into a panel for multiplex IF testing
At this point, researchers encounter a challenge: What technology enables spatial protein profiling with sufficient throughput and multiplexing capacity to derive clinically relevant spatial biomarkers backed by the statistics provided by large cohort studies?
Human Breast Invasive Ductal Carcinoma. Dense triple-positive tumor showing complete membranous staining of HER2, with nuclear staining of P53 (blue), ER (red), PR (green) or combinations thereof.
“Discovery work performed with upstream transcriptomics tools has revealed a tremendous number of biomarkers with potential clinical value. The current challenge is to integrate useful RNA leads into improved biomarker panels that can then be applied to large cohort studies to establish clinical utility.”
— Tad George, Senior Vice President Biology R&D at RareCyte, Inc.
Overcoming Traditional Limitations
Spatial biology for translational research requires development of useful and reliable panels with sufficient plex to resolve microenvironments, and sample testing with sufficient throughput and plex to get statistically powered microenvironment-level clinical insights.
To establish clinically relevant biomarker panels for large cohort studies, high-throughput protein analysis is crucial, yet throughput is often limited by the number of markers that can be measured in a single imaging round. Traditional multiplex IF technologies, typically restricted to 2–6 markers per round, limit the depth of clinical research. Increasing the number of protein markers detected per round enables more comprehensive biological insights and improves data quality. The Orion™ platform addresses this limitation by capturing 20 channels (18 markers + DNA + autofluorescence) per round, significantly expanding panel capacity. When panels exceed the capacity of a single round, cycling on a small subset of samples can help identify a subset of markers that are compatible for single-round measurement – however, each additional cycle adds time, reduces throughput, and increases the risk of tissue degradation. By capturing more markers per round, Orion minimizes the number of cycles needed, streamlining workflows and improving data quality.
What plex is ideal for clinical research? Dr. Peter Sorger’s team at Harvard University explained in this article that the current standard in clinical research is 5-6 plex imaging, but that a minimum of 10-16 markers are required for tumor profiling.
Panel design in multiplex IF experiments presents additional challenges that go beyond antibody selection.
- Each antibody must be rigorously validated for compatibility with the specific platform to ensure accurate and reproducible results. The availability of a broad range of pre-validated reagents is essential to streamline panel development and reduce experimental risk.
- For studies requiring novel targets, the ability to create and validate custom reagents becomes critical.
- In multi-round experiments, it is also necessary to verify that signal removal is complete and that antigen integrity is preserved throughout the process, ensuring reliable detection across all cycles.
Addressing these requirements is vital for generating high-quality, reproducible data in translational spatial biology studies.
Orion is uniquely suited to bridge the translational gap in spatial biology
The Orion™ platform overcomes barriers in spatial biology by enabling simultaneous detection of 20 channels per round. This high-plex, high-throughput capability allows researchers to efficiently transition from RNA discovery to protein translational studies – without compromising sample integrity or data quality.
- Flexible, High-Quality, Reliable Panels
Orion’s comprehensive panel development toolkit includes pre-validated reagents, off-the-shelf panels, and easy-to-master labeling kits for incorporating custom markers, minimizing your panel development time. The ability to stain all your antibodies in a single round simplifies validation and improves data quality. - High-Throughput and High-Plex for Large Cohorts
Orion has the throughput and plex necessary to resolve microenvironments across large cohorts of whole specimen samples for statistical power. Process tens to hundreds of samples quickly, generating robust, quantitative, statistically powered data tied to clinical outcomes. -
One Platform for Discovery and Translational
Single platform for high-plex discovery panels and single-round translational panels. Image 20 channels in a single round, or cycle Orion to achieve an even higher plex when needed. This flexibility allows you to start broad (e.g., 51-plex discovery in three rounds), then focus on a streamlined, clinically relevant single-round panel for high-throughput validation – all on the same platform.
In Summary
Orion empowers researchers to perform high-plex, high-throughput spatial protein analysis across large sample numbers, supporting robust biomarker validation and meeting the demands of clinical trials. By seamlessly connecting spatial transcriptomics discovery with functional protein validation, Orion bridges the gap between biomarker discovery and clinical research – accelerating the translation of spatial biology insights into patient impact.
