Moving from Spatial Transcriptomics to Protein Profiling
von RareCyte
The Path to Clinical Relevance
Spatial biology is rapidly transforming human health through advanced imaging. This field covers the entire research spectrum, from mapping the whole transcriptome to developing the precise, single-protein biomarker tests that drive clinical decisions. Read RareCyte's blog here.
Translational researchers seeking to derive clinically useful protein profiling panels from whole transcriptome insights face significant challenges, like:
- Deciding which biomarkers to include in the panel
- Validating the reagents for reliable results
- Testing large numbers of clinical samples for statistically powered results tied to clinical outcomes
Figure 1 - 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.
To provide better patient care, translational spatial biology maps out tissue environments on a large scale, enabling insights that help prognose and predict. Focusing on proteins within these spaces remains the gold standard for researchers trying to measure a patient’s response to new therapies and disease mechanisms.
The central challenge for researchers is how can they design a clinically relevant biomarker panel that captures sufficient biological complexity to assess efficacy, while at the same time maintaining the throughput required for large preclinical studies and clinical trials?
Moving Discoveries into the Clinic
Spatial transcriptomics technologies has uncovered a wealth of new microenvironment biomarkers over the last decade, but the real challenge lies in proving their clinical worth. Because proteins expressions drive cellular function and phenotype, the first step is validating RNA leads at the protein level, followed by microenvironment analysis. These findings must then be backed by large-scale cohort studies to ensure statistical power.
Moving from initial spatial results to a multiplex IF panel testing panel involves:
- Targeting: Identifying a short list of key RNA leads within the tissue with spatial transcriptomics.
- Validating: Using immunochemistry (IHC) to validate those RNA leads at the protein level.
- Integration: Developing a multiplex IF panel testing that combines new and established protein markers.
However, a bottleneck remains when talking about deriving clinically relevant spatial biomarkers backed by the statistics provided by large cohort studies: what technology enables spatial protein profiling with sufficient throughput and multiplexing capacity in order to achieve this?
“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.
Figure 2 - High-plex spatial imaging example obtained with the RareCyte Orion platform
Going beyond Limitations
The succes of 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.
Large-scale studies depend on high-throughput protein analysis, but researchers are often held back by how few markers they can measure in a single imaging round. Standard imaging techniques are usually limited to 2–6 markers per round, which restricts the scope of clinical research. By breaking through this limit and increasing the number of protein markers detected per round, we can capture a more complete biological picture and significantly improve data accuracy.
What plex is ideal for clinical research? Dr. Peter Sorger’s team at Harvard University explained that a minimum of 10-16 markers are required for tumor profiling. You can access to the article here.
The Orion™ platform overcomes these hurdles by detecting 20 channels in just one round (18 markers + DNA + autofluorescence), vastly increasing what a single panel can capture. While other methods require multiple cycles to reach this depth, which wastes time and risks damaging the tissue, Orion’s high capacity per round keeps workflows fast. By minimizing the need for repeated cycling, it protects tissue from the risk of degradation and ensures higher data quality.
Designing a multiplex IF panel involves much more than just picking the right antibodies. To get accurate and repeatable results, every antibody has to be strictly tested to ensure it is compatible with the specific platform. Having access to a wide library of pre-validated tools is a game-changer, since it speeds up the setup process and reduces experimental risk. Also, for researchers requiring new targets, the flexibility to build and verify custom reagents is just as vital. Furthermore, in multiple round experiments, there must be certainty that signal removal is completed, and that antigen integrity is preserved, so every cycle delivers trustable data.
Addressing these requirements is vital for generating high-quality, reproducible data in translational spatial biology studies.
Figure 3 - RareCyte Orion Platform
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.
To sum up
Orion gives researchers the power to perform deep spatial analysis at the scale required for modern clinical trials. By bridging the gap between transcriptomics and protein validation, it streamlines the journey from lab discovery to real patient impact.