Patient samples are precious – as is the information they yield. Current assays present a choice between spatial information, precision, and plex. But compromise may not be necessary; digital spatial profiling (DSP) allows highly multiplexed, multi-analyte quantification of RNA and protein from FFPE tissue. With a non-destructive approach, you can do more with less.
By Dr. Alessandra Cesano, Chief Medical Officer, nanoString, Seattle, WA, USA.
Understanding cancerous tumors and their microenvironments permits more detailed and comprehensive research, potentially leading to more accurate prognoses, personalized treatment decisions and disease monitoring.
The problem
The tumor microenvironment plays a vital part in cancer’s progression and responsiveness to treatment – which makes it a key target in both the laboratory and the clinic. Typically, imaging studies are used to understand the microenvironment in biopsy samples, but the techniques used are fraught with difficulties. They offer limited dynamic range, poor precision, and require significant time and effort to analyze a single target.
Conversely, RNA or protein expression profiling assays are quantitative, precise, and can be performed at high plex. Due to the “grind and bind” nature of the assay, however, all of the valuable spatial information is lost.
For precision oncology, that is not good enough. Researchers need the ability to quantitatively evaluate and characterize RNA and protein while maintaining spatial information. This allows them to establish the overall morphology of the tumor tissue, and conduct further high-plex profiling if necessary. Observing the spatial distribution of abnormal cells – and their subtypes – allows researchers to determine whether a tumor is benign or malignant, immune “hot” or “cold,” and whether or not current treatments are effectively controlling or eliminating disease. Without this information, it is difficult for health care teams to make appropriate diagnostic, prognostic and treatment decisions.
But this view is difficult to obtain with imaging or profiling capabilities alone – and all of these assays consume precious patient samples. This presents pathologists with a dilemma: what is most important to preserve? Is it sample, spatial information, or high-plex target information?
With laboratories already under stress and the need for pathology services only increasing, is there a way around this dilemma? What pathologists need is a practical way to overcome these challenges and provide maximum information from precious tissue samples.
The solution
Digital spatial profiling (DSP) is a novel platform, based on analyte barcoding technology, that enables the spatially resolved characterization of RNA and protein in a highly multiplexed, nondestructive assay. The instrument is capable of examining up to 800 analytes at once, and RNA or protein can be profiled on a single FFPE slide section (see Figure 1).
Figure 1. An overview of the DSP workflow demonstrating how the DSP instrument prepares multiplexed assays from a single tissue biopsy slide.
Figure 2. Immune characterization of a colorectal cancer excisional biopsy by DSP (1). Tumor tissue (left) was fluorescently stained for pancytokeratin (PanCK), CD45 and DNA. Different regions of interest were selected for high-plex protein expression profiling (right). Matching expression levels to regions of interest allows tumor and microenvironment characterization and, potentially, treatment personalization.
Once the analytes of interest have been quantified, the counts can be mapped back to their original location on the tissue sample, providing spatial resolution for the quantitative data (see Figure 2).
- N Confuorto, Presented at the 4th Digital Pathology Congress; November 20, 2017; London, UK.
