A user's perspective on GeoMxTM digital spatial profiling

Abstract

Characterization of spatial protein expression for multiple targets from a single tissue is difficult to perform, especially due to the limitations of multiplex immunohistochemistry and tissue heterogeneity. Therefore, a new technology is required that permits detailed and simultaneous expression profiling of proteins within a defined region of interest (ROI). To address this unmet need, NanoString Technologies developed a new technology, GeoMx^TM digital spatial profiling (DSP), which currently enables simultaneous and guided detection of up to 40 antibodies (probes) from a single formalin-fixed paraffin-embedded (FFPE) tissue. DSP probes are tagged with unique photocleavable DNA oligos that are released after guided ultraviolet exposure in specific ROIs. Digital quantification of the released oligos by NanoString's nCounter® system provides a detailed expression profile of proteins within these discrete ROIs. In this article, we will describe our experience with the GeoMx DSP platform using cancer FFPE tissues. These expression profiles will provide better characterization and understanding of tumor heterogeneity and the tumor micro-environment, enabling the improvement of patient therapy and the identification of potential biomarker signatures. The purpose of this article is to offer potential future users an independent insight into the DSP platform and a comprehensive idea of usability, including advantages and current limitations of the technology based on our current experience with the beta version of NanoString's DSP platform as part of the DSP beta-testing program. The GeoMx^TM Digital Spatial Profiling (DSP) platform is a non-destructive technique for regional in-depth protein expression profiling. Using oligonucleotide detection technologies, the GeoMx^TM DSP enables simultaneous high-level multiplexing on a single FFPE tissue. Here, we focus on our current experience derived from our biomarker research using the beta version of the DSP instrument.

Keywords: DSP; IHC; Multiplex; NanoString; Region of interest; Translational research.

Figure 1

Protein digital spatial profiling (DSP) working procedure. Formalin-fixed paraffin-embedded tissue slide preparation involves incubation with an antibody mixture which contains up to four visualization markers and 40 DSP probes. Following imaging, regions of interest (ROIs) are selected based on visualization of the tissue. Sequential ultraviolet (UV) light exposure of each ROI results in the release of indexing oligos from the DSP probes, allowing their quantification on NanoString's nCounter® system.

Figure 2

Comparison of staining efficiency before and after oligo conjugation of antibodies. (A) Standard immunohistochemical staining for CD16 and CD39 before and after oligo conjugation of the antibodies. Rabbit immunoglogulin G (IgG) was used as the background control. Scale bar 100 μm. (B) Housekeeping (HK)-normalized digital spatial profiling counts after oligo conjugation of antibodies from three discrete regions of interest (ROI1–3). Violet bars, rabbit IgG; pink bars (upper figure), CD16; pink bars (lower figure), CD39.

Figure 3

Selection of type of region of interest (ROI). Three types of regions can be selected within the digital spatial profiling platform. Tissue biopsy was stained with S100B/PMEL17 (green), LDH (red) and CD45 (yellow) visualization markers. (A–C) Geometric ROIs can be selected, ranging from circles (A) to rectangles (B) to user-defined polygons (C). (D,E) Segmentation within a geometric ROI is generated based on visualization markers, and can currently distinguish between tumor and stroma (D) or specific cell type populations (E). (F) Single-cell ROIs are generated based on visualization markers which allow the analysis of either one or multiple single cells within a field of view. Scale bar 100 μm.

Figure 4

Precise ultraviolet (UV) guidance by digital mirror devices. (A) CAGE-dye-stained tonsil tissue with geometric region of interest (ROI) before and after UV exposure. Scale bar 100 μm. (B) Circular ROIs (200-μm diameter) on cell pellet array and ‘glass’ and respective protein expression levels after digital spatial profiling (DSP) analysis. DSP counts are normalized to immunoglobulin G (IgG) controls to correct for noise. Scale bar 100 μm. (C) Geometric ROI on colorectal cancer tissue with internal segmentation for ‘tumor’ (red) and ‘stroma’ (green). Scale bar 100 μm. Heatmap of region-specific nCounter counts normalized to nuclei. (D) Circular ROI (200-μm diameter) with segmentation on ‘PanCK+ CD45- CD3-’ (blue), ‘PanCK- CD45+ CD3-’ (yellow) and ‘PanCK- CD45+ CD3+’ (red) cells and respective DSP counts after normalization to IgG controls. Scale bar 100 μm.

Figure 5

Reproducibility of digital spatial profiling analysis. Independent expression analyses of depicted proteins were performed on two serial sections of (A) cell pellet array and (B) colorectal cancer tissue (B). Expression levels are shown for one 200-μm-diameter circular region of interest (ROI)/section and counts were normalized to nuclei and housekeeping proteins. ROIs of serial sections were chosen in the same tissue area to allow close comparison. r² value indicates correlation between expression profiles from sections 1 and 2. Section 1, dark grey bars; section 2, light grey bars.

Figure 6

Correlation of digital spatial profiling (DSP) counts with immunofluorescent or standard immunohistochemical staining. (A) Tonsil tissue stained with PanCK (green), CD45 (red) and CD3 (yellow) visualization markers. Scale bar 100 μm. Graphs depict nuclei and housekeeping (HK)-normalized DSP counts of indicated proteins in ‘tumor’ or ‘immune’-enriched regions of interest (ROIs). (B) Nuclei and HK-normalized counts for CD163 and PD-L1 obtained from melanoma patient groups 1 (n=22) and 2 (n=32). Each dot represents one ROI/patient selected by similar tissue morphology. *P<0.005, unpaired t-test. ns, non-significant. (C) Representative images for CD163 and PD-L1 were obtained from melanoma tissue samples from groups 1 and 2 using standard immunohistochemistry. Scale bar 200 μm.