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Proteomic dysregulation plays an important role in the spread of diffusely infiltrating gliomas, but several relevant proteins remain unidentified. Digital spatial processing (DSP) offers an efficient, high-throughput approach for characterizing the differential expression of candidate proteins that may contribute to the invasion and migration of infiltrative gliomas.
Diffusely infiltrating gliomas are associated with high morbidity and mortality due to the infiltrative nature of tumor spread. They are morphologically complex tumors, with a high degree of proteomic variability across both the tumor itself and its heterogenous microenvironment. The malignant potential of these tumors is enhanced by the dysregulation of proteins involved in several key pathways, including processes that maintain cellular stability and preserve the structural integrity of the microenvironment. Although there have been numerous bulk and single-cell glioma analyses, there is a relative paucity of spatial stratification of these proteomic data. Understanding differences in spatial distribution of tumorigenic factors and immune cell populations between the intrinsic tumor, invasive edge, and microenvironment offers valuable insight into the mechanisms underlying tumor proliferation and propagation. Digital spatial profiling (DSP) represents a powerful technology that can form the foundation for these important multilayer analyses.
DSP is a method that efficiently quantifies protein expression within user-specified spatial regions in a tissue specimen. DSP is ideal for studying the differential expression of multiple proteins within and across regions of distinction, enabling multiple levels of quantitative and qualitative analysis. The DSP protocol is systematic and user-friendly, allowing for customized spatial analysis of proteomic data. In this experiment, tissue microarrays are constructed from archived glioblastoma core biopsies. Next, a panel of antibodies is selected, targeting proteins of interest within the sample. The antibodies, which are preconjugated to UV-photocleavable DNA oligonucleotides, are then incubated with the tissue sample overnight. Under fluorescence microscopy visualization of the antibodies, regions of interest (ROIs) within which to quantify protein expression are defined with the samples. UV light is then directed at each ROI, cleaving the DNA oligonucleotides. The oligonucleotides are microaspirated and counted within each ROI, quantifying the corresponding protein on a spatial basis.
Diffusely infiltrating gliomas are the most common type of malignant brain tumor in adults and are invariably lethal. The propensity for glioma cells to migrate extensively in the brain is a major therapeutic challenge. The mechanism by which they spread involves directed migration and unchecked invasion. Invasive glioma cells have been shown to exhibit tropism and migration along white matter tracts1, with recent research implicating demyelination of these tracts as an active, protumorigenic feature2. Invasion is mediated by an epithelial-to-mesenchymal transition, in which glioma cells acquire mesenchymal properties by....
The protocol outlined below follows the guidelines of the Dartmouth-Hitchcock Human Research Ethics Committee. Informed consent was obtained from the patients whose tissue samples were included in this study. See the Table of Materials section for details related to all materials, reagents, equipment, and software used in this protocol.
1. Slide preparation17
Figure 4 shows the representative results from a DSP experiment performed on samples of glioblastoma. A heat map is presented, illustrating one of the methods by which to capture data visually using the DSP software. Rows represent protein targets, and each column corresponds to a region of interest. A color range of blue to red denotes low to high expression, respectively. Variability of color within a row reflects regional protein heterogeneity and suggests a possible spatial association w.......
Given the diversity of proteins that could potentially influence the aggressiveness of gliomas and the notion that several of these proteins remain undiscovered, a high-throughput protein quantification method is an ideal technologic approach. Additionally, given that spatial data in oncologic samples often correlates with differential expression18, incorporating spatial profiling into the protein quantification approach allows for more effective analysis.
The high-thro.......
The authors have no conflicts of interest to disclose.
The authors acknowledge the support of the Laboratory for Clinical Genomics and Advanced Technology in the Department of Pathology and Laboratory Medicine of the Dartmouth Hitchcock Health System. The authors also acknowledge the Pathology Shared Resource at the Dartmouth Cancer Center with NCI Cancer Center Support Grant 5P30 CA023108-37.
....Name | Company | Catalog Number | Comments |
BOND Research Detection System | Leica Biosystems, Wetzlar, Germany | DS9455 | Open detection system containing open containers in a reagent tray |
BOND Wash | Leica Biosystems, Wetzlar, Germany | AR950 | 10X concentrated buffer solution for washing fixed tissue |
Buffer W | NanoString, Seattle, WA | contact company | Blocking reagent |
Cy3 conjugation kit | Abcam, Cambridge, UK | AB188287 | Cy3 fluorescent antibody conjugation kit |
GeoMx Digital Spatial Profiler (DSP) | NanoString, Seattle, WA | contact company | System for imaging and characterizing protein and RNA targets |
GeoMx DSP Instrument BufferKit | NanoString, Seattle, WA | 100471 | Buffer kit for GeoMX DSP (including buffers for sample processing and preparation) |
GeoMx Hyb Code Pack_Protein | NanoString, Seattle, WA | 121300401 | Controls for running GeoMX DSP experiemtns |
GeoMx Immune Cell Panel (Imm Cell Pro_Hs) | NanoString, Seattle, WA | 121300101 | Protein module with targets for human immune cells and immuno-oncologic targets |
GeoMx Pan-Tumor Panel (Pan-Tumor_Hs) | NanoString, Seattle, WA | 121300105 | Protein module with targets for multiple human tumor types and for markers of epithelial-mesenchymal transition |
GeoMx Protein Slide Prep FFPE | NanoString, Seattle, WA | 121300308 | Sample preparation reagents for GeoMX DSP protein analysis |
IDH1-R132H antibody | Dianova, Hamburg, Germany | DIA-H09 | Monoclonal antibody against human IDH1 R132H |
LEICA Bond RX | Leica Biosystems, Wetzlar, Germany | contact company | Fully automated IHC stainer |
Master Kit--12 reactions | NanoString, Seattle, WA | 100052 | Materials and reagents for use with the nCounter Analysis system |
nCounter Analysis System | NanoString, Seattle, WA | contact company | Automated system for multiplex target expression quantification (to be used with GeoMx DSP) |
TMA Master II | 3DHistech Ltd., Budapest, Hungary | To create the tissue microarray block |
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