Resolving the intricate cellular diversity within tumors is crucial for advancing cancer research and developing treatment strategies. MERSCOPE®, with its high sensitivity and industry-leading resolution, offers the power to spatially map and quantify up to 1000 genes simultaneously at a single-cell resolution. This powerful platform provides comprehensive tumor profiling, including mapping gene expression across entire tissues, which enhances your understanding of cellular composition, tumor biology, and treatment responses to better understand patient outcomes.
Explore the capabilities of MERSCOPE® inside our human immuno-oncology data release. The platform uses formalin-fixed paraffin-embedded (FFPE) cancer samples to perform single-cell spatial transcriptomics. This release also features 16 MERFISH datasets across eight human tumor types, including two colon, two liver, two melanoma, four ovarian, two prostate, two lung, one breast, and one uterine cancer sample(s).
Each dataset features the analysis of 500 genes to represent about 4 billion transcripts within 9 million cells in total. This robust dataset allows you to delve into detailed immune cell characterization within the tumor microenvironment. Access this rich dataset to see how MERFISH can perform high multiplexing, high-resolution single-cell, and spatial genomics analysis for your FFPE samples.
FFPE Sample Preparation with MERSCOPE®
Formalin fixed-paraffin-embedded tissue processing is the most economical form of archivable tissue storage. To expand the scope of your potential discovery, MERSCOPE® supports tumor profiling using your FFPE samples. This protocol can be used to maintain nucleic acid integrity within your FFPE samples to get the most out of them during mapping with MERSCOPE®:
Our MERSCOPE® PanCancer Pathways (human) panel comes predesigned with 500 genes from cancer-related pathways to simplify your experimental design process.
The MERSCOPE®-compatible PanCancer Pathways (human) panel revolutionizes your approach to cancer research by spatially visualizing gene expressions in each cell across whole tumors. The panel includes 500 genes; 261 genes from canonical cancer pathways, 48 from oncological pathways, 69 for immune-specific markers, and 122 genes with mutational significance. This varied data set helps you view specific oncogenes, uncover potential therapeutic targets, and understand the molecular underpinnings of cancer progression.
Profiling tumors with the PanCancer panel sheds light on the heterogeneity within tumors, allowing you to detect variations in gene expression that are key to personalizing treatment strategies. This heterogeneity, coupled with the detailed mapping of the tumor’s cellular organization, provides critical insights into how cancer develops and interacts with surrounding tissues. Such understanding is pivotal in exploring new methods to disrupt cancer growth and metastasis.
Figure: Clustered cells are spatially displayed across a Human Breast Cancer tissue section.
Likewise, you can use the panel to monitor changes within tumor cells in response to treatment. By observing genetic expression changes within different cell types of a tumor, researchers can study treatment strategies with greater precision to enhance patient outcomes. The MERSCOPE®– PanCancer Pathways panel offers a comprehensive solution to unravel the complexities of tumor biology and forge a new era of personalized cancer therapies.
Unlock the secrets of cancer with a comprehensive suite of 500 genes, revealing deep insights into canonical signaling pathways.
Dive into the complexity of tumor dynamics to understand progression and response mechanisms through spatial gene analysis.
Illuminate the intricate interactions between tumor, immune, and stromal cells to reveal the full landscape of human cancers.
Grow your research potential with a panel compatible with multiple human cancers, including breast, lung, liver, prostate, colon, ovarian, brain cancers, and melanoma.
Leverage proven performance across fresh frozen, fixed frozen, cell culture, and FFPE samples, maximizing the potential of your research.
Figure: The PanCancer Pathways Panel allows researchers to explore tumor biology and the interactions of tumor cells with stromal and immune cells.
Using combinatorial labeling, sequential imaging, and error-resistant barcoding, MERSCOPE® allows you to observe the expression location of tens of thousands of specific genes tumor-wide, down to the single-cell scale. This variable-scale tumor profiling empowers you to observe the location of your gene of interest within individual cells and detect heterogeneity within a whole tumor in staggering detail.
Figure A: Spatial distribution of select genes, including ACTA2 (green), CD3D (red), LGR5 (light green), MKI67 (magenta), and PECAM1 (blue) from 500 genes analyzed across the tissue. Scale bar: 1mm. Figure B: Zoom-in of the boxed region in A. Scale bar: 1 mm. Figure C: Zoom-in of the boxed region in B, with cell boundary polygon masks shown in grey. Scale bar: 250 µm.
MERSCOPE® offers a clear assessment of tumor development by showing you the arrangement of specific cell types within the tumor microenvironment of any tumor type. Many sample types are compatible with MERSCOPE®, including fresh frozen, fixed frozen, cell culture, and even FFPE samples. Our goal is to make data like this possible for your samples.
Figure: FFPE cancer samples, including breast cancer, colon cancer, melanoma, lung cancer, liver cancer, ovarian cancer, prostate cancer, and uterine cancer, were analyzed by MERSCOPE® using the Human Immuno-Oncology predesigned panel together with cell boundary staining kit to label the cell boundary. Cells are segmented and subjected to single-cell analysis. Identified cells in each sample are colored to show the spatial distribution of different cells across the sample. Scale bar: 1mm.
Have confidence in the results of your tumor profiling efforts. MERSCOPE data is highly accurate, as shown by high correlation between counts from replicates from the same tumor and a strong correlation between MERFISH counts and bulk RNA-seq. Map tumor expression with transcript quantification measurements you can rely on.
Figure A Correlation of MERSCOPE® data between two human ovarian cancer slices from the same patient. The correlation coefficient is 0.99, indicating the measurement is highly reproducible.
Figure B Correlation analysis between MERFISH counts and FPKM values from bulk RNA sequencing on Human Ovarian Cancer 1. The correlation coefficient is 0.82, indicating the measurement is highly accurate.
Crafting a gene panel that targets the intricate mechanisms of cancer biology demands both precision and a deep understanding of oncogenic processes. To streamline this process and help you save time, we’ve developed the 500-gene PanCancer Pathways Panel, which integrates insights from leading oncology databases like OncoKB, MutSigCV, and The Cancer Genome Atlas. This panel offers a robust and resource-efficient solution for insights into the spatial transcriptomics of cancer while unveiling the molecular underpinnings and interactions that drive tumorigenesis and progression.
The MERSCOPE® platform produces subcellular spatial transcriptomic data for whole tissue sections, making it ideal for tumor profiling. This empowers researchers and clinicians to assess the heterogeneity within a cross-sectional tumor sample, quantify oncogenes of interest, and predict tumor development.
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