Our expertise & capacities in Digital Spatial Profiling (DSP)

digital spatial profiling DSP services immuno-oncology CRO services

Flexible tissue sampling, in-house capacities

  • Preclinical (mouse) or clinical specimens (human): frozen & FFPE tissue samples, including biopsies
  • On-site capacities: fixation & paraffin embedding (FFPE tissues), slicing
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Tissue Preparation: morphological & profiling markers

  • Fluorescent morphological markers: eg. Nuclei (Sytox), Immune cells (CD45), Tumor cells (PanCK). 4 channels available. Custom immunostainings
  • Digital Spatial Profiling probes: in situ hybridization probes (RNA) targeting over 18,000 protein-coding genes from Whole Transcriptome Atlas (WTA – both mouse and human)
nanostring spatial transcriptomics CRO services Immuno-oncology markers

Acquisition with GeoMx® DSP platform by Nanostring

  • Whole slide imaging 
  • Definition of regions of interest and segmentation strategy based on morphological markers and assisted by a trained pathologist. Eg. Tumor compartment (PanCK+) vs Stroma compartment (PanCK-)
  • Virtual session with sponsor for tailored analysis
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Bioinformatics & data representation

  • Digital quantitation with integrated data normalization
  • Differential gene expression – production of heatmaps and volcano plots
  • In-depth statistical analysis to decipher MoA, explore signaling pathways, gene signatures, immune cell estimation (data deconvolution) etc…

Why working with Explicyte?

Experts
in Immuno-Oncology

  • 100+ samples already analyzed by spatial transcriptomics in the context of preclinical & clinical studies to discover and validate novel targets, biomarkers, and characterize the response to cancer immunotherapies
  • 10+ peer-reviewed papers based on spatial transcriptomic data generated by Explicyte

Personalized
approach

  • Custom morphological markers and profiling panels (cancer transcriptome, immune pathways, immuno-oncology protein panels)
  • A dedicated study director (PhD) to tailor the experimental plan to your need and discuss results
  • In-house data analysis capacities and complementary technologies (digital pathology, proteomics, flow cytometry, …)

Illustrative data: Spatial Transcriptomics for Immuno-Oncology

The GeoMX platform allows profiling the transcriptomes of specific cell types within tissues. Multiplex panels with Sytox/PanCK/CD8 or Sytox/PanCK/CD45/αSMA were used to characterize the transcriptome of tumor cells (PanCK-positive / green), CD8+ T cells (CD8-positive / red), immune cells (CD45-positive / yellow), and fibroblasts (αSMA-positive / purple).

GEOMX Nanostring services CRO immuno-oncology DSP

Spatial transcriptomic analysis reveals differentially expressed genes in tumor microenvironments. This study analyzed the tumor bed and microenvironment of six patients (divided into two groups of 3) using whole transcriptome Atlas Panel on the GeoMX DSP platform. Spatial transcriptomics allowed researchers to identify genes differentially expressed between the two groups (B – Volcano plot). Notably, top variant genes within the immune microenvironment effectively predicted patient clustering (C).

Spatial transcriptomic analysis tumor CRO services

Estimation of immune cell composition based on data deconvolution.  Tertiary lymphoid structure from sarcoma patient was segmented in CD20+ and CD20- areas on the GeoMX DSP platform and analyzed using the whole transcriptome atlas panel (A). Estimation of immune cell composition using SpatialDecon algorithm (Nanostring) (B).

digital spatial profiling analysis services immuno-oncology tumor biopsies TLS

Pathway analysis, to capture the bigger picture. This technique relies on databases of known gene signatures (A) that are used in gene set enrichment analyses (B) to identify biological processes that are dysregulated in the groups you studied (C).

pathway analysis spatial transcriptomics CRO

Your contacts

explicyte team 2024

Jean-Philippe Guégan, PhD (Study Director), Imane Nafia, PhD (Chief Scientific Officer), Alban Bessede, PhD (Chief Executive Officer), Loic Cerf, MSc (Chief Operations Officer), Paul Marteau, PharmD (Study Director)

Tell us about your project !

    Select department:

    Spatial Transcriptomics CRO Services I GeoMx platform by Nanostring I DSP

    In the era of immuno-oncology, it’s critical to unravel mechanisms of action underlying sensitivity or resistance to current immunotherapies in order to i) identify predictive biomarkers of response and then ii) discover novel actionable therapeutic targets. However, cancer biology, particularly anti-tumor immunity, is complex and is characterized by a continuous interaction between tumor cells and their microenvironment – both characterized by specific features, which occurs heterogeneously within the space. It therefore becomes primordial to benefit from a technological platform that allows to deal with the tumor biology complexity/heterogeneity and get specific investigations in compartments of interest (e.g. tumor vs stroma). Thanks to the GeoMx platform (Nanostring Inc.), which combines the spatial resolution of immunohistofluorescence with the high-plex gene/protein expression analysis, the Digital Spatial Profiling (DSP) revolution has started. Starting from specimens as simple as FFPE tissue samples, this novel technology offers through selected panels the simultaneous analysis of up to 96 mRNAs or 10’s-100’s proteins in several regions of interest (ROIs) divided in two compartments. In addition to these panels, the comprehensive Cancer Transcriptome Atlas (CTA) – covering 1,800 genes and more than 50 cancer-related pathways -, as well as the Whole Transcriptome Atlas (WTA) – covering 18,000 protein-coding human genes – are now running.

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