Explicyte provides standalone bioinformatics services for transcriptomic and digital pathology datasets used in translational research. While data analysis is often the final step of a study, it can become a bottleneck that delays decision-making when the right expertise is not available. With a strong focus on fast and robust processing of large datasets, our data science team analyzes raw data from Bulk RNA-seq & GeoMx DSP, 10x Genomics single-cell and spatial transcriptomics, and digitized pathology slides (IHC/IF).
- Fast turnaround: receive your custom data analysis report within 4 weeks.
- Human expertise and AI: we automate whenever relevant, while keeping biological interpretation in the hands of experienced bioinformaticians
- Strong expertise in FFPE-based oncology: helping uncover and validate new targets and biomarkers
To better understand the mechanisms underlying UPS metastasis, a team led by Prof. Antoine Italiano (Institut Bergonié, University of Bordeaux, INSERM U1312 BRIC) performed an integrated multi-omics analysis of paired primary and metastatic UPS samples, followed by functional validation in relevant patient-derived models.
Spatial biology (Explicyte)
As part of this work, Explicyte performed spatial transcriptomic profiling using the GeoMx Digital Spatial Profiler (Whole Transcriptome Atlas; >18K genes). The spatial analyses were conducted on 3 paired primary tumors and matched metastases enabling a direct comparison of tumor and microenvironmental programs across disease stages.
Key observations included:
- Upregulation of hypoxia, glycolysis, and EMT-related programs in metastases, consistent with a more aggressive, metastasis-associated biology.
- Enrichment of endothelial-cell signatures in metastatic samples, suggesting increased angiogenesis compared with primary tumors.
- Higher immune infiltration in primary tumors (including CD8+ T cells, NK cells, and memory B cells), supporting the notion of a more immune-suppressive / immune-excluded state in metastatic lesions.
To further support these findings, we confirmed a reduction in CD8+ T-cell infiltration in metastases using a multiplex immunohistofluorescence (mIHF) panel in five paired primary/metastatic cases.
Bulk RNAseq
In parallel, the team analyzed paired primary and metastatic tumor samples from 13 patients using bulk RNA-seq to capture global transcriptomic changes associated with metastatic progression. This analysis confirmed an enrichment of metastasis-associated pathways and identified 690 genes significantly altered between primary tumors and metastases. Among the top candidates, ADORA2B emerged as particularly compelling because:
- ADORA2B encodes a G protein–coupled adenosine receptor (A2B) implicated in metastatic progression in several epithelial cancers,
- ADORA2B is druggable, with inhibitors already being evaluated in clinical development programs.
Using public and third-party sarcoma datasets, the team further showed that ADORA2B is overexpressed in UPS and is associated with features of an immune-suppressive microenvironment in metastatic UPS—supporting ADORA2B as a promising therapeutic target in this indication.
Functional validation
To test whether ADORA2B plays a causal role in UPS aggressiveness, the authors generated ADORA2B knockout models using CRISPR-Cas9 in two patient-derived UPS cell lines.
- Transcriptomic profiling of ADORA2B-knockout cells confirmed downregulation of key pathways involved in metastatic biology.
- Functional assays demonstrated that ADORA2B loss reduces UPS cell proliferation, migration, and invasion, supporting a direct role in tumor aggressiveness.
The in vivo impact was then evaluated in Rag2-/- γc-/- mice:
- In an orthotopic model, tumors derived from ADORA2B-knockout cells showed markedly impaired growth, leading to significantly smaller, low-proliferating tumors compared with controls.
- In a forced metastasis model (tail-vein injection), ADORA2B-knockout cells produced substantially fewer metastases, translating into a striking survival benefit (100% survival in the knockout arm vs 0% in controls in this experimental setting).
Finally, the team evaluated a dual ADORA2A/ADORA2B inhibitor, M1069 (EMD Serono), currently assessed in early-phase trials. In vitro, M1069 reduced proliferation and invasion in UPS models, providing pharmacological support for the genetic findings.
Impact
Overall, this work identifies ADORA2B as a critical regulator of primary tumor growth and metastatic dissemination in UPS. It also highlights the therapeutic promise of targeting the adenosine axis, and specifically ADORA2B, as a strategy to disrupt metastatic progression and improve outcomes in this rare and aggressive cancer.
Read the paper
This research received funding from the Agence Nationale de la Recherche (“France 2030” / ANR 21 RHUS 0010).
Using single-cell and spatial transcriptomics profiling of vitiligo patient biopsies, the team demonstrates that similar CD8+ T-cell clusters infiltrate both lesional and non-lesional skin. The difference lies in the “regulatory layer”: normal-appearing skin is characterized by an enrichment in immune regulatory pathways (increased Treg infiltration and higher PD-1 expression on CD8+ T cells), consistent with tighter regulation of inflammation.
Building on the Phase 2 BARVIT trial (NCT04822584), which showed a clinical benefit of baricitinib combined with phototherapy for repigmentation, ImmunoConcEpT partnered with Explicyte to perform a paired pre/post immune profiling of skin biopsies using our automated multiplex IF workflow.
Our multiplex IF data support the proposed mechanism; after 9 months of treatment, non-lesional skin exhibits:
• reduced CD8+ T-cell infiltration
• increased PD-1 on CD8+ T cells and PD-L1 on dendritic cells
• an increased FOXP3+ / CD8+ T-cell ratio
Together, these results highlight the critical role of immune regulatory mechanisms to prevent inflammation & depigmentation in vitiligo.
> Read the article
Beyond the headline result, these findings reinforce a key idea: TLS can be pursued as a therapeutic objective—with the right engineering and delivery, CD40 agonism can reprogram the tumor microenvironment into a self-sustaining immune ecosystem.
Explicyte supported this work with multiplex IHF staining, enabling direct visualization of TLS formation in tumor tissue. This study highlights how our translational research platform helps partners measure and interpret the impact of new immunomodulatory agents—from TLS induction and maturation to dendritic-cell activation, HEV density, and chemokine programs—leveraging spatial biology + multiplex IHF with integrated analytics.
Explore our translational research platform
What types of datasets can Explicyte analyze?
At Explicyte, we provide bioinformatics support for a broad range of datasets used in translational research. This includes Bulk RNA-seq, GeoMx DSP, 10x Genomics single-cell and spatial transcriptomics datasets, as well as digitized pathology slides for image analysis in spatial biology workflows.
Can you analyze datasets generated outside Explicyte?
Yes. Our data analysis services are available as standalone offerings, so we can work on datasets generated by your internal team, a core facility, or another service provider. We regularly support clients who need expert interpretation of already generated data.
Do you support FFPE-based studies?
Yes. We have strong expertise in FFPE-based oncology studies, including biomarker-oriented transcriptomic and spatial biology projects. Our team is familiar with the specific analytical challenges associated with FFPE material and can help generate robust biological insight from these datasets.
How long does a typical data analysis project take?
Project timelines depend on the dataset type, the complexity of the study, and the level of analysis required. As a general rule, we aim to deliver custom data analysis reports within 4 weeks, with shorter timelines possible for more focused analysis packages.
Do you combine automated workflows with expert interpretation?
Yes. At Explicyte, we combine automation and AI-driven workflows with scientist-led interpretation. We automate wherever relevant to gain speed and robustness, while ensuring that the biological interpretation remains in the hands of experienced bioinformaticians.
Do you provide publication-ready outputs?
Yes. Our goal is not only to process datasets, but to generate results that are directly usable by scientific teams. Depending on the project, our deliverables can include structured reports, clear visualizations, publication-ready figures, and processed datasets to support internal decisions, partner discussions, abstracts, or manuscripts.
Can you adapt the analysis to our scientific objectives?
Yes. We do not apply a one-size-fits-all workflow. Our analyses are tailored to your study design, dataset structure, scientific question, timeline, and reporting needs. Whether your objective is biomarker discovery, treatment-response analysis, spatial interpretation, or figure generation, we adapt our approach accordingly.
Who do you work with?
We support biotech companies, pharmaceutical companies, academic teams, and translational research groups looking for fast and expert analysis of complex transcriptomic and digital pathology datasets.
Why work with Explicyte for data analysis services?
We combine a dedicated data science team, strong expertise in transcriptomics and digital pathology, recognized experience in FFPE-based oncology, and a commitment to delivering robust, actionable results. Our role is to help you turn complex raw data into insights that support real scientific and strategic decisions.
Talk to our team
Talk to our team !
Paul Marteau, PharmD (preclinical study director), Imane Nafia, PhD (CSO), Loïc Cerf, MSc (COO), Alban Bessede, PhD (founder, CEO), Jean-Philippe Guégan, PhD (CTO)