Tumor Organoids & Fragments
Patient-Derived 3D Tumor Models: Immune-Native Organoids and Tumor Fragments
Explicyte establishes short-term 3D tumor models directly from fresh patient tumor tissue, retaining endogenous immune populations for functional immunotherapy testing.
By capturing patient-specific tumor and immune features, these models provide a human-relevant in vitro platform to investigate treatment response, reduce reliance on animal models and strengthen translational evidence before clinical studies.
TUMOR ORGANOIDS AND FRAGMENTS
Why immune-native 3D tumor models ?
Patient-derived 3D tumor models are in vitro cultures grown directly from a patient's tumor — as organoids or intact tumor fragments — that preserve both the tumor cells and their native immune populations for functional immunotherapy testing.
Custom 3D models
Through our biobank network, we source fresh tumor tissue from biopsies or surgical resections and establish short-term patient-derived 3D models tailored to the program - early-passage organoids or intact tumor fragments.
Translational relevance
Both formats preserve patient-specific tumor features and heterogeneity. Early organoids retain the native immune fraction short-term; intact fragments additionally preserve tissue architecture and TME spatial organization.
Mechanistic readouts
Beyond supernatant analysis and kinetic functional readouts, we bring spatial biology — digital pathology and single-cell spatial transcriptomics — to resolve where and how an agent acts, down to mechanism of action.
For immunotherapy testing, patient-derived 3D models are most informative when they retain the immune context in which the treatment is expected to act. Our early organoid and tumor-fragment models preserve patient-derived immune populations over short experimental windows, while tumor fragments additionally retain native tissue architecture. Combined with functional and spatial readouts, these models allow us to characterize where immune responses emerge within the tumor and which cellular programs are associated with treatment response.
Imane Nafia, PhD
Chief Scientific Officer, Explicyte
Early tumor organoids
Immune-native tumor organoids (PDTOs)
Short-term patient-derived tumor organoids established directly from fresh tumor tissue with no or minimal passage, retaining a fraction of endogenous immune populations during the experimental window.
At a glance
Core features of early PDTOs
- Origin
- Fresh patient tumor tissues, no/minimal passage
- Immune content
- Fraction of endogenous immune populations retained
- Experimental window
- ~7 days
- Readouts
- Flow cytometry · cytokines · functional response kinetics
- Best for
- Early immunotherapy testing on patient-proximal organoids
Organoid — 1 week
TNBC patient tumor
Preserved immune fraction, IL2-sustained CD8 persistence
Early immune-native TNBC organoids retain a fraction of T cells relative to the parent tumor. Under IL2, the CD8 compartment persists through day 7, where the untreated condition declines — native immune dynamics that respond to culture conditions rather than a static endpoint.
Early immune-native TNBC PDOs are immunotherapy-responsive
Early immune-native TNBC PDOs show treatment-induced immune modulation. CD3 stimulation and nivolumab modulate the CD45, CD3, CD4 and CD8 compartments, providing a functional readout of immune engagement in patient-derived 3D cultures.
PDTF MODELS
Patient-Derived Tumor Fragments
A highly patient-proximal 3D model that retains intact tissue architecture and the native immune infiltrate.
At a glance
Core features of PDTFs
- Origin
- Fresh patient tumor tissues
- Immune content
- Endogenous infiltrate retained in situ
- Architecture
- Native tumor/TME architecture preserved
- Experimental window
- 2–5 days
- Readouts
- Flow cytometry · cytokines · pathology · spatial profiling
- Best for
- Immunotherapy response and biomarker evaluation on intact tumor tissue before clinical trial initiation
2-day colorectal cancer fragment, treated with anti-CD3
A quantifiable native immune infiltrate
Flow cytometry of a CRC fragment resolves the native immune infiltrate directly from patient tissue — T cells (CD8, CD4), a dominant myeloid compartment (CD11b, CD11c), NK (CD16), and B cells (CD19) — each measurable as a fraction of viable CD45⁺ cells before any treatment.
Immune subsets modulated under immunotherapy
Native immune cells in CRC fragments shift under treatment. Across 2- and 5-day windows, aCD3 and aCD3 + nivolumab modulate the CD45, CD8, CD11b, and CD11c compartments — the native infiltrate responding, not just persisting.
Functional IFN-γ response
Fragments are functionally responsive to immunotherapy: aCD3 + nivolumab drives a marked IFN-γ release over untreated and single-agent conditions at both 2 and 5 days — a functional secretome readout on intact patient tissue.
Making a difference as a preclinical CRO in oncology
Why work with Explicyte
Proven experience
>10 years in preclinical immuno-oncology, with deep expertise in functional assays and tumor microenvironment profiling across in vitro and ex vivo models.
Built around your program
A PhD-level study director designs your study around your indication, tumor model, and immunotherapy, sourcing fresh biopsies through our biobank network.
Beyond functional readouts
A multiomic platform to resolve mechanism of action alongside the functional data — flow cytometry, secretome analysis, digital pathology, and single-cell spatial transcriptomics.
Reports you can act on
Progress reports let you adjust the plan as the study runs; final reports arrive with ready-to-publish data that holds up in due diligence.
Paul Marteau, PharmD (study director), Imane Nafia, PhD (CSO), Loïc Cerf, MSc (COO), Alban Bessede, PhD (founder, CEO), Jean-Philippe Guégan, PhD (CTO)
Contact our team
Discuss your 3D tumor model study
Tell us about your indication, therapeutic modality and the biological questions you want the model to answer. We can help select the appropriate patient-derived model, experimental window and readouts.
Patient-derived 3D tumor models: common questions
Frequently asked questions
What are patient-derived 3D tumor models?
Patient-derived 3D tumor models are established directly from fresh human tumor tissue and retain patient-specific tumor characteristics during short-term ex vivo culture. At Explicyte, we use two complementary formats: early immune-native tumor organoids, which retain a fraction of endogenous immune cells, and patient-derived tumor fragments, which additionally preserve native tissue architecture and the immune infiltrate in situ.
How do organoids and tumor fragments differ?
Early tumor organoids provide a flexible short-term 3D system retaining tumor cells together with a fraction of the endogenous immune compartment. Patient-derived tumor fragments require minimal tissue processing and additionally preserve native tissue architecture and spatial organization of the tumor microenvironment. The choice between formats depends on the biological question, therapeutic mechanism and readouts required.
Do these models keep a functional immune compartment?
These models are designed to retain endogenous tumor-infiltrating immune populations over the short experimental window. Immune composition and viability are characterized by flow cytometry, and functional responsiveness can be evaluated through treatment-induced changes in immune phenotype and cytokine secretion. As expected for ex vivo models, immune-cell persistence depends on the tumor sample, culture conditions and experimental duration.
What immunotherapies can be tested?
The models can be configured to evaluate immunotherapies whose mechanism depends on interactions within the tumor microenvironment. Our current datasets include PD-1 checkpoint blockade, T-cell stimulation and combination conditions. Additional modalities can be evaluated depending on target expression, tissue availability and the biological requirements of the therapeutic.
What readouts are available?
Readouts can combine flow-cytometry immune profiling, secretome analysis including cytokine measurements, treatment-response kinetics and spatial biology. Digital pathology and single-cell-resolution spatial transcriptomics can map treatment-associated cellular states and transcriptional programs within the tissue, supporting mechanistic interpretation of the functional response.
Can these models reduce reliance on in vivo studies?
Patient-derived 3D models provide a complementary human-relevant system that can reduce reliance on animal studies for selected mechanistic and efficacy questions. They preserve patient-specific tumor and immune features that are difficult to reproduce in animal models, while in vivo studies remain important when systemic exposure, pharmacokinetics, biodistribution or whole-organism immune responses need to be assessed.
Which indications and tumor types can you work with?
Through our biobank network, we can source fresh tumor tissue from biopsies or surgical resections, subject to tissue availability and study-specific inclusion criteria. We have generated immune-native models from TNBC and colorectal cancer and can assess the feasibility of additional solid-tumor indications according to the program.
How do you qualify patient-derived samples before treatment?
Because each patient sample is unique, model qualification is built into the study. Depending on the format, baseline assessments can include tissue or organoid viability, immune-cell content and composition, tumor characteristics and sample availability. These parameters are used to confirm assay suitability and support interpretation of treatment-induced responses.