Tumor Organoids & Fragments
Patient-Derived 3D Tumor Models: Immune-Native Organoids and Tumor Fragments
Our team builds 3D tumor models from fresh patient tumor tissues (biopsies or surgical resections), with the native immune compartment preserved.
Reflecting real in-human sensitivity and resistance, they offer an in vitro route to replace in vivo studies and strengthen evidence before trials.
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 obtain fresh tumor biopsies for your indication of interest and grow them in 3D at low passage — organoids or intact fragments, built around your program.
Translational relevance
The models preserve tissue architecture, the native tumor microenvironment, and patient heterogeneity. Sensitivity and resistance patterns emerge on human tumor material — reflecting the patient, not a surrogate host.
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.
A patient-derived 3D model is only useful if it still contains the patient’s own immune system — ours do. Working in three dimensions also lets us study how a drug penetrates the tumor, and pairing that with spatial platforms shows us where it acts and how the immune response plays out, cell by cell.
Imane Nafia, PhD
Chief Scientific Officer, Explicyte
Early TUMOR organoids
Immune-native tumor organoids (PDTOs)
True early-stage organoids derived directly from patient tissue, with no or minimal passage — so the native immune compartment is still present and functional when you test on them.
At a glance
Core features of early PDTOs
- Origin
- Fresh patient tumor tissues, no/minimal passage
- Immune content
- Native — CD45, CD3, CD4, CD8 identifiable
- Readouts
- Flow immune profiling, treatment-response kinetics
- Timeline
- Short (early / ~1-week window)
- 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
The same organoids respond to immunotherapy in vitro: CD3 activation and nivolumab shift the CD45, CD3, CD4, and CD8 compartments, giving a functional readout of immune engagement on patient-proximal material.
PDTF MODELS
Patient-Derived Tumor Fragments
The closest 3D model to the patient tumor — intact fragments that recapitulate tissue features and architecture, with the native immune infiltrate preserved in place.
At a glance
Core features of PDTFs
- Origin
- Fresh patient tumor tissues, tissue architecture retained
- Immune content
- Native infiltrate in place — CD45, CD8, myeloid (CD11b/c), CD16, CD19
- Readouts
- Flow immune profiling, IFN-γ / secretome, treatment-response
- Timeline
- Short (2–5 day windows)
- 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, the immunotherapy you're testing, and the questions you want the model to answer — we'll scope the right model (organoids or fragments), readouts, and reporting, and send a fit-for-purpose proposal.
Patient-derived 3D tumor models: common questions
Frequently asked questions
What are patient-derived 3D tumor models?
They are in vitro cultures grown directly from a patient’s tumor that preserve both the tumor cells and their native immune populations. Explicyte offers two formats: immune-native organoids (PDOs), grown from patient tissue at no or minimal passage, and patient-derived tumor fragments, which keep the tissue architecture and immune infiltrate intact. Both allow functional immunotherapy testing on patient-proximal material, in vitro.
How do organoids and tumor fragments differ?
Organoids are early-stage cultures grown from patient tissue with no or minimal passage, suited to short-timeline immunotherapy testing where a preserved immune fraction is enough. Tumor fragments are the closest model to the patient tumor: they retain intact tissue architecture, the native tumor microenvironment, and the immune infiltrate in place, making them well suited to studying immune-cell modulation and functional response on genuine tissue. We help you choose the format that fits your program and question.
Do these models keep a functional immune compartment?
Yes. Native immune populations survive into culture and stay identifiable and functional — including T cells (CD3, CD4, CD8), myeloid cells (CD11b, CD11c), NK cells (CD16), and B cells (CD19), quantified by flow cytometry as a fraction of viable CD45⁺ cells. In organoids, the CD8 compartment can be sustained under IL2; in fragments, the native infiltrate is modulated under immunotherapy rather than simply persisting.
What immunotherapies can be tested?
The models respond to a range of immunotherapy approaches in vitro, including checkpoint inhibitors such as anti-PD-1 (nivolumab), T-cell–activating agents such as anti-CD3, and combinations. Each study is configured to the mechanism the therapeutic depends on. Contact us to discuss whether your modality fits the model.
What readouts are available?
Readouts span three layers: flow-cytometry immune profiling of native populations, functional secretome analysis of the supernatant including kinetic cytokine readouts such as IFN-γ, and spatial biology — digital pathology and single-cell spatial transcriptomics — to resolve where and how an agent acts, down to mechanism of action.
Can these models replace in vivo studies?
They offer an in vitro alternative to animal models that keeps what animal models cannot: intact human tissue architecture, the native tumor microenvironment, and real patient heterogeneity. Sensitivity and resistance patterns emerge on human tumor material rather than in a surrogate host, which can reduce reliance on in vivo work and strengthen evidence ahead of trials.
Which indications and tumor types can you work with?
Through our biobank network, we obtain fresh tumor biopsies matched to your indication of interest. We have generated immune-native models from indications including triple-negative breast cancer (TNBC) and colorectal cancer (CRC), and can scope other solid-tumor indications on request.