How to Choose Immunodeficient Mice for Human Disease Research
Updated on 2026/10/30
The right immunodeficient mouse is the one whose remaining immunity, lifespan, and biology match your graft and your endpoints. There is no universal best strain. A host that works well for a fast-growing tumor cell line can fail a months-long PDX study or an irradiation-conditioned HSC humanization.
Since the first SCID-hu and hu-PBL-SCID models were reported in the late 1980s, researchers have used immunodeficient hosts to study human tumors, immune cells, hematopoiesis, and infection in vivo. If you need background on each strain first, see our introduction to common immunodeficient mouse models, which compares nude, SCID, NOD-SCID, and NKG mice side by side.
This guide focuses on the decision itself. It walks through six steps, from defining your research question to checking model characteristics, and ends with a checklist you can use when planning a study.
Step 1: Define the research question and readouts
Start by writing down the exact question the model must answer. Model choice follows from that question, not from which strain is most immunodeficient.
Then specify how the model will answer it:
- What will be engrafted: a tumor cell line, patient tumor tissue, PBMCs, CD34+ HSCs, or engineered cells such as CAR-T cells
- How long the study must run: weeks for a tumor efficacy or PBMC study, months for HSC humanization or slow-growing PDX
- What will be measured: tumor volume, survival, human cell chimerism, cytokines, persistence of therapeutic cells, toxicity
- What treatment will be given: antibodies, small molecules, cell therapies, radiation, or DNA-damaging chemotherapy
These four answers narrow the candidate strains before any other factor is considered.
Step 2: Match the graft and study design to a host
The graft is the single strongest driver of host choice. As a rule, the more primary or immune-derived the human material, the more severe the immunodeficiency it needs. Use the table below as a starting point, then confirm with Steps 3–6.
| Study type | Host options to consider | Why | Watch for |
|---|---|---|---|
| Human tumor cell line xenograft (CDX) | Nude mice | T cell deficiency is usually enough for established lines; low cost, easy tumor monitoring in hairless mice | Active NK cells can reject some lines; move to NKG if take rate is low |
| Patient-derived xenograft (PDX) | NKG mice | Primary tumor tissue engrafts poorly when NK cells or B cells remain | Take rate varies by tumor; composition can shift over passages |
| Hematologic malignancies | NKG mice | Primary leukemia/lymphoma cells need a host without T, B, and NK cells | Limited patient material, so engraftment efficiency matters |
| CAR-T or other cell therapy efficacy | Tumor-bearing NKG mice | No host lymphocytes to reject or compete with human effector cells | Xenogeneic GvHD narrows the readout window |
| PBMC humanization | NKG mice | Rapid, T cell-dominated human engraftment | GvHD develops within weeks; plan short studies |
| HSC (CD34+) humanization | NKG mice | NOD background plus Il2rg loss supports multilineage human reconstitution | Takes months to build; some human lineages develop poorly without human cytokines |
| Irradiation or DNA-damaging chemotherapy | Consider Rag1/Rag2 knockout hosts | Normal DNA repair tolerates higher doses | scid strains are radiosensitive; titrate dose if using them |
For HSC humanization, conditioning such as sublethal irradiation is common. That makes radiosensitivity (Step 4) part of the host decision, not just the protocol.
Step 3: Check which host immune components remain
Whatever immunity a host keeps is what can reject or clear your graft. For each candidate, check T cells, B cells, NK cells, macrophages, dendritic cells, and complement.
| Host | T cells | B cells | NK cells | Other innate defects |
|---|---|---|---|---|
| Nude (Foxn1 mutant) | Very few | Present | Retained*, elevated activity | None notable |
| Rag1/Rag2 knockout | Absent | Absent | Present | Depends on background |
| NOD-SCID | Absent | Absent | Reduced but present | NOD background: complement deficiency, impaired macrophages and APCs |
| NKG (NOD-scid Il2rg−/−) | Absent | Absent | Absent | NOD defects, plus loss of IL-2, IL-4, IL-7, IL-9, IL-15, and IL-21 signaling |
*activity depends on strain background and experimental conditions
Why genetic background matters
The same mutation behaves differently on different backgrounds. The NOD background is one reason NOD-based strains engraft human cells so well. Its SIRPα variant binds human CD47 and sends a “don’t eat me” signal, so mouse macrophages phagocytose fewer human cells. NOD mice also lack complement component C5 and have weaker NK and antigen-presenting cell function.
Background also sets MHC haplotype, behavior, and disease susceptibility. NOD mice develop spontaneous type 1 diabetes, but NOD-SCID and NKG mice do not, because the disease requires T cells [1].
Host–graft interactions
Human cells rely on mouse cytokines and growth factors that cross-react with human receptors. Where cross-reactivity is poor, some human lineages, such as myeloid cells and NK cells, develop weakly. If those lineages are your readout, consider strains engineered to express human cytokines.
Step 4: Check model characteristics that limit study design
Two strains with similar immune profiles can still differ in ways that decide whether a study works. Check these four properties before committing.
Leakiness. Some scid strains are “leaky”: a proportion of mice develop functional T and B cells, and this proportion increases with age [1]. Leakiness is relatively common in C.B-17-scid mice and less common in NOD-SCID mice. NKG mice show an extremely low incidence of T- and B-cell leakiness. Rag1- or Rag2-knockout mice do not exhibit scid-associated leakiness. For long-term studies, or when residual host lymphocytes could confound results, select a strain with minimal leakiness and consider screening for host T and B cells and serum immunoglobulins.
Radiosensitivity. The scid mutation impairs DNA-PKcs, encoded by Prkdc, compromising DNA double-strand break repair through non-homologous end joining. Scid-based strains, including NOD-SCID and NKG, are therefore highly sensitive to irradiation and certain DNA-damaging drugs [2]. Rag1- or Rag2-knockout mice do not have this scid-associated DNA repair defect and generally tolerate higher irradiation doses than scid-based strains. Nevertheless, conditioning doses should be validated for the specific strain and experimental protocol.
Breeding. Homozygous nude females have underdeveloped mammary glands, lactate poorly, and have reduced fertility. Nude colonies are usually maintained by mating heterozygous (nu/+) females with homozygous (nu/nu) males. Plan lead time and cohort size accordingly.
Husbandry. All immunodeficient strains are highly susceptible to infection. They need barrier housing with sterilized food, water, bedding, and cages [3]. Budget for this when comparing models, since facility constraints can rule out an otherwise ideal strain.
Step 5: Control extrinsic factors
Extrinsic factors are not part of the host–graft biology, but they often explain why the same model gives different results in different labs. Define them in the protocol before the study starts.
| Factor | What to define | Why it matters |
|---|---|---|
| Graft preparation | Viability, cell number or fragment size, passage, time from collection | Low viability or delayed processing reduces take rate |
| Administration | Route (subcutaneous, intravenous, intrafemoral, orthotopic), injection volume | Route changes homing, growth kinetics, and metastasis |
| Conditioning | Irradiation dose or chemical conditioning, timing before engraftment | Needed for many HSC models; scid hosts tolerate less |
| Donor variability | Number of PBMC, HSC, or tumor donors; donor matching across arms | One donor can bias efficacy or GvHD timing |
| Animal factors | Age, sex, body weight at engraftment | Affects engraftment, residual immunity, and drug exposure |
| Environment | Housing, bedding, temperature, light cycle, diet, health status | Influences infection risk and pharmacokinetics |
Step 6: Review Published Evidence and Validate Your Choice
A short, structured literature search turns the factors above into evidence. It shows which hosts others have used for the same graft and endpoint, and which factors actually changed outcomes.
- Run a quick scoping review. Use free databases such as PubMed to find studies with the same graft type, disease, and readout. Note which strains, doses, and timelines they used.
- Add human clinical context. Check whether the endpoint you plan to measure has translated to patients, so the model answers a clinically relevant question.
- Design a systematic search. Turn what you learned into defined search terms and inclusion criteria, and search more than one source.
- Add vendor characterization data. Ask suppliers for engraftment rates, lifespan, leakiness, and baseline immune profiles for each candidate strain. No public database holds all of this.
- Shortlist and pilot. Narrow to one or two hosts and, where possible, run a small pilot to confirm take rate and timing before the full study.
Immunodeficient mouse selection checklist
Use this list when planning a study or briefing a model supplier.
- The research question and primary endpoint are written down.
- The graft type is defined: cell line, PDX, PBMC, HSC, or engineered cells.
- The study length is estimated, including time to engraft.
- Host immune components that could reject the graft have been ruled out.
- Strain lifespan exceeds the planned study length with margin.
- Leakiness is acceptable for the study length and readout.
- Any irradiation or DNA-damaging treatment is compatible with the host’s DNA repair.
- Needed human lineages can develop with the cytokines the host provides.
- Graft preparation, route, conditioning, and donors are specified.
- Barrier housing and breeding lead time are confirmed.
- Published studies and vendor data support the chosen host.
Need help choosing a model?
Cyagen’s scientists can help match your graft, timeline, and endpoints to the right host, from nude and NOD-SCID mice to NKG and humanized NKG models. Explore Cyagen's immunodeficient mouse models to find options for your study.
👉 [Discuss Your Immunodeficient Mouse Model Requirements with Our Scientists]
👉 [Explore Full Validation Data of Our Immunodeficient Mouse Models]
References
[1] Chen J, Liao S, Xiao Z, Pan Q, Wang X, Shen K, Wang S, Yang L, Guo F, Liu HF, Pan Q. The development and improvement of immunodeficient mice and humanized immune system mouse models. Front Immunol. 2022 Oct 19;13:1007579. doi: 10.3389/fimmu.2022.1007579. PMID: 36341323; PMCID: PMC9626807.
[2] van der Zalm AP, Bootsma S, Rodermond HM, Oei AL, Bijlsma MF. Local irradiation of patient-derived tumors in immunodeficient mice. STAR Protoc. 2023 Mar 17;4(1):102098. doi: 10.1016/j.xpro.2023.102098. Epub 2023 Feb 7. PMID: 36825807; PMCID: PMC9929630.
[3] Monzavi SM, Muhammadnejad S, Mansouri V, Ashraf H, Ahmadbeigi N. Unwanted disorders and xenogeneic graft-versus-host disease in experimental immunodeficient mice: How to evaluate and how to report. Animal Model Exp Med. 2025 Jan;8(1):20-29. doi: 10.1002/ame2.12509. Epub 2024 Nov 27. PMID: 39601130; PMCID: PMC11798742.
Frequently Asked Questions (FAQs)
Should I use male or female immunodeficient mice?
At what age should mice be engrafted?
Can I evaluate antibody-mediated effector functions, such as ADCC and ADCP, in immunodeficient mice?
Can I test immune checkpoint inhibitors in immunodeficient mice?
Will the same tumor grow the same way in different hosts?
