Here, we present a rapid, pure, and cost-effective method for establishing tumor organoids from the A549 cell line, suitable for preliminary tests and educational purposes.
Method Article
June 12th, 2026
Corresponding Authors: Xinhua Lin <xlin@fudan.edu.cn>, Bin Guo <binguo@fudan.edu.cn>
* These authors contributed equally
Here, we present a rapid, pure, and cost-effective method for establishing tumor organoids from the A549 cell line, suitable for preliminary tests and educational purposes.
Here, we describe a protocol for generating Cell Line-Derived Tumor Organoids (CDTOs) from the A549 human lung adenocarcinoma cell line. The protocol involves embedding 2D-expanded A549 cells in Matrigel and maintaining them in 3D culture medium for long-term culture. Recommended seeding density of 500 cells/µL was determined to support consistent organoid formation. The resulting CDTOs were characterized by hematoxylin and eosin (H&E) staining and immunofluorescence (IF). The organoids maintained high expression of the lung adenocarcinoma markers Thyroid Transcription Factor 1 (TTF-1), adhesion protein E-Cadherin (ECAD), and cytoskeleton protein Keratin 7 (KRT7). Furthermore, tight junction protein Zona Occludens 1 (ZO-1) expression showed dysregulated polarity of tumor organoids. This protocol offers a technically straightforward, cost-effective, and purely tumorous organoid platform for lung adenocarcinoma research. Its simplicity and reproducibility also make it suitable for undergraduate laboratory teaching, where it can help students acquire fundamental 3D tumor organoid culture techniques within a limited lab schedule.
Organoids are in vitro. self-organized three-dimensional (3D) structures that originate from stem cells and are capable of recapitulating biological complexities of real organs to a considerable extent1. The cells constituting organoids may derive from induced pluripotent stem cells or tissue-derived cells, the latter including normal stem/progenitor cells, differentiated cells, and tumor cells2. Compared with traditional two-dimensional culture systems and animal models, organoids can more closely mimic the physiological characteristics of the human body while offering greater experimental flexibility. Consequently, organoid technology has been widely applied in drug development3, personalized medicine4, and disease modeling5.
Numerous studies have established organoid models for a broad spectrum of cancers, including colorectal6, prostate7, pancreatic8, gastric9, hepatic10, biliary11, breast12, and neuroendocrine tumors. However, one of the major challenges in tumor organoid research lies in maintaining purity. For instance, a study on non-small cell lung cancer revealed that only 17% of the established organoids were purely tumorous, as tumor samples often contain a mixture of normal and malignant cells that are difficult to fully separate prior to culture13. This impurity issue can cause elimination of tumor cells by outgrowth of non-tumor cells, interfere with readouts of drug susceptibility tests, and lead to inaccurate molecular analyses, such as RT-qPCR or Western blot, where RNAs and proteins from tumor cells are diluted by uncontrollable proportions of contaminating cells.
To address this issue, researchers have explored the design of selective culture media that exploit the reduced dependency of tumor cells on certain growth factors, thereby inhibiting normal cell growth while promoting tumor cell expansion14. In addition, strategies such as cell sorting or monoclonal identification are being developed to construct pure tumor organoids.
This protocol describes the generation of Cell line-Derived Tumor Organoids (CDTOs) using the A549 human lung adenocarcinoma cell line, which has been reported to partially exhibit cancer stem cell-like properties, as well as enhanced clonogenicity, proliferative potential, and tumorigenicity in vitro.15. The resulting CDTOs maintained expression of lineage-specific biomarkers Thyroid Transcription Factor 1 (TTF-1)16, adhesion protein E-Cadherin (ECAD)17, and cytoskeleton protein Keratin 7 (KRT7)16 and exhibited physiological features characteristic of tumor organoids. This model is easy to establish and contains defined cancer cell components, making it suitable for researchers new to the tumor organoid field or those challenged by loss of tumor identity in primary tumor organoid cultures. Potential applications include preliminary drug susceptibility testing18, tumor microenvironment studies19, and educational training in 3D culture techniques.
The room temperature in the lab is 22–24 °C and is referred to as RT. Using a swing-bucket centrifuge is recommended. The reagents and the equipment used are listed in the Table of Materials.
1. Establishment of primary A549 organoids
2. Fixation, embedding, and sectioning of organoids
3. Hematoxylin and Eosin (H&E) staining
4. Whole-mount immunofluorescence staining
The general process of this protocol includes expanding 2D A549 cells into the exponential stage (Supplementary Figure 1A) and passage into 3D Matrigel to form organoids (Figure 1A). Upon encapsulation in Matrigel, cells proliferated and self-assembled, predominantly forming monoclonal organoids (Figure 1B). Its dense and convoluted morphology was uniform across passage (Supplementary Figure 1C). In comparison, most of these structures were spherical and increased in size with continued culture; a fraction adhered to the plate bottom from the outset, giving rise to 2D clones (Figure 1C). This adherent morphology was more frequently observed in high-serum conditions, such as organoids cultured with DMEM supplemented with 10% FBS (Supplementary Figure 1B). Seeding density gradients from 50–5000 cells/µL were conducted to assess their influence on colony-forming efficiency (CFE) and organoid size (Figure 1D). Figure 1E,F showcased the two statistics at day 7, and group 5000 cells/µL was excluded from the statistical analysis because the cells were too dense, resulting in poor light transmission and making accurate counting difficult. At the lowest density tested, organoids are poorly formed, manifested by a smaller colony size and lower forming efficiency. At 2000 and 5000 cells/µL, organoids began to shrink and fragment (Figure 1D) in the center of the gel during culture, resulting from limited nutrient diffusion. Combining the two statistics, 500 cells/µL showed optimal organoid growth with only a slightly lower CFE. Seeding at 500 cells/µL can also generate a clear visual appearance and enhance the yield of organoids per well within the same plate format.
H&E staining was performed to validate the morphological features of A549 CDTOs. As shown in Figure 2A, the organoids exhibited solid spheroidal structures with varying sizes and architectural heterogeneity. Critically, the majority of organoids lacked a defined central lumen and instead presented as densely packed cell masses with dysregulated polarity, demonstrating a strong morphological correspondence with primary lung adenocarcinoma organoids21. Further immunofluorescence (IF) staining showed positive expression of lung adenocarcinoma markers transcription factor TTF-1, adhesion protein ECAD, and cytoskeleton KRT7 (Figure 2B). Positive ZO-1 and ECAD signals showed a tightly connected structure with dysregulated polarity of the CDTOs, similar to primary lung adenocarcinoma organoid features21. Hypoxia-Inducible Factor 1-Alpha (HIF1α) was also positive in the culture22 (Supplementary Figure 1D).
In conclusion, these results confirmed that this protocol can successfully generate structured A549 organoids that retain key lung adenocarcinoma molecular markers. The positive expression of TTF-1/ECAD/KRT7 serves as an indicator for successful modeling and cellular identity. The seeding density is a critical parameter, with low densities failing to initiate organoid formation and high densities resulting in aberrant growth.

Figure 1: Establishment of A549 CDTOs from 2D-cultured cells. (A) Schematic workflow for generating tumor organoids from 2D-cultured A549 cells. 2D A549 cells were digested into single cells and then embedded into Matrigel domes for 3D culture. (B) Time-series images showing the progression from single cells to mature organoids at the same location. Seeding density: 500 cells/µL. CDTOs in (B), (C), and (D) were maintained in a 6 µL gel in a 48-well plate. Scale bar: 100 µm. (C) Representative image of A549 CDTOs at day 7. Arrowhead: 2D adherent clone. Arrow: 3D organoid. Scale bar: 100 µm. (D) Center image of A549 CDTOs of different seeding densities from the automated imaging device. The images were captured by automation to reduce bias and were used to generate quantification data in (E)and (F). Scale bar: 100 µm. (E,F) Quantification data of colony-forming efficiency (CFE) and mean organoid area per well of (D). 5000 cells/µL were excluded for inaccuracy and difficulty in quantification. Organoids were counted and divided by the total seeding amount to generate CFE. Areas in one well were measured and averaged by counts. Data are presented as mean ± SD, with N = 4–8. Statistical significance was assessed using one-way ANOVA followed by Tukey's post-hoc test for multiple comparisons correction. Significance levels are denoted as: ****, padj < 0.0001; ***, padj < 0.0005; **, padj < 0.001; ns, not significant. Please click here to view a larger version of this figure.

Figure 2: Histological and molecular characterization of A549 organoids. (A) H&E staining reveals the overall architecture and cytomorphology of the organoids, resembling primary lung adenocarcinoma organoid features. Scale bar: 50 µm. (B) Immunofluorescence analysis reveals positive expression of key lung adenocarcinoma markers: TTF1, ECAD, and KRT7. Positive ZO-1 expression showed tight junctions of tumor organoids. Nuclei are labeled with DAPI. Scale bar: 50 µm. Please click here to view a larger version of this figure.
| Plate Type | Matrigel Volume (μL/dome) | Domes per Well | Medium Volume (μL) | Seeding Density |
| 96-well | 2-3 | 1 | 100 | 500 cells/μL |
| 48-well | 6-10 | 1 | 200 | |
| 24-well | 20-30 | 1 | 500 | |
| 12-well | 20-30 | 3-4 | 1500 |
Table 1: Recommended Matrigel droplet configuration for 3D organoid culture. Due to Matrigel viscosity, preparing 10%–20% excess volume is recommended. Generally, the maximum volume within the recommended range should be used.
Supplementary Figure 1: Additional characterization of A549 organoids. (A) Representative image of A549 cells at 70% confluence in 2D culture. Scale bar: 100 µm. (B) Representative images of organoids cultured at 1000 cells/µL in 3D medium and in Dulbecco ‘s Modified Eagle’s Medium containing 10% fetal bovine serum. Arrowhead: 2D adherent clone. Scale bar: 100 µm. (C) Passaged A549 CDTOs showed consistent morphology with Figure 1C. Scale bar: 100 µm. (D) HIF1α-positive expression revealed a potential hypoxic microenvironment. Nuclei are labeled with DAPI. Scale bar: 50 µm. Please click here to download this file.
This protocol describes a method for generating A549 lung adenocarcinoma Cell line-Derived Tumor Organoids optimized for technical simplicity, reproducibility, and educational use. Three parameters critically determine success: initial cell state, medium formulation, and matrix composition. Additionally, culture duration is not recommended to exceed 14 days. Listed below are key parameters and troubleshooting.
Initial cell state
The cells were maintained at a low passage number (<20 passages) to minimize genetic drift and clonal selection. Cells were harvested during the logarithmic growth phase (70%–80% confluence) to ensure optimal organoid-forming capacity. During cell counting, the harvested cells were confirmed to be in a single-cell suspension, as clumping affected quantification in downstream assays, although it generally did not interfere with colony formation; persistent clumps were filtered through a 40 µm cell strainer.
Matrigel scaffolding
After seeding, the plate was transferred to the incubator immediately to minimize cell sedimentation and early adherence, with adherence of up to 10% of the input cell number considered tolerable. Matrigel droplets were incubated at 37 °C for at least 40 min to ensure complete gelation before the addition of medium. Matrigel was thawed overnight on ice at 4 °C, aliquoted into precooled sterile microcentrifuge tubes to avoid repeated freeze–thaw cycles, and stored at −20 °C for short-term use (within 1 month) or −80 °C for long-term storage. Aliquots were thawed on ice for approximately 1–2 h and were never exposed to temperatures above 0 °C. During handling, Matrigel was kept on ice at all times, and precooled pipette tips and tubes were used to prevent premature gelation; the gel–cell mixture was maintained on ice during seeding and gently resuspended five times to ensure even distribution, with pipette tips changed every 10 wells to prevent gel residue condensation. Adequate medium volume was maintained, and edge wells were filled with PBS to prevent evaporation-induced edge effects, as uneven gel–cell distribution and evaporation adversely affected organoid formation. Bubble formation was minimized by pressing the pipette only to the first stop and dispensing slowly; portions containing fine, dense bubbles were discarded, as bubbles could interfere with imaging and size measurements, even though one or two bubbles typically did not affect cell growth. Occasional cracking or floating of Matrigel droplets was observed despite careful handling, and lot numbers were recorded to identify and avoid problematic batches.
Medium formulation
The culture medium was prepared fresh or used within 14 days when stored at 4 °C, with preparation aligned to the experimental schedule to avoid prolonged storage. The medium was replaced every 3 days, and early yellowing of the medium was interpreted as an indicator of high metabolic activity, requiring immediate replacement and more frequent subsequent changes to maintain optimal growth conditions.
Limitations
This current model lacks patient heterogeneity, tumor microenvironment components, and is subject to genetic drift with extended passage (use cells <20 passages). Organoid-forming capacity requires intrinsic stem-like subpopulations (e.g., CD133⁺/ABCG2⁺ in A549)16, limiting applicability to other cell lines.
Applications
The protocol serves primarily for undergraduate teaching (results within 7–10 days), graduate training in 3D techniques, and as a positive control for method development. Research usages include preliminary drug screening18, extracellular matrix studies19, and other proof-of-concept organoid experiments, though findings usually require validation in more physiologically relevant models. By defining critical parameters and providing troubleshooting guidance, this protocol offers a reproducible, cost-effective platform for educational and preliminary research applications in 3D cancer modeling.
The authors have no conflicts of interest to disclose.
This work was supported by the Fudan Good Practice Program of Teaching and Learning, the National Research Institute for Teaching Materials, and the National Program for Talent Training in Basic Disciplines (No. J1210012), as well as the Program for Cultivating Top-Notch Students in Basic Disciplines from the Ministry of Education (No. 20211021). Figure 1A was created in BioRender (Joe, Z. (2026) https://BioRender.com/0qi2gmd).
| Name | Company | Catalog Number | Comments |
|---|---|---|---|
| 1.5 mL Micro Centrifuge tube | Biofil | CFT003015 | |
| A549 [A-549]human non-small cell lung cancer cells | ZQXZbio | ZQ0003 | STR: Amelogenin: X,Y; CSF1PO: 10,12; D13S317: 11; D16S539: 11,12; D5S818: 11; D7S820: 8,11; TH01: 8,9.3; TPOX: 8,11; vWA: 14. Mycoplasma was negetive when purchased was tested every 2 weeks. Passage number within 10 passages from the P1 aliquots of the purchased batch was used. |
| Advanced DMEM/F12 | Gibco | 12634010 | |
| Anti-E Cadherin antibody | Abcam | ab231303 | |
| Anti-Fade Mounting Medium | YEASEN | 36307ES08 | |
| Anti-HIF-1 alpha antibody | Abcam | ab51608 | |
| Biological Safety Cabinet | Nuaire LABGARD | NU-540 | |
| Biological Tissue Embedding Machine | KEDEE | KD-BM | |
| BSA | Sigma | A1933 | |
| Cell-Grade BSA | Sigma | A1933-100G | |
| Centrifuge | Eppendorf | Centrifuge 5702 R | Swing bucket; Mild to low speed. |
| Centrifuge tube | Biofil | CFT920150 | |
| Citrate Antigen Retrieval Solution (pH 6.0) | ZSGB-BIO | ZLI-9065 | |
| Cryostage | KEDEE | KD-BL | |
| Cytation 5 Cell Imaging Multimode Reader | Biotek | Cytation 5 | |
| Cytokeratin 7 (KRT7) Rabbit mAb | Abclonal | A4357 | |
| DMEM | Gibco | 11965092 | |
| DMSO | Solarbio | D8371 | |
| Donkey Serum | Solarbio | SL050 | |
| Dulbecco's Modified Eagle Medium | Gibco | 11965118 | |
| Eclipse Ts2 Inverted Microscope | Nikon | Eclipse Ts2 | |
| Eosin Staining Solution (Alcohol-Soluble) | Servicebio | G1001 | |
| FBS | Nobimpex | B118-500 | |
| Forma Steri-Cycle i160 CO2 Incubator | Thermo Scientific | i60 | |
| Hematoxylin Bluing Solution | Servicebio | G1040 | |
| Hematoxylin Differentiation Solution | Servicebio | G1040 | |
| Hematoxylin Staining Solution | Servicebio | G1004 | |
| Hemocytometer | Solarbio | YA0810 | |
| Human Lung Adenocarcinoma Organoid Medium (3D medium) | PMO Bio | HC1001 | |
| Immunohistochemistry (IHC) Pen | ZSGB-BIO | ZLI-9305 | Store in 4°C |
| Laser Confocal Microscope FV3000 | Olympus | FV3000 | Usual parameter range: PMT Voltage: 500 ± 200 V; Laser Transmissivity: 5 ± 3%; Offset: 3 % |
| Manual Rotary Microtome | Leica | RM2235 | |
| Metal Bath | ALLSHENG | MK-3000 | |
| Microwave Oven | Galanz | ||
| Nail Polish | Lete | ||
| Neutral Balsam (Mounting Medium for Microscopy) | Beyotime | C0173 | |
| Organoid-Specific Extracellular Matrix Gel | PMO Bio | BM1001 | |
| PBS | WISENT | 311-010-CL | |
| Peroxidase Blocking Solution | Beyotime | P0100A | |
| Pipettes | Eppendorf | 312300063/312300020/312400083 | |
| Pipettes tips | Axygen | 14-222-692/14-222-723/14-222-869 | Consider using low retention tips if possible. |
| Three-Dimensional Shaker | SCILOGEX | SK-D3309-Pro | Low speed. |
| Tissue Flotation Water Bath | KEDEE | KD-P | |
| Triton X-100 | VWR | 92046-34-9 | |
| Trypan Blue | Gibco | 15250061 | |
| TryPLE | Gibco | 12605028 | |
| TTF1 Recombinant Monoclonal Antibody | HUABIO | HA720067 |
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