# Biomimetic 3D-Bioprinted organoids of thymic epithelial tumors for translational drug screening and biomarker identification

**Authors:** Beibei Liu, Huiyan Cheng, Keke Yu, Wen Xu, Xiaoting Tian, Yuhan Xu, Yanbin Kuang, Jun Lu, Rong Li, Xiao Zhang, Min Tang, Jianxin Xue, Yuqing Lou

PMC · DOI: 10.1016/j.mtbio.2026.102878 · 2026-02-11

## TL;DR

Researchers created 3D-printed tumor models of thymic epithelial tumors to test drugs and identify biomarkers for better treatment.

## Contribution

The first 3D bioprinted organoid model of thymic epithelial tumors using proteomic data to guide biomaterial design.

## Key findings

- 3D-bioprinted organoids better replicate tumor properties than traditional Matrigel models.
- Lurbinectedin was identified as a potent therapeutic candidate for thymic epithelial tumors.
- PBX3, REPS2, and CXCR4 are potential biomarkers for treatment efficacy.

## Abstract

Thymic epithelial tumors (TETs), including thymic carcinoma and thymoma, are rare malignancies lacking both effective therapies and validated biomarkers to guide treatment. Here, we report the first 3D (three-dimensional) bioprinted organoid model of TETs, established through a proteomic data-driven biomaterial design strategy. Patient tumor tissues were first decellularized and analyzed by proteomics to determine their extracellular matrix (ECM) composition. The results revealed distributions of ECM proteins which guided the formulation of photocurable bioinks. The resulting 3D-bioprinted organoids supported primary TET cell proliferation, and more faithfully replicated the biophysical properties and molecular characteristics of native tumors than traditional Matrigel-cultured organoids. Leveraging this biomimetic platform, we conducted high-throughput drug screening and identified lurbinectedin as a potent therapeutic candidate for TETs. Transcriptomic profiling revealed its anti-TET mechanism. Integrating RNAseq data with TCGA survival analysis further identified PBX3, REPS2, and CXCR4 as potential efficacy-predictive biomarkers. This study establishes a translational framework linking 3D bioprinted TET models with biomarker discovery, offering a standardized platform for precision drug screening and mechanistic exploration in thymic epithelial tumors.

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## Linked entities

- **Genes:** PBX3 (PBX homeobox 3) [NCBI Gene 5090], REPS2 (RALBP1 associated Eps domain containing 2) [NCBI Gene 9185], CXCR4 (C-X-C motif chemokine receptor 4) [NCBI Gene 7852]
- **Chemicals:** lurbinectedin (PubChem CID 57327016)
- **Diseases:** thymic carcinoma (MONDO:0006451), thymoma (MONDO:0006456)

## Full-text entities

- **Genes:** CXCL12 (C-X-C motif chemokine ligand 12) [NCBI Gene 6387] {aka IRH, PBSF, SCYB12, SDF1, TLSF, TPAR1}, IL2 (interleukin 2) [NCBI Gene 3558] {aka IL-2, TCGF, lymphokine}, SMARCD1 (SWI/SNF related BAF chromatin remodeling complex subunit D1) [NCBI Gene 6602] {aka BAF60A, CRACD1, CSS11, Rsc6p}, CXCR4 (C-X-C motif chemokine receptor 4) [NCBI Gene 7852] {aka CD184, D2S201E, FB22, HM89, HSY3RR, LCR1}, MMRN1 (multimerin 1) [NCBI Gene 22915] {aka ECM, EMILIN4, GPIa*, MMRN}, CMPK1 (cytidine/uridine monophosphate kinase 1) [NCBI Gene 51727] {aka CK, CMK, CMPK, UMK, UMP-CMPK, UMPK}, NES (nestin) [NCBI Gene 10763] {aka Nbla00170}, EGFR (epidermal growth factor receptor) [NCBI Gene 1956] {aka ERBB, ERBB1, ERRP, HER1, NISBD2, NNCIS}, PIK3CB (phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit beta) [NCBI Gene 5291] {aka P110BETA, PI3K, PI3KBETA, PIK3C1}, GAPDH (glyceraldehyde-3-phosphate dehydrogenase) [NCBI Gene 2597] {aka G3PD, GAPD, HEL-S-162eP}, CD8A (CD8 subunit alpha) [NCBI Gene 925] {aka CD8, CD8alpha, IMD116, Leu2, p32}, FGF2 (fibroblast growth factor 2) [NCBI Gene 2247] {aka BFGF, FGF-2, FGFB, HBGF-2}, KIT (KIT proto-oncogene, receptor tyrosine kinase) [NCBI Gene 3815] {aka C-Kit, CD117, MASTC, PBT, SCFR}, ALK (ALK receptor tyrosine kinase) [NCBI Gene 238] {aka ALK1, CD246, NBLST3}, TP63 (tumor protein p63) [NCBI Gene 8626] {aka AIS, B(p51A), B(p51B), EEC3, KET, LMS}, ARID1A (AT-rich interaction domain 1A) [NCBI Gene 8289] {aka B120, BAF250, BAF250a, BM029, C1orf4, CSS2}, NOTCH1 (notch receptor 1) [NCBI Gene 4851] {aka AOS5, AOVD1, TAN1, hN1}, FGFR3 (fibroblast growth factor receptor 3) [NCBI Gene 2261] {aka ACH, CD333, CEK2, HSFGFR3EX, JTK4}, EGF (epidermal growth factor) [NCBI Gene 1950] {aka HOMG4, URG}, TP53 (tumor protein p53) [NCBI Gene 7157] {aka BCC7, BMFS5, LFS1, P53, TRP53}, MYBL2 (MYB proto-oncogene like 2) [NCBI Gene 4605] {aka B-MYB, BMYB}, IGF1 (insulin like growth factor 1) [NCBI Gene 3479] {aka IGF, IGF-I, IGFI, MGF}, RSPO1 (R-spondin 1) [NCBI Gene 284654] {aka CRISTIN3, RSPO}, WNT3A (Wnt family member 3A) [NCBI Gene 89780], PBX3 (PBX homeobox 3) [NCBI Gene 5090], BCL11A (BCL11 transcription factor A) [NCBI Gene 53335] {aka CTIP1, DILOS, EVI9, HBFQTL5, SMARCM1, ZNF856}, NCAM1 (neural cell adhesion molecule 1) [NCBI Gene 4684] {aka CD56, MSK39, NCAM}, DNTT (DNA nucleotidylexotransferase) [NCBI Gene 1791] {aka TDT}, PLAG1 (PLAG1 zinc finger) [NCBI Gene 5324] {aka PSA, SGPA, SRS4, ZNF912}, JAK3 (Janus kinase 3) [NCBI Gene 3718] {aka JAK-3, JAK3_HUMAN, JAKL, L-JAK, LJAK}, PTPRC (protein tyrosine phosphatase receptor type C) [NCBI Gene 5788] {aka B220, CD45, CD45R, GP180, IMD105, L-CA}, REPS2 (RALBP1 associated Eps domain containing 2) [NCBI Gene 9185] {aka POB1}, AKT1 (AKT serine/threonine kinase 1) [NCBI Gene 207] {aka AKT, PKB, PKB-ALPHA, PRKBA, RAC, RAC-ALPHA}, FGF10 (fibroblast growth factor 10) [NCBI Gene 2255] {aka LADD3}
- **Diseases:** brain tumor (MESH:D001932), A THYM (MESH:D013945), TC-Tumor (MESH:D013953), cytotoxic (MESH:D064420), neuroendocrine carcinoma (MESH:D018278), immune (MESH:D007154), rare (MESH:D035583), metastasis (MESH:D009362), non-small cell lung cancer (MESH:D002289), squamous cell carcinoma (MESH:D002294), neuroendocrine tumor (MESH:D018358), TETs (MESH:C536905), lung tumors (MESH:D008175), Tumor (MESH:D009369), small-cell lung cancer (MESH:D055752), inflammatory (MESH:D007249)
- **Chemicals:** DMSO (MESH:D004121), DAPI (MESH:C007293), lithium phenyl-2,4,6-trimethylbenzoylphos phinate (MESH:C546776), PFA (MESH:C003043), Lenvatinib (MESH:C531958), agarose (MESH:D012685), BCA (MESH:C047117), CO2 (MESH:D002245), ammonium bicarbonate (MESH:C027043), A83-01 (MESH:C507011), etoposide (MESH:D005047), Alexa Fluor 488 (MESH:C000711379), carboplatin (MESH:D016190), Alexa Fluor 647 (MESH:C569686), penicillin (MESH:D010406), ABC (MESH:C106538), Adamas-beta (-), Y-27632 (MESH:C108830), H&amp;E (MESH:D006371), CAA (MESH:C013874), Lurbinectedin (MESH:C568606), glutamax (MESH:C054122), ethanol (MESH:D000431), HA (MESH:D006820), Alcian Blue (MESH:D000423), DTT (MESH:D004229), ACN (MESH:C084683), SDS (MESH:D012967), TRIzol (MESH:C411644), water (MESH:D014867), Triton X-100 (MESH:D017830), acetonitrile (MESH:C032159), streptomycin (MESH:D013307), DPBS (MESH:C012939), polysaccharide (MESH:D011134), F-12 (MESH:C007782), paclitaxel (MESH:D017239), salt (MESH:D012492), formic acid (MESH:C030544), platinum (MESH:D010984), NaCl (MESH:D012965), methanol (MESH:D000432)
- **Species:** Homo sapiens (human, species) [taxon 9606], Mycoplasma (genus) [taxon 2093]
- **Cell lines:** IU-TAB-1 — Homo sapiens (Human), Thymoma type AB, Cancer cell line (CVCL_D551), IU-tab-1 — Mus musculus (Mouse), Hybridoma (CVCL_J620), THYM — Mus musculus (Mouse), Mouse lymphoma, Cancer cell line (CVCL_2Z87), Ty-82 — Homo sapiens (Human), NUT carcinoma, Cancer cell line (CVCL_3220), -L — Mus musculus (Mouse), Spontaneously immortalized cell line (CVCL_0462)

## Figures

8 figures with captions in the complete paper: https://tomesphere.com/paper/PMC12924735/full.md

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Source: https://tomesphere.com/paper/PMC12924735