# Personalized pharmacokinetic–pharmacodynamic guided therapy via an induced pluripotent stem cell–derived multi-organoid platform in NF1-mutant breast cancer

**Authors:** Jung Hwa Lim, Seon Ju Mun, Hyun Mi Kang, Won Dong Yu, Soo Jin Oh, Ji-Yoon Lee, Ye Seul Son, Sugi Lee, Dae Soo Kim, Jaeseo Lee, Su Jeong Kim, Hyun-Soo Cho, Myung Jin Son, Mi-Young Son, Cho-Rok Jung

PMC · DOI: 10.1038/s41392-026-02595-7 · 2026-03-05

## TL;DR

A new personalized cancer treatment model uses organoids from stem cells to guide drug therapy for NF1-mutant breast cancer.

## Contribution

A multi-organoid platform integrating PK/PD and genomic data enables personalized therapy for NF1-mutant breast cancer.

## Key findings

- The NOCS platform enabled individualized assessment of drug metabolism and excretion.
- Paxalisib combined with exon skipping therapy showed synergistic anticancer effects in tumor models.
- The approach integrates PK/PD modeling with genotype-driven strategies for precision oncology.

## Abstract

Effective precision oncology demands integration of pharmacokinetics/pharmacodynamics (PK/PD) profiling with tumor-specific genomic features. Here, we present a personalized treatment model using a patient-derived Networking Organoid Culture System (NOCS) composed of intestinal, liver, and kidney organoids differentiated from induced pluripotent stem cells (iPSCs) of an NF1-mutant breast cancer patient. This multi-organoid system enabled individualized assessment of drug absorption, distribution, metabolism, and excretion. Integrative genomic and pathway analyses uncovered therapeutic vulnerabilities, including responsiveness to a novel exon skipping therapy targeting NF1. PK/PD-guided screening on the NOCS prioritized Paxalisib, which, when combined with the exon skipping approach, demonstrated synergistic anticancer efficacy in patient-derived tumor models. These findings establish a clinically relevant framework that integrates multi-organ PK/PD modeling with genotype-driven therapeutic strategies, highlighting the potential of combining targeted gene correction with small-molecule therapy for personalized treatment. This platform offers broad applicability in precision oncology and drug development across diverse genetic contexts.

## Linked entities

- **Genes:** NF1 (neurofibromin 1) [NCBI Gene 4763]
- **Chemicals:** Paxalisib (PubChem CID 57384863)
- **Diseases:** breast cancer (MONDO:0004989)

## Full-text entities

- **Genes:** EGF (epidermal growth factor) [NCBI Gene 1950] {aka HOMG4, URG}, BMP7 (bone morphogenetic protein 7) [NCBI Gene 655] {aka OP-1}, RHOA (ras homolog family member A) [NCBI Gene 387] {aka ARH12, ARHA, EDFAOB, RHO12, RHOH12}, ABCB11 (ATP binding cassette subfamily B member 11) [NCBI Gene 8647] {aka ABC16, BRIC2, BSEP, PFIC-2, PFIC2, PGY4}, SLC15A2 (solute carrier family 15 member 2) [NCBI Gene 6565] {aka PEPT2}, FABP2 (fatty acid binding protein 2) [NCBI Gene 2169] {aka FABPI, I-FABP}, HGF (hepatocyte growth factor) [NCBI Gene 3082] {aka DFNB39, F-TCF, HGFB, HPTA, SF}, BMP4 (bone morphogenetic protein 4) [NCBI Gene 652] {aka BMP2B, BMP2B1, MCOPS6, OFC11, ZYME}, PGP (phosphoglycolate phosphatase) [NCBI Gene 283871] {aka AUM, G3PP, PGPase}, HNF4A (hepatocyte nuclear factor 4 alpha) [NCBI Gene 3172] {aka FRTS4, HNF4, HNF4a7, HNF4a8, HNF4a9, HNF4alpha}, ITGA6 (integrin subunit alpha 6) [NCBI Gene 3655] {aka CD49f, ITGA6A, ITGA6B, JEB6, VLA-6}, UMOD (uromodulin) [NCBI Gene 7369] {aka ADMCKD2, ADTKD1, FJHN, HNFJ, HNFJ1, MCKD2}, FGF19 (fibroblast growth factor 19) [NCBI Gene 9965], MAP2K7 (mitogen-activated protein kinase kinase 7) [NCBI Gene 5609] {aka JNKK2, MAPKK7, MEK, MEK 7, MKK7, PRKMK7}, ABCC4 (ATP binding cassette subfamily C member 4 (PEL blood group)) [NCBI Gene 10257] {aka MOAT-B, MOATB, MRP4}, JAG1 (jagged canonical Notch ligand 1) [NCBI Gene 182] {aka AGS, AGS1, AHD, AWS, CD339, CMT2HH}, SLC10A1 (solute carrier family 10 member 1) [NCBI Gene 6554] {aka FHCA2, NTCP}, VIL1 (villin 1) [NCBI Gene 7429] {aka D2S1471, VIL}, ACTA2 (actin alpha 2, smooth muscle) [NCBI Gene 59] {aka ACTSA, SMDYS}, NPHS1 (NPHS1 adhesion molecule, nephrin) [NCBI Gene 4868] {aka CNF, NPHN, nephrin}, HAVCR1 (hepatitis A virus cellular receptor 1) [NCBI Gene 26762] {aka CD365, HAVCR, HAVCR-1, KIM-1, KIM1, TIM}, ZHX2 (zinc fingers and homeoboxes 2) [NCBI Gene 22882] {aka AFR1, RAF}, ERBB2 (erb-b2 receptor tyrosine kinase 2) [NCBI Gene 2064] {aka CD340, HER-2, HER-2/neu, HER2, MLN 19, MLN-19}, CASP3 (caspase 3) [NCBI Gene 836] {aka CPP32, CPP32B, SCA-1}, CYP2C8 (cytochrome P450 family 2 subfamily C member 8) [NCBI Gene 1558] {aka CPC8, CYP2C8DM, CYPIIC8, MP-12/MP-20}, ACTA1 (actin alpha 1, skeletal muscle) [NCBI Gene 58] {aka ACTA, ASMA, CFTD, CFTD1, CFTDM, CMYO2A}, POU5F1 (POU class 5 homeobox 1) [NCBI Gene 5460] {aka OCT3, OCT4, OCT4Borf1, OTF-3, OTF3, OTF4}, ANXA5 (annexin A5) [NCBI Gene 308] {aka ANX5, CPB-I, ENX2, HEL-S-7, PP4, RPRGL3}, GCLC (glutamate-cysteine ligase catalytic subunit) [NCBI Gene 2729] {aka CNSHA7, GCL, GCS, GLCL, GLCLC}, ABCC2 (ATP binding cassette subfamily C member 2) [NCBI Gene 1244] {aka ABC30, CMOAT, DJS, MRP2, cMRP}, OSM (oncostatin M) [NCBI Gene 5008], WNT3A (Wnt family member 3A) [NCBI Gene 89780], NPHS2 (NPHS2 stomatin family member, podocin) [NCBI Gene 7827] {aka PDCN, SRN1}, SLCO1A2 (solute carrier organic anion transporter family member 1A2) [NCBI Gene 6579] {aka OATP, OATP-A, OATP1A2, SLC21A3}, KRT18 (keratin 18) [NCBI Gene 3875] {aka CK-18, CYK18, K18}, RSPO1 (R-spondin 1) [NCBI Gene 284654] {aka CRISTIN3, RSPO}, CYP2C19 (cytochrome P450 family 2 subfamily C member 19) [NCBI Gene 1557] {aka CPCJ, CYP2C, CYPIIC17, CYPIIC19, P450C2C, P450IIC19}, VIM (vimentin) [NCBI Gene 7431], KLF4 (KLF transcription factor 4) [NCBI Gene 9314] {aka EZF, GKLF}, LCN2 (lipocalin 2) [NCBI Gene 3934] {aka 24p3, MSFI, NGAL, p25}, PLSCR4 (phospholipid scramblase 4) [NCBI Gene 57088] {aka TRA1}, INS (insulin) [NCBI Gene 3630] {aka IDDM, IDDM1, IDDM2, ILPR, IRDN, MODY10}, NQO1 (NAD(P)H quinone dehydrogenase 1) [NCBI Gene 1728] {aka DHQU, DIA4, DTD, NMOR1, NMORI, QR1}, KRT7 (keratin 7) [NCBI Gene 3855] {aka CK7, K2C7, K7, SCL}, ADA2 (adenosine deaminase 2) [NCBI Gene 51816] {aka ADGF, CECR1, IDGFL, PAN, SNEDS, VAIHS}, PPIG (peptidylprolyl isomerase G) [NCBI Gene 9360] {aka CARS-Cyp, CYP, SCAF10, SRCyp}, CYP4F3 (cytochrome P450 family 4 subfamily F member 3) [NCBI Gene 4051] {aka CPF3, CYP4F, CYPIVF3, LTB4H}, FGF10 (fibroblast growth factor 10) [NCBI Gene 2255] {aka LADD3}, SLC22A8 (solute carrier family 22 member 8) [NCBI Gene 9376] {aka OAT3}, AKT1 (AKT serine/threonine kinase 1) [NCBI Gene 207] {aka AKT, PKB, PKB-ALPHA, PRKBA, RAC, RAC-ALPHA}, CD44 (CD44 molecule (IN blood group)) [NCBI Gene 960] {aka CDW44, CSPG8, ECM-III, ECMR-III, H-CAM, HCELL}, UGT1A1 (UDP glucuronosyltransferase family 1 member A1) [NCBI Gene 54658] {aka BILIQTL1, GNT1, HUG-BR1, UDPGT, UDPGT 1-1, UGT1}, FGF4 (fibroblast growth factor 4) [NCBI Gene 2249] {aka FGF-4, HBGF-4, HST, HST-1, HSTF-1, HSTF1}, SOX2 (SRY-box transcription factor 2) [NCBI Gene 6657] {aka ANOP3, MCOPS3}, MUC2 (mucin 2, oligomeric mucus/gel-forming) [NCBI Gene 4583] {aka MLP, MUC-2, SMUC}, SLCO2B1 (solute carrier organic anion transporter family member 2B1) [NCBI Gene 11309] {aka OATP-B, OATP2B1, OATPB, SLC21A9}, AQP2 (aquaporin 2) [NCBI Gene 359] {aka AQP-2, AQP-CD, NDI2, WCH-CD}, TJP1 (tight junction protein 1) [NCBI Gene 7082] {aka ZO-1}, CHGA (chromogranin A) [NCBI Gene 1113] {aka CGA, PHE5, PHES}, SLC15A1 (solute carrier family 15 member 1) [NCBI Gene 6564] {aka HPECT1, HPEPT1, PEPT1}
- **Diseases:** malignant spindle cell tumor of the sarcoma type (MESH:D012509), DE (MESH:D003635), NF1 deficiency (MESH:D009456), Duchenne muscular dystrophy (MESH:D020388), genetic diseases (MESH:D030342), tumorigenesis (MESH:D063646), hypoxic (MESH:D002534), spinal muscular atrophy (MESH:D009134), Tumor (MESH:D009369), PD (MESH:D010300), mastectomy (MESH:D000072656), inflammation (MESH:D007249), glioblastoma (MESH:D005909), neuromuscular disorders (MESH:D009468), IO (MESH:D007410), MPS (MESH:D015619), DhLOs (MESH:D017093), HM (MESH:D056486), kidney disease (MESH:D007674), BCs (MESH:D001943), invasive ductal carcinoma (MESH:D044584), pleomorphic lobular carcinoma (MESH:D018275), cytotoxic (MESH:D064420)
- **Chemicals:** FITC-dextran (MESH:C015219), B- (MESH:D001895), ethanol (MESH:D000431), GlutaMAX (MESH:C054122), hIOs (MESH:C081961), Acyclovir (MESH:D000212), SDS (MESH:D012967), Gentamycin (MESH:D005839), GDP (MESH:D006153), Tipifarnib (MESH:C402769), DTT (MESH:D004229), PGE2 (MESH:D015232), vitamin A (MESH:D014801), Chlorothiazide (MESH:D002740), CHIR99021 (MESH:C473711), nicotinamide (MESH:D009536), Paxalisib (MESH:C000630586), 2-hydroxypropyl beta-cyclodextrin (MESH:D000073738), silane (MESH:D012821), water (MESH:D014867), streptomycin (MESH:D013307), rapamycin (MESH:D020123), Alpelisib (MESH:C585539), acetonitrile (MESH:C032159), Triton X-100 (MESH:D017830), EDTA (MESH:D004492), N (MESH:D009584), F-12 (MESH:C007782), RepSox (MESH:C550621), FITC (MESH:D016650), NP-40 (MESH:C010615), xylene (MESH:D014992), cimetidine (MESH:D002927), DPBS (MESH:C012939), Apitolisib (MESH:C569670), Acetaminophen (MESH:D000082), GTPgammaS (MESH:D016244), Gedatolisib (MESH:C549060), formic acid (MESH:C030544), P (MESH:D010758), NaCl (MESH:D012965), MgCl2 (MESH:D015636), Paraffin (MESH:D010232), Epothilone B (MESH:C093788), calcium (MESH:D002118), formalin (MESH:D005557), glucose (MESH:D005947), DMSO (MESH:D004121), DAPI (MESH:C007293), magnesium (MESH:D008274), Cremophor-EL (MESH:C000515), PVDF (MESH:C024865), heparin (MESH:D006493), DAB (MESH:C000469), N-acetyl L-cysteine (MESH:D000111), Tween 20 (MESH:D011136), PBS (MESH:D007854), carbamazepine (MESH:D002220), Sepharose (MESH:D012685), polybrene (MESH:D006583)
- **Species:** Saccharomyces cerevisiae (baker's yeast, species) [taxon 4932], Mus musculus (house mouse, species) [taxon 10090], Sendai virus [taxon 11191], Homo sapiens (human, species) [taxon 9606]
- **Mutations:** p.D904V, p.I55fsX, c.2711 A > T, c.165_166insCT, c.3139 C > T
- **Cell lines:** U7-AON2/12 — Mus musculus (Mouse), Hybridoma (CVCL_C2BY), 293 T — Homo sapiens (Human), Transformed cell line (CVCL_0063), HE — Homo sapiens (Human), Finite cell line (CVCL_2922), HEK293 — Homo sapiens (Human), Transformed cell line (CVCL_0045), IM — Rattus norvegicus (Rat), Transformed cell line (CVCL_8809), Caco-2 — Homo sapiens (Human), Colon adenocarcinoma, Cancer cell line (CVCL_0025)

## Figures

8 figures with captions in the complete paper: https://tomesphere.com/paper/PMC12960935/full.md

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Source: https://tomesphere.com/paper/PMC12960935