# Engineered romidepsin biosynthetic pathways in Escherichia coli Nissle 1917 improve the efficacy of bacteria-mediated cancer therapy

**Authors:** Chenghao Ma, Geng Li, Tao Sun, Ximi Tang, Tong Qiu, Jingwen Song, Hailong Wang, Youming Zhang, Tianyu Jiang

PMC · DOI: 10.1371/journal.pbio.3003657 · PLOS Biology · 2026-03-17

## TL;DR

Scientists engineered a probiotic bacteria to produce an anticancer drug inside tumors, improving treatment effectiveness and reducing side effects.

## Contribution

The study introduces a novel method of using engineered bacteria to biosynthesize and deliver romidepsin directly to tumors.

## Key findings

- Engineered EcN strains produced romidepsin with a maximum in vitro yield of 1.5 mg/L.
- Recombinant strains outperformed wild-type EcN in tumor models and reduced cardiotoxicity and mortality.
- Intratumoral FK228 production combined with EcN's inflammatory response improved treatment outcomes.

## Abstract

The probiotic strain Escherichia coli Nissle 1917 (EcN), a potential member of tumor-targeting bacteria, shows great promise for cancer treatment. By leveraging engineered EcN, we can design a bacteria-assisted, tumor-targeted therapy for the biosynthesis and targeted delivery of small-molecule anticancer agents. In this study, we aimed to use EcN as a base for synthesizing Romidepsin (FK228), an FDA-approved drug originally made by Chromobacterium violaceum No. 96. Through gene cluster reconstruction, promoter optimization, and genome modification, we created FK228-producing strains to boost anticancer efficacy. The engineered strain achieved a maximum in vitro yield of 1.5 mg/L. In 4T1 tumor-bearing BALB/c mouse xenograft models, six recombinant strains outperformed the wild-type EcN. Proteome showed that inflammatory response induced by EcN combined with intratumoral FK228 production improved treatment results. Also, targeted synthesis reduced FK228's cardiotoxicity and mortality. Engineered EcN enables drug biosynthesis and precise delivery, offering powerful anticancer activity.

Bacteria-mediated cancer therapy exploits the ability of bacterial strains to specifically colonize tumors and deliver therapeutic molecules. This study engineers Escherichia coli Nissle 1917 strains to biosynthesize and deliver the anticancer drug romidepsin, achieving improved intratumoral efficacy and reduced systemic toxicity in tumor models.

## Linked entities

- **Chemicals:** romidepsin (PubChem CID 5352062), FK228 (PubChem CID 5352062)
- **Diseases:** cancer (MONDO:0004992)
- **Species:** Escherichia coli Nissle 1917 (taxon 316435), Mus musculus (taxon 10090)

## Full-text entities

- **Genes:** CRSA (Craniosynostosis, Adelaide type) [NCBI Gene 7885] {aka CRS3}, Gpr84 (G protein-coupled receptor 84) [NCBI Gene 80910] {aka EX33}, Uck1 (uridine-cytidine kinase 1) [NCBI Gene 22245] {aka URK1, Umpk}, Pf4 (platelet factor 4) [NCBI Gene 56744] {aka Cxcl4, Scyb4}, Psen1 (presenilin 1) [NCBI Gene 19164] {aka Ad3h, PS-1, PS1, S182}, Ecd (ecdysoneless cell cycle regulator) [NCBI Gene 70601] {aka 5730461K03Rik, Hsgt1}, Trp53-ps (transformation related protein 53, pseudogene) [NCBI Gene 22060], Fbn1 (fibrillin 1) [NCBI Gene 14118] {aka B430209H23, Fib-1, Tsk}, Iglv2 (immunoglobulin lambda variable 2) [NCBI Gene 110612] {aka Igl-V2}, Adap2 (ArfGAP with dual PH domains 2) [NCBI Gene 216991] {aka Centa2}, Dhx9 (DExH-box helicase 9) [NCBI Gene 13211] {aka Ddx9, HEL-5, NDHII, RHA, mHEL-5}, Mecp2 (methyl CpG binding protein 2) [NCBI Gene 17257] {aka 1500041B07Rik, D630021H01Rik, Mbd5, WBP10}, Sting1 (stimulator of interferon response cGAMP interactor 1) [NCBI Gene 72512] {aka 2610307O08Rik, ERIS, MPYS, Mita, STING, STING-beta}, Gcsh (glycine cleavage system protein H (aminomethyl carrier)) [NCBI Gene 68133] {aka 1100001L02Rik, 5730591C18Rik}, Faah (fatty acid amide hydrolase) [NCBI Gene 14073], Dhx34 (DExH-box helicase 34) [NCBI Gene 71723] {aka 1200013B07Rik, 1810012L18Rik, Ddx34, mKIAA0134}, Cd163 (CD163 antigen) [NCBI Gene 93671] {aka CD163v2, CD163v3}, Stfa2 (stefin A2) [NCBI Gene 20862] {aka Stf2}, Pdcd1 (programmed cell death 1) [NCBI Gene 18566] {aka Ly101, PD-1, Pdc1}, Got2 (glutamatic-oxaloacetic transaminase 2, mitochondrial) [NCBI Gene 14719] {aka FABP-pm, Got-2, Kyat4, mAspAT}, Ptma (prothymosin alpha) [NCBI Gene 19231] {aka Thym}, Taf1a (TATA-box binding protein associated factor, RNA polymerase I, A) [NCBI Gene 21339] {aka TAFI48, mTAFI48}, Lrp6 (low density lipoprotein receptor-related protein 6) [NCBI Gene 16974] {aka C030016K15Rik, Cd, Gw, ska26, ska<m26Jus>, skax26}, Ctsh (cathepsin H) [NCBI Gene 13036], Cd274 (CD274 antigen) [NCBI Gene 60533] {aka A530045L16Rik, B7h1, Pdcd1l1, Pdcd1lg1, Pdl1}, Siglece (sialic acid binding Ig-like lectin E) [NCBI Gene 83382] {aka Cd170, Siglec12, Siglec5, Siglec9, Siglecl1, mSiglec-E}, Mylk (myosin, light polypeptide kinase) [NCBI Gene 107589] {aka 9530072E15Rik, A930019C19Rik, KRP, MLCK108, MLCK210, Mlck}, Ybx3 (Y box protein 3) [NCBI Gene 56449] {aka Csda, Dpba, MSY3, MSY4, Yb2, dbpA}, Phf11c (PHD finger protein 11C) [NCBI Gene 628705] {aka EG628705, Gm6907, Phf11}, Rpl36a (ribosomal protein L36A) [NCBI Gene 19982] {aka L44L, Rpl44}, Ighg3 (Immunoglobulin heavy constant gamma 3) [NCBI Gene 380795] {aka IgG3}, Mettl2 (methyltransferase 2, methylcytidine) [NCBI Gene 52686] {aka 2810438F06Rik, C130031G21Rik, D11Ertd768e, METL, PSENIP1}, Cyth1 (cytohesin 1) [NCBI Gene 19157] {aka CLM1, CTH-1, CYTIP, Pscd1}, B2m (beta-2 microglobulin) [NCBI Gene 12010] {aka Ly-m11, beta2-m, beta2m}, Ppp3cb (protein phosphatase 3, catalytic subunit, beta isoform) [NCBI Gene 19056] {aka 1110063J16Rik, Calnb, CnAbeta, Cnab}, Fn1 (fibronectin 1) [NCBI Gene 14268] {aka E330027I09, Fn, Fn-1}, Zfp871 (zinc finger protein 871) [NCBI Gene 208292] {aka 4732483N19, 9030612M13Rik, mKIAA3006}, Taf12 (TATA-box binding protein associated factor 12) [NCBI Gene 66464] {aka 20kDa, 2810422D08Rik, Taf2J}, Rps25 (ribosomal protein S25) [NCBI Gene 75617] {aka 2810009D21Rik}, Ptrh1 (peptidyl-tRNA hydrolase 1 homolog) [NCBI Gene 329384] {aka 2210013M04Rik, PTH}, Kif14 (kinesin family member 14) [NCBI Gene 381293] {aka D1Ertd367e, E130203M01}, Sepsecs (Sep (O-phosphoserine) tRNA:Sec (selenocysteine) tRNA synthase) [NCBI Gene 211006] {aka D5Ertd135e, SLA, SecS}, Igkc (immunoglobulin kappa constant) [NCBI Gene 16071] {aka Igk-C}, Col4a1 (collagen, type IV, alpha 1) [NCBI Gene 12826] {aka Bru, Col4a-1, Raw, Svc}, Adamtsl4 (ADAMTS-like 4) [NCBI Gene 229595] {aka ADAMTSL-4, Tsrc1}, Zfp729b (zinc finger protein 729b) [NCBI Gene 100416706], Prss23 (serine protease 23) [NCBI Gene 76453] {aka 2310046G15Rik, 4930479H08Rik, Spuve}, Ighm (immunoglobulin heavy constant mu) [NCBI Gene 16019] {aka Igh-6, Igh-M, Igh6, Igm, TC1460681, muH}, Igkv9-120 (immunoglobulin kappa chain variable 9-120) [NCBI Gene 434025] {aka EG434025, Gm5571}, Ahsa2 (AHA1, activator of heat shock protein ATPase 2) [NCBI Gene 268390], Anxa3 (annexin A3) [NCBI Gene 11745] {aka Anx3}, Ighg2b (immunoglobulin heavy constant gamma 2B) [NCBI Gene 16016] {aka IgG2b, Igh-3, gamma2b}, Csnk1g2 (casein kinase 1, gamma 2) [NCBI Gene 103236] {aka 2810429I12Rik}, Hfe (homeostatic iron regulator) [NCBI Gene 15216] {aka MR2}, Fxn (frataxin) [NCBI Gene 14297] {aka FA, FARR, Frda, X25}
- **Diseases:** dislocation (MESH:D004204), Tumor (MESH:D009369), hypoxia (MESH:D000860), necrotic (MESH:D009336), breast cancer (MESH:D001943), cardiotoxicity (MESH:D066126), hypoxic (MESH:D002534), inflammatory (MESH:D007249), cutaneous T-cell lymphoma (MESH:D016410), R (MESH:C580424), PKSs (MESH:D020159), bacterial (MESH:D001424), deaths (MESH:D003643), metastases (MESH:D009362), EcN (MESH:D004927), AT (MESH:C537607), peripheral T-cell lymphoma (MESH:D016411), toxicity (MESH:D064420), pancreatic cancer (MESH:D010190)
- **Chemicals:** isoflurane (MESH:D007530), reactive oxygen species (MESH:D017382), ACN (MESH:C032159), PBS (MESH:D007854), TA (MESH:D013635), methanol (MESH:D000432), CO2 (MESH:D002245), Tet (MESH:D013752), sucrose (MESH:D013395), ammonia (MESH:D000641), formic acid (MESH:C030544), araC (MESH:D003561), sodium chloride (MESH:D012965), FK228 (MESH:C087123), H2O (MESH:D014867), 4-mercaptobutanyl-S-PCP (-), dep (MESH:C007268), Colibactin (MESH:C569566), chloramphenicol (MESH:D002701), oxygen (MESH:D010100), Herceptin (MESH:D000068878), CCK-8 (MESH:D012844), L-arginine (MESH:D001120), F12 (MESH:C007782), depsipeptide (MESH:D047630), spectinomycin (MESH:D000198), L-arabinose (MESH:D001089), cyclic-di-AMP (MESH:C528998), agar (MESH:D000362), AHT (MESH:C016229)
- **Species:** Bifidobacterium (genus) [taxon 1678], Chromobacterium (genus) [taxon 535], Saccharomyces cerevisiae (baker's yeast, species) [taxon 4932], Bacillus subtilis (species) [taxon 1423], Escherichia coli (E. coli, species) [taxon 562], Listeria (genus) [taxon 1637], Pseudomonas aeruginosa PAO1 (strain) [taxon 208964], Mus musculus (house mouse, species) [taxon 10090], Escherichia coli Nissle 1917 (strain) [taxon 316435], Bacteria Latreille et al. 1825 (Bacteria stick insect, genus) [taxon 629395], Pseudomonas sp. (species) [taxon 306], Homo sapiens (human, species) [taxon 9606], Salmonella (genus) [taxon 590], Escherichia coli BL21 (strain) [taxon 511693], Enterococcus faecium (species) [taxon 1352]
- **Cell lines:** WM3064 — Homo sapiens (Human), Melanoma, Cancer cell line (CVCL_C281), EcN-25 — Homo sapiens (Human), Transformed cell line (CVCL_9I02), 4T1 — Mus musculus (Mouse), Malignant neoplasms of the mouse mammary gland, Cancer cell line (CVCL_0125), )-23 — Cricetulus griseus (Chinese hamster), Spontaneously immortalized cell line (CVCL_K265), HC11 — Mus musculus (Mouse), Spontaneously immortalized cell line (CVCL_0288)

## Full text

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## Figures

12 figures with captions in the complete paper: https://tomesphere.com/paper/PMC12994790/full.md

## References

90 references — full list in the complete paper: https://tomesphere.com/paper/PMC12994790/full.md

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Source: https://tomesphere.com/paper/PMC12994790