VASN-Linked Paclitaxel Resistance in Triple-Negative Breast Cancer

Key Takeaways

• In TNBC, higher VASN expression was associated with paclitaxel resistance in resistant models and with less favorable response to paclitaxel-based therapy in clinical specimens.
• Paclitaxel-resistant MDA-MB-231R and CAL-51R cells showed about sixfold higher paclitaxel IC50 values, along with less paclitaxel-induced apoptosis and G2/M arrest than parental cells.
• The authors reported that CCAAT/enhancer-binding protein beta (CEBPB) activated VASN transcription and linked VASN to insulin-like growth factor 2 binding protein 3 (IGF2BP3), ATP-binding cassette subfamily B member 1 (ABCB1) signaling, and phosphatidylinositol 3-kinase/protein kinase B (PI3K/AKT) activation in TNBC cells.
• Computational screening identified trametinib, and trametinib plus paclitaxel suppressed resistant xenograft growth with reported synergy and no obvious toxicity in the model.

Paclitaxel is a mainstay in triple-negative breast cancer (TNBC), but resistance can sharply narrow benefit in a subtype with few targetable markers of nonresponse. That problem is especially consequential when treatment decisions still rely more on broad clinicopathologic features than on resistance-specific biology. Investigators therefore examined how paclitaxel resistance might be traced across public datasets, clinical specimens, resistant cell models, and xenografts.

In a single preclinical study, detailed in the VASN paclitaxel-resistance study in the International Journal of Biological Sciences, investigators combined The Cancer Genome Atlas (TCGA)-BRCA, Gene Expression Omnibus (GEO) resistance datasets including GSE90564 and GSE25066, single-cell RNA sequencing (scRNA-seq) data from GSE169246, resistant cell models, and xenografts; GSE169246 included tissues from 22 patients with advanced TNBC, and TCGA comparisons spanned 1,097 primary tumors and 114 normal breast tissues. They then generated paclitaxel-resistant MDA-MB-231R and CAL-51R sublines through stepwise drug exposure and evaluated them with flow cytometry, viability and colony assays, quantitative real-time polymerase chain reaction, and western blotting. Promoter-binding and interaction work extended to chromatin immunoprecipitation (ChIP), co-immunoprecipitation (Co-IP), liquid chromatography-tandem mass spectrometry (LC-MS/MS), molecular dynamics (MD), and Cellular Thermal Shift Assay (CETSA), and resistant xenograft testing included paclitaxel 5 mg/kg intraperitoneally every 2 days for 5 cycles and trametinib 1 mg/kg/day by oral gavage for 14 consecutive days. Together, the design linked discovery screening to functional and in vivo validation.

VASN emerged as an overlapping candidate from neoadjuvant-resistance data, GSE90564 paclitaxel-resistant cells, and scRank analysis of GSE169246. In resistant sublines, the paclitaxel half-maximal inhibitory concentration increased from 4.64 nM to 26.44 nM in MDA-MB-231R, a 6.59-fold rise, and from 8.11 nM to 49.27 nM in CAL-51R, a 6.07-fold rise, while paclitaxel-induced apoptosis and G2/M arrest were attenuated. Across human material, VASN expression was higher in tumor than adjacent tissue, higher in estrogen receptor-negative than estrogen receptor-positive disease, and higher in patients with stable or progressive disease than in those with partial or complete response or pathological complete response after paclitaxel-based therapy. Functional experiments moved in the same direction, with VASN knockdown reducing proliferation, enhancing paclitaxel sensitivity, and slowing xenograft growth, whereas overexpression promoted the resistant phenotype.

CCAAT/enhancer-binding protein beta (CEBPB) emerged as the upstream regulator, and the authors reported direct binding at the VASN promoter with reduced promoter activity after mutation of the core site. RNA sequencing of VASN-overexpressing cells highlighted ATP-binding cassette subfamily B member 1 (ABCB1) and phosphatidylinositol 3-kinase/protein kinase B (PI3K/AKT) pathway enrichment, while VASN manipulation altered ABCB1 expression and PI3K/AKT phosphorylation. Co-IP, immunofluorescence, ubiquitination assays, and related experiments supported a model in which VASN interacted with insulin-like growth factor 2 binding protein 3 (IGF2BP3) and recruited ubiquitin-specific peptidase 10 (USP10) to reduce K48-linked polyubiquitination, stabilize IGF2BP3, and support N6-methyladenosine (m6A)-dependent ABCB1 messenger RNA stabilization. Trametinib was identified through computational screening, and resistant xenografts randomized to four treatment arms with n = 5 mice per group showed suppressed growth with trametinib plus paclitaxel, a Bliss-defined synergistic effect, and no obvious toxicity in the model.

The evidence remains preclinical, built from cell lines, xenografts, public datasets, and clinical specimen analyses rather than prospective patient intervention. That framing positions VASN as a mechanistic and biomarker candidate rather than a validated treatment-selection tool, and the reported response and prognostic associations still require external confirmation. The trametinib signal is likewise bounded to resistant models, so the observed lack of obvious toxicity in mice does not establish patient safety, dosing feasibility, or clinical benefit.

The authors concluded that paclitaxel resistance in TNBC can be organized around a proposed CEBPB-VASN-IGF2BP3-USP10-ABCB1 network that converges on drug-efflux and survival signaling. They further framed trametinib plus paclitaxel as a preclinical sensitization signal derived from that mechanism rather than a practice-ready regimen. In the authors' interpretation, VASN linked the dataset-derived signal to the resistant behavior seen in TNBC models.

Clinician Questions

What evidence identified VASN as a paclitaxel-resistance candidate in triple-negative breast cancer?

VASN emerged as an overlapping candidate across neoadjuvant-resistance data, GSE90564 paclitaxel-resistant cells, and scRank analysis of GSE169246, and resistant MDA-MB-231R and CAL-51R TNBC models showed attenuated paclitaxel-induced apoptosis and G2/M arrest plus marked IC50 increases versus parental cells.

How did the investigators connect CEBPB, VASN, IGF2BP3, USP10, and ABCB1 in TNBC cells?

The authors reported direct CEBPB binding at the VASN promoter in TNBC cells, then linked VASN to IGF2BP3 through protein interaction and USP10 recruitment that reduced K48-linked polyubiquitination and stabilized IGF2BP3; stabilized IGF2BP3 was in turn linked to m6A-dependent ABCB1 mRNA stabilization with associated changes in PI3K/AKT signaling.

Where was higher VASN expression associated with less favorable disease features or treatment response in breast cancer specimens?

Higher VASN expression was reported in breast tumor tissue versus adjacent tissue, in estrogen receptor-negative versus estrogen receptor-positive disease, and in TNBC cases with stable or progressive disease after paclitaxel-based therapy compared with partial or complete response or pathological complete response.

What preclinical evidence supported trametinib plus paclitaxel in resistant TNBC models?

Trametinib was identified through computational drug screening as a VASN-associated candidate and then tested with paclitaxel in resistant TNBC xenografts that compared vehicle, paclitaxel, trametinib, and combination therapy; the authors reported suppressed tumor growth, a Bliss-defined synergistic effect, and no obvious toxicity in the model.