REFERENCES
1. Kim J, Harper A, McCormack V, et al. Global patterns and trends in breast cancer incidence and mortality across 185 countries. Nat Med. 2025;31:1154-62.
2. Loibl S, André F, Bachelot T, et al.; ESMO Guidelines Committee. Early breast cancer: ESMO Clinical Practice Guideline for diagnosis, treatment and follow-up. Ann Oncol. 2024;35:159-82.
3. Early Breast Cancer Trialists’ Collaborative Group (EBCTCG). Long-term outcomes for neoadjuvant versus adjuvant chemotherapy in early breast cancer: meta-analysis of individual patient data from ten randomised trials. Lancet Oncol. 2018;19:27-39.
4. Cottu P, D’Hondt V, Dureau S, et al. Letrozole and palbociclib versus chemotherapy as neoadjuvant therapy of high-risk luminal breast cancer. Ann Oncol. 2018;29:2334-40.
5. Yau C, Osdoit M, van der Noordaa M, et al.; I-SPY 2 Trial Consortium. Residual cancer burden after neoadjuvant chemotherapy and long-term survival outcomes in breast cancer: a multicentre pooled analysis of 5161 patients. Lancet Oncol. 2022;23:149-60.
6. Almendro V, Cheng YK, Randles A, et al. Inference of tumor evolution during chemotherapy by computational modeling and in situ analysis of genetic and phenotypic cellular diversity. Cell Rep. 2014;6:514-27.
7. Yates LR, Gerstung M, Knappskog S, et al. Subclonal diversification of primary breast cancer revealed by multiregion sequencing. Nat Med. 2015;21:751-9.
8. Yin G, Liu L, Yu T, et al. Genomic and transcriptomic analysis of breast cancer identifies novel signatures associated with response to neoadjuvant chemotherapy. Genome Med. 2024;16:11.
9. Seo ES, Park S, Cho EY, et al. Spatial and genomic profiling of residual breast cancer after neoadjuvant chemotherapy unveil divergent fates for each breast cancer subtype. Cell Rep Med. 2025;6:102164.
10. Venizelos A, Engebrethsen C, Deng W, et al. Clonal evolution in primary breast cancers under sequential epirubicin and docetaxel monotherapy. Genome Med. 2022;14:86.
11. Varna M, Soliman H, Feugeas JP, et al. Changes in allelic imbalances in locally advanced breast cancers after chemotherapy. Br J Cancer. 2007;97:1157-64.
12. Marine JC, Dawson SJ, Dawson MA. Non-genetic mechanisms of therapeutic resistance in cancer. Nat Rev Cancer. 2020;20:743-56.
13. Gonçalves AC, Richiardone E, Jorge J, et al. Impact of cancer metabolism on therapy resistance - clinical implications. Drug Resist Updat. 2021;59:100797.
14. Winter M, Nait Eldjoudi A, Guette C, et al. Mitochondrial adaptation decreases drug sensitivity of persistent triple negative breast cancer cells surviving combinatory and sequential chemotherapy. Neoplasia. 2023;46:100949.
15. Goldman A, Khiste S, Freinkman E, et al. Targeting tumor phenotypic plasticity and metabolic remodeling in adaptive cross-drug tolerance. Sci Signal. 2019;12:eaas8779.
16. Echeverria GV, Ge Z, Seth S, et al. Resistance to neoadjuvant chemotherapy in triple-negative breast cancer mediated by a reversible drug-tolerant state. Sci Transl Med. 2019;11:eaav0936.
17. Hangauer MJ, Viswanathan VS, Ryan MJ, et al. Drug-tolerant persister cancer cells are vulnerable to GPX4 inhibition. Nature. 2017;551:247-50.
18. Derouane F, Desgres M, Moroni C, et al. Metabolic adaptation towards glycolysis supports resistance to neoadjuvant chemotherapy in early triple negative breast cancers. Breast Cancer Res. 2024;26:29.
19. Kenicer J, Spears M, Lyttle N, et al. Molecular characterisation of isogenic taxane resistant cell lines identify novel drivers of drug resistance. BMC Cancer. 2014;14:762.
20. Michaelis M, Rothweiler F, Barth S, et al. Adaptation of cancer cells from different entities to the MDM2 inhibitor nutlin-3 results in the emergence of p53-mutated multi-drug-resistant cancer cells. Cell Death Dis. 2011;2:e243.
21. Braunstein M, Liao L, Lyttle N, et al. Downregulation of histone H2A and H2B pathways is associated with anthracycline sensitivity in breast cancer. Breast Cancer Res. 2016;18:16.
22. Tsugawa H, Cajka T, Kind T, et al. MS-DIAL: data-independent MS/MS deconvolution for comprehensive metabolome analysis. Nat Methods. 2015;12:523-6.
23. Patro R, Duggal G, Love MI, Irizarry RA, Kingsford C. Salmon provides fast and bias-aware quantification of transcript expression. Nat Methods. 2017;14:417-9.
24. Robinson MD, McCarthy DJ, Smyth GK. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. 2010;26:139-40.
25. Ritchie ME, Phipson B, Wu D, et al. limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res. 2015;43:e47.
26. Hoogstraat M, Lips EH, Mayayo-Peralta I, et al. Comprehensive characterization of pre- and post-treatment samples of breast cancer reveal potential mechanisms of chemotherapy resistance. NPJ Breast Cancer. 2022;8:60.
27. Park YH, Lal S, Lee JE, et al. Chemotherapy induces dynamic immune responses in breast cancers that impact treatment outcome. Nat Commun. 2020;11:6175.
28. van Veen S, Kourti A, Ausloos E, et al. ATP13A4 upregulation drives the elevated polyamine transport system in the breast cancer cell line MCF7. Biomolecules. 2023;13:918.
29. Chen X, Zhou X, Meng Y, et al. Deubiquitinase UCH-L1 confers paclitaxel resistance via stabilizing PKM2 to promote glycolysis in triple-negative breast cancer. Cell Death Dis. 2026;17:261.
30. Deng Y, Chen Z, Chen P, et al. ALKBH3-regulated m1A of ALDOA potentiates glycolysis and doxorubicin resistance of triple negative breast cancer cells. Acta Pharm Sin B. 2025;15:3092-106.
31. Uslu C, Kapan E, Lyakhovich A. OXPHOS inhibition overcomes chemoresistance in triple negative breast cancer. Redox Biol. 2025;83:103637.
32. Evans KW, Yuca E, Scott SS, et al. Oxidative phosphorylation is a metabolic vulnerability in chemotherapy-resistant triple-negative breast cancer. Cancer Res. 2021;81:5572-81.
33. Yang R, Yi M, Xiang B. Novel insights on lipid metabolism alterations in drug resistance in cancer. Front Cell Dev Biol. 2022;10:875318.
34. Wang Z, Wang M, Dong B, Wang Y, Ding Z, Shen S. Drug-tolerant persister cells in cancer: bridging the gaps between bench and bedside. Nat Commun. 2025;16:10048.
35. Pan H, Gray R, Braybrooke J, et al.; EBCTCG. 20-year risks of breast-cancer recurrence after stopping endocrine therapy at 5 years. N Engl J Med. 2017;377:1836-46.
36. Dent R, Trudeau M, Pritchard KI, et al. Triple-negative breast cancer: clinical features and patterns of recurrence. Clin Cancer Res. 2007;13:4429-34.
37. Holbert CE, Cullen MT, Casero RA Jr, Stewart TM. Polyamines in cancer: integrating organismal metabolism and antitumour immunity. Nat Rev Cancer. 2022;22:467-80.
38. Kahi M, Mazzu A, Batistic L, et al. Hypusination of the translation factor eIF5A regulates mitochondrial tRNA processing to promote prostate cancer aggressiveness. Nat Commun. 2026;17:4892.
39. Borsky P, Holmannova D, Soukup O, et al. Distinct roles of urolithin A and spermidine in mitophagy and autophagy: implications for dietary supplementation. Nutr Res Rev. 2025;39:e8.
40. Zhou J, Pang J, Tripathi M, et al. Spermidine-mediated hypusination of translation factor EIF5A improves mitochondrial fatty acid oxidation and prevents non-alcoholic steatohepatitis progression. Nat Commun. 2022;13:5202.
41. Ji G, Liu J, Zhao Z, et al. Polyamine anabolism promotes chemotherapy-induced breast cancer stem cell enrichment. Adv Sci. 2024;11:e2404853.
42. Park BS, Jeon H, Kim Y, et al. Polyamine and EIF5A hypusination downstream of c-Myc confers targeted therapy resistance in BRAF mutant melanoma. Mol Cancer. 2024;23:136.
43. Piha-Paul SA, Tolcher AW, Vandross AL, Spira AI, Burns MR. Phase I dose-escalation trial of AMXT 1501 dicaprate plus difluoromethylornithine: a dual-agent approach targeting immunosuppressive polyamine metabolism. ESMO Open. 2025;10:105576.
44. Gamble LD, Purgato S, Murray J, et al. Inhibition of polyamine synthesis and uptake reduces tumor progression and prolongs survival in mouse models of neuroblastoma. Sci Transl Med. 2019;11:eaau1099.
45. Khan A, Gamble LD, Upton DH, et al. Dual targeting of polyamine synthesis and uptake in diffuse intrinsic pontine gliomas. Nat Commun. 2021;12:971.
46. Casero RA Jr, Murray Stewart T, Pegg AE. Polyamine metabolism and cancer: treatments, challenges and opportunities. Nat Rev Cancer. 2018;18:681-95.
47. Iqbal MA, Siddiqui S, Smith K, et al. Metabolic stratification of human breast tumors reveal subtypes of clinical and therapeutic relevance. iScience. 2023;26:108059.
48. Shahnazari P, Kavousi K, Khorshid HRK, Minuchehr Z, Goliaei B, Salek RM. Uncovering subtype-specific metabolic signatures in breast cancer through multimodal integration, attention-based deep learning, and self-organizing maps. Sci Rep. 2025;15:21775.
