# Epigenetic Activity of Cancer Therapy Drugs Revealed by HeLa TI Cell-Based Assay

**Authors:** Varvara Maksimova, Valeriia Popova, Alyona Kholodova, Julia Makus, Olga Usalka, Eugenia Lylova, Aleksandr Kudriashov, Gennady Belitsky, Marianna Yakubovskaya, Kirill Kirsanov

PMC · DOI: 10.3390/epigenomes10010014 · 2026-02-23

## TL;DR

This study shows that many cancer drugs affect the epigenetic state of cancer cells, which could improve treatment strategies and help overcome drug resistance.

## Contribution

The study reveals the epigenetic activity of 15 widely used cancer therapy drugs using a HeLa TI cell-based assay.

## Key findings

- Epigenetic activity was observed in 15 drugs with diverse mechanisms, including chemotherapeutics, targeted agents, and corticosteroids.
- Drugs like chlorambucil, cisplatin, and docetaxel significantly increased GFP-positive cells, indicating epigenetic reactivation.
- The findings suggest that epigenetic modulation by these drugs may enhance treatment efficacy and combination therapies.

## Abstract

Background/Objectives: The aberrant epigenetic landscape of cancer cells has attracted wide attention, motivating the search for new epigenetically active drugs both for anticancer therapy and for overcoming the drug resistance promoted by epigenetic changes. The use of epi-drugs in cancer therapy requires consideration of the influence of applied treatment on epigenetic regulation of gene expression. Therefore, it is reasonable to screen epigenetically active compounds among the drugs widely used in clinical oncology. Methods: We applied the HeLa TI cell-based assay to analyze the epigenetic activity of 40 drugs including 22 chemotherapeutic, 2 immunotherapeutic, 13 targeted, and 3 palliative agents. Reactivation of the epigenetically silenced GFP reporter gene integrated into the genome of HeLa TI cells was assessed using flow cytometry. Results: Statistically significant increases in the proportions of GFP-positive cells were demonstrated for the alkylating agent chlorambucil; the antimetabolites cytarabine, fluorouracil, gemcitabine, and pemetrexed; the platinum-based compounds cisplatin, and oxaliplatin; the topoisomerase inhibitor topotecan; and the antimicrotubule agents docetaxel, vincristine, and eribulin. Epigenetic activity was also detected for the targeted-therapy agents AZD8055, wortmannin, and cetuximab, as well as for the corticosteroid dexamethasone. Thus, epigenetic activity was revealed for 15 drugs widely used in cancer therapy, which possess different modes of action. Conclusions: Our findings show that many anticancer therapy agents modulate the epigenetic landscape of cancer cells, providing a rationale for expanding their therapeutic applications and enhancing the efficacy of combination strategies by overcoming epigenetically driven chemoresistance.

## Linked entities

- **Genes:** NAL1 (Protein NARROW LEAF 1) [NCBI Gene 4336986]
- **Chemicals:** chlorambucil (PubChem CID 2708), cytarabine (PubChem CID 6253), fluorouracil (PubChem CID 3385), gemcitabine (PubChem CID 60750), pemetrexed (PubChem CID 135410875), cisplatin (PubChem CID 5460033), oxaliplatin (PubChem CID 9887053), topotecan (PubChem CID 60700), docetaxel (PubChem CID 148124), vincristine (PubChem CID 5978), eribulin (PubChem CID 11354606), AZD8055 (PubChem CID 25262965), wortmannin (PubChem CID 312145), dexamethasone (PubChem CID 5743)
- **Diseases:** cancer (MONDO:0004992)

## Full-text entities

- **Genes:** KDM1A (lysine demethylase 1A) [NCBI Gene 23028] {aka AIMAH3, AOF2, BHC110, CPRF, KDM1, LSD1}, CDKN2A (cyclin dependent kinase inhibitor 2A) [NCBI Gene 1029] {aka ARF, CAI2, CDK4I, CDKN2, CMM2, INK4}, SMARCA2 (SWI/SNF related BAF chromatin remodeling complex subunit ATPase 2) [NCBI Gene 6595] {aka BAF190, BIS, BRM, NCBRS, SAMRCA2, SNF2}, KMT5C (lysine methyltransferase 5C) [NCBI Gene 84787] {aka SUV420H2, Suv4-20h2}, CHAF1A (chromatin assembly factor 1 subunit A) [NCBI Gene 10036] {aka CAF-1, CAF1, CAF1B, CAF1P150, P150}, AKT1 (AKT serine/threonine kinase 1) [NCBI Gene 207] {aka AKT, PKB, PKB-ALPHA, PRKBA, RAC, RAC-ALPHA}, EHMT2 (euchromatic histone lysine methyltransferase 2) [NCBI Gene 10919] {aka BAT8, C6orf30, G9A, GAT8, KMT1C, NG36}, PARP1 (poly(ADP-ribose) polymerase 1) [NCBI Gene 142] {aka ADPRT, ADPRT 1, ADPRT1, ARTD1, PARP, PARP-1}, KMT5B (lysine methyltransferase 5B) [NCBI Gene 51111] {aka CGI-85, CGI85, MRD51, SUV420H1}, PDSS1 (decaprenyl diphosphate synthase subunit 1) [NCBI Gene 23590] {aka COQ1, COQ10D2, COQ1A, DPS, SPS, TPRT}, HDAC1 (histone deacetylase 1) [NCBI Gene 3065] {aka GON-10, HD1, KDAC1, RPD3, RPD3L1}, GSTP1 (glutathione S-transferase pi 1) [NCBI Gene 2950] {aka DFN7, FAEES3, GST3, GSTP, GSTP1-1, HEL-S-22}, NR3C1 (nuclear receptor subfamily 3 group C member 1) [NCBI Gene 2908] {aka GCCR, GCR, GCRST, GR, GRL}, TWSG1 (twisted gastrulation BMP signaling modulator 1) [NCBI Gene 57045] {aka TSG}, PRMT5 (protein arginine methyltransferase 5) [NCBI Gene 10419] {aka HRMT1L5, HSL7, IBP72, JBP1, SKB1, SKB1Hs}, EGFR (epidermal growth factor receptor) [NCBI Gene 1956] {aka ERBB, ERBB1, ERRP, HER1, NISBD2, NNCIS}, TET3 (tet methylcytosine dioxygenase 3) [NCBI Gene 200424] {aka BEFAHRS, hCG_40738}, KDM2A (lysine demethylase 2A) [NCBI Gene 22992] {aka CXXC8, FBL11, FBL7, FBXL11, JHDM1A, LILINA}, CD274 (CD274 molecule) [NCBI Gene 29126] {aka ADMIO5, B7-H, B7H1, PD-L1, PDCD1L1, PDCD1LG1}, HDAC9 (histone deacetylase 9) [NCBI Gene 9734] {aka HD7, HD7b, HD9, HDAC, HDAC7B, HDAC9B}, MLH1 (mutL homolog 1) [NCBI Gene 4292] {aka COCA2, FCC2, HNPCC, HNPCC2, LYNCH2, MLH-1}, PDGFRA (platelet derived growth factor receptor alpha) [NCBI Gene 5156] {aka CD140A, PDGFR-2, PDGFR2}, CASC3 (CASC3 exon junction complex subunit) [NCBI Gene 22794] {aka BTZ, MLN51}, PDCD1 (programmed cell death 1) [NCBI Gene 5133] {aka ADMIO4, AIMTBS, CD279, PD-1, PD1, SLEB2}, ESR1 (estrogen receptor 1) [NCBI Gene 2099] {aka ER, ESR, ESRA, ESTRR, Era, NR3A1}, SUV39H1 (SUV39H1 histone lysine methyltransferase) [NCBI Gene 6839] {aka H3-K9-HMTase 1, KMT1A, MG44, SUV39H}, CISH (cytokine inducible SH2 containing protein) [NCBI Gene 1154] {aka BACTS2, CIS, CIS-1, G18, SOCS}, EREG (epiregulin) [NCBI Gene 2069] {aka EPR, ER, Ep}, HNMT (histamine N-methyltransferase) [NCBI Gene 3176] {aka HMT, HNMT-S1, HNMT-S2, MRT51}, TMPRSS11D (transmembrane serine protease 11D) [NCBI Gene 9407] {aka ASP, HAT}, DNMT3A (DNA methyltransferase 3 alpha) [NCBI Gene 1788] {aka DNMT3A2, HESJAS, M.HsaIIIA, TBRS}, SUV39H2 (SUV39H2 histone lysine methyltransferase) [NCBI Gene 79723] {aka KMT1B}, SMARCA4 (SWI/SNF related BAF chromatin remodeling complex subunit ATPase 4) [NCBI Gene 6597] {aka BAF190, BAF190A, BRG1, CSS4, MRD16, OTSC12}, FDPS (farnesyl diphosphate synthase) [NCBI Gene 2224] {aka FPPS, FPS, POROK9}, DOT1L (DOT1 like histone lysine methyltransferase) [NCBI Gene 84444] {aka DOT1, KMT4, NDNS}, PHC2 (polyhomeotic homolog 2) [NCBI Gene 1912] {aka EDR2, HPH2, PH2}, MTOR (mechanistic target of rapamycin kinase) [NCBI Gene 2475] {aka FRAP, FRAP1, FRAP2, RAFT1, RAPT1, SKS}, DNMT1 (DNA methyltransferase 1) [NCBI Gene 1786] {aka ADCADN, AIM, CXXC9, DNMT, HSN1E, MCMT}, SETDB1 (SET domain bifurcated histone lysine methyltransferase 1) [NCBI Gene 9869] {aka ESET, H3-K9-HMTase4, KG1T, KMT1E, TDRD21}, TET1 (tet methylcytosine dioxygenase 1) [NCBI Gene 80312] {aka CXXC6, LCX, bA119F7.1}, PRDM9 (PR/SET domain 9) [NCBI Gene 56979] {aka KMT8B, MEISETZ, MSBP3, PFM6, ZNF899}, SOX10 (SRY-box transcription factor 10) [NCBI Gene 6663] {aka DOM, PCWH, SOX-10, WS2E, WS4, WS4C}, VEGFA (vascular endothelial growth factor A) [NCBI Gene 7422] {aka L-VEGF, MVCD1, VEGF, VPF}, EZH2 (enhancer of zeste 2 polycomb repressive complex 2 subunit) [NCBI Gene 2146] {aka ENX-1, ENX1, EZH2b, KMT6, KMT6A, WVS}, PIK3CB (phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit beta) [NCBI Gene 5291] {aka P110BETA, PI3K, PI3KBETA, PIK3C1}, SLAMF7 (SLAM family member 7) [NCBI Gene 57823] {aka 19A, CD319, CRACC, CS1}, TOP2A (DNA topoisomerase II alpha) [NCBI Gene 7153] {aka TOP2, TOP2alpha, TOPIIA, TP2A}, PRC1 (protein regulator of cytokinesis 1) [NCBI Gene 9055] {aka ASE1, MAP65}, DNMT3B (DNA methyltransferase 3 beta) [NCBI Gene 1789] {aka FSHD4, ICF, ICF1, M.HsaIIIB}, KDM5A (lysine demethylase 5A) [NCBI Gene 5927] {aka NEDEHC, RBBP-2, RBBP2, RBP2}, RING1 (ring finger protein 1) [NCBI Gene 6015] {aka RING1A, RNF1}
- **Diseases:** prostate cancer (MESH:D011471), acute myeloid leukemia (MESH:D015470), triple-negative (MESH:D064726), injury to (MESH:D014947), epithelioid sarcoma (MESH:D012509), small-cell lung cancer (MESH:D055752), rhabdomyosarcoma (MESH:D012208), epithelial malignancies (MESH:D002277), colorectal cancer (MESH:D015179), cytotoxicity (MESH:D064420), non-small cell lung cancer (MESH:D002289), tumor suppressor (OMIM:601308), Cancer (MESH:D009369), lymphoblastic leukemia (MESH:D054198), ovarian cancer (MESH:D010051), inflammatory (MESH:D007249), hematological malignancies (MESH:D019337), breast cancer (MESH:D001943), lymphomas (MESH:D008223)
- **Chemicals:** PTX (MESH:D017239), triazenes (MESH:D014226), ER (MESH:C490954), RAPA (MESH:D020123), methionine (MESH:D008715), carbon (MESH:D002244), nitrogen mustard (MESH:D008466), N-nitrosodimethylamine (MESH:D004128), EtOH (MESH:D000431), L-glutamine (MESH:D005973), WMN (MESH:D000077191), PCZ (MESH:D011344), BNZ (MESH:C571386), CAS (MESH:D002118), streptomycin (MESH:D013307), anthracyclines (MESH:D018943), pyrimidine (MESH:C030986), CAS 137281-23-3 (-), PMX (MESH:D000068437), AZD (MESH:C546624), DEX (MESH:D003907), 5-FU (MESH:D005472), EDTA (MESH:D004492), cisplatin (MESH:D002945), VPA (MESH:D014635), OPB (MESH:C531550), CA (MESH:D002699), DOX (MESH:D004317), IRI (MESH:D000077146), topotecan (MESH:D019772), formazan (MESH:D005562), methylhydrazine (MESH:D009002), vorinostat (MESH:D000077337), Platinum (MESH:D010984), OXPT (MESH:D000077150), DNR (MESH:D003630), DTX (MESH:D000077143), OLA (MESH:C000589393), VCR (MESH:D014750), penicillin (MESH:D010406), DMSO (MESH:D004121), bortezomib (MESH:D000069286), BVZ (MESH:D000068258), DCZ (MESH:D003606), PBS (MESH:D007854), TMZ (MESH:D000077204), ETZ (MESH:C546027), 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MESH:C022616), CTX (MESH:D000068818), VIS (MESH:C538724), tazemetostat (MESH:C000593333), IFO (MESH:D007069), taxane (MESH:C080625), NAD+ (MESH:D009243), FVP (MESH:C077990), TSA (MESH:C012589), MTT (MESH:C070243), N-nitrosodiphenylamine (MESH:C023649), ZOL (MESH:D000077211), GEM (MESH:D000093542)
- **Species:** Homo sapiens (human, species) [taxon 9606], Rattus norvegicus (brown rat, species) [taxon 10116], Schizosaccharomyces pombe (fission yeast, species) [taxon 4896]
- **Cell lines:** Walker 256 — Rattus norvegicus (Rat), Adenocarcinoma of the rat mammary gland, Cancer cell line (CVCL_3537), HeLa — Homo sapiens (Human), Human papillomavirus-related endocervical adenocarcinoma, Cancer cell line (CVCL_0030), HCT116 — Homo sapiens (Human), Colon carcinoma, Cancer cell line (CVCL_0291), HeLa TI — Mus musculus (Mouse), Hybridoma (CVCL_B7NK), HL-60 — Homo sapiens (Human), Adult acute myeloid leukemia with maturation, Cancer cell line (CVCL_0002), S2 — Drosophila melanogaster (Fruit fly), Spontaneously immortalized cell line (CVCL_Z232), CaSki — Homo sapiens (Human), Human papillomavirus-related cervical squamous cell carcinoma, Cancer cell line (CVCL_1100), Ascites Sarcoma — Rattus norvegicus (Rat), Rat sarcoma, Cancer cell line (CVCL_4U54), MDA-MB-231 — Homo sapiens (Human), Breast adenocarcinoma, Cancer cell line (CVCL_0062)

## Figures

5 figures with captions in the complete paper: https://tomesphere.com/paper/PMC13025751/full.md

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Source: https://tomesphere.com/paper/PMC13025751