Cancer drug response and resistance: molecular mechanisms and combating strategies

Altered drug transport and metabolism

One of the central barriers to effective chemotherapy is the development of MDR, wherein tumor cells acquire cross-resistance to structurally and mechanistically distinct agents (Fig. 2a).18 A hallmark of MDR is the dysregulation of intracellular drug availability, primarily through impaired drug uptake and enhanced drug efflux, involving the SLC and ABC transporter families.138,139,140 These transport mechanisms, often coupled with vesicular trafficking and metabolic reprogramming, significantly reduce intracellular drug accumulation, attenuate target engagement and contribute to immune evasion, collectively undermining therapeutic efficacy.

Fig. 2

Molecular mechanisms and combating strategies in cancer drug resistance: drug transport, metabolism, and signaling pathways. a Altered drug transport and metabolism, including decreased uptake mediated by solute carrier (SLC) transporters, enhanced efflux via ATP-binding cassette (ABC) transporters, and dysregulated pharmacokinetics/metabolic enzymes. b Alterations in DNA damage repair (DDR) mechanisms and corresponding therapeutic vulnerabilities. c Aberrant activation of major signaling pathways, including PI3K-AKT/mTOR, MAPK, NF-κB, TGF-β, Wnt, JAK/STAT, Notch, Hippo, and GAS6/AXL, along with potential targeted intervention strategies

Drug uptake: the role of SLC

SLC transporters, a large superfamily of membrane proteins responsible for nutrient and metabolite transport, also mediate the uptake of various chemotherapeutics (Fig. 2a).141 Their downregulation or functional loss has been implicated in primary and acquired resistance.140 For instance, decreased expression of the organic cation transporter OCT2 (SLC22A2) confers resistance to platinum-based drugs in pancreatic and ovarian cancers by reducing cellular drug accumulation.138,139 Similarly, the itaconate transporter SLC13A3 facilitates the uptake of itaconate (ITA), a TAM-derived immunometabolite. Elevated SLC13A3 expression in tumor cells stabilizes PD-L1 through ITA-mediated posttranslational modification, promoting immune escape and resistance to checkpoint blockade.142 Targeting SLC13A3 restores PD-L1 degradation and improves ICI responsiveness, highlighting a direct link between metabolite transport and immunotherapeutic resistance.142

Enhanced drug efflux: ABC transporters and MDR

ABC transporters constitute the most prominent efflux systems driving MDR (Fig. 2a).143 Powered by ATP hydrolysis, they actively extrude cytotoxic agents from tumor cells, thereby reducing intracellular drug concentrations below therapeutic thresholds.144 Among them, P-gp/ABCB1,145 MDR-associated proteins (MRPs/ABCCs),146 and BCRP/ABCG2147 are most extensively studied.

P-gp, encoded by ABCB1, is broadly expressed in various tumor types and correlates with disease progression, therapy resistance, and poor prognosis.148 P-gp substrates are structurally diverse, including paclitaxel, doxorubicin, vincristine, imatinib, and olaparib.149 Beyond tumors, P-gp is physiologically expressed in the gastrointestinal tract, renal tubules, liver, and blood–brain barrier, contributing to systemic drug clearance.150 Notably, paclitaxel-induced P-gp overexpression in mitochondria has been implicated in acquired resistance in ovarian cancer.151 Elevated MDR1/MRP1 expression is frequently associated with tumor recurrence and metastasis, and metastatic lesions often display higher P-gp levels than corresponding primary tumors.152 Proteomic profiling further identifies MDR1 upregulation as a critical driver of both intrinsic and acquired resistance to proteolysis-targeting chimeras (PROTACs), extending its relevance to emerging targeted protein degradation strategies.153

Complementing MDR1-mediated drug efflux, the multidrug resistance-associated protein (MRP) subfamily comprises nine members (MRP1–9) that confer resistance through partially distinct yet overlapping mechanisms.154,155,156 MRPs preferentially export drug–glutathione conjugates and promote drug sequestration into perinuclear vesicles, thereby restricting intracellular and nuclear drug availability.157 For example, MRP1 mediates resistance to methotrexate, cisplatin, and vinca alkaloids and is frequently overexpressed in lung, ovarian, and hematologic malignancies.158 MRP4 and MRP5 facilitate the efflux of cyclophosphamide and 5-fluorouracil and are transcriptionally regulated by Nrf2 signaling and therapeutic stress.154

BCRP, a half-transporter encoded by ABCG2, functions as a homodimer and mediates the efflux of topotecan, SN-38, mitoxantrone, and several TKIs, such as imatinib and osimertinib.147,159 Elevated BCRP expression is associated with chemoresistance and unfavorable prognosis in leukemia, breast, and ovarian cancers.160,161

Drug pharmacokinetics and metabolism

Pharmacokinetics, the study of drug absorption, distribution, metabolism, and excretion, is increasingly recognized as a determinant of therapeutic efficacy (Fig. 2a).44 Interpatient variability in PK, influenced by genetic polymorphisms, organ function, and TME characteristics, profoundly affects drug response.45 The lung resistance protein (LRP), encoded by the major vault protein (MVP) gene, contributes to MDR by mediating intracellular vesicular sequestration of drugs.162 By trafficking cytotoxic agents into exocytic vesicles or blocking nuclear entry, LRP prevents engagement with nuclear DNA or enzymes.162 The kinesin KIF4A regulates LRP trafficking, and elevated LRP expression has been associated with resistance in lung and ovarian cancers.163 CYP450 enzymes in the liver regulate the metabolism of many anticancer drugs (e.g., imatinib and erlotinib), and altered activity can lead to reduced efficacy or increased toxicity.46 High intratumoral expression of CYP3A4 can accelerate the metabolic inactivation of chemotherapeutic agents such as paclitaxel and docetaxel, thereby reducing local drug bioavailability, diminishing therapeutic efficacy, and ultimately contributing to drug resistance.164 Conversely, the loss of CYP3A4 expression in hepatocellular carcinoma impairs the bioactivation of prodrugs, leading to treatment failure. In addition, tumor-associated systemic inflammation can suppress hepatic CYP3A4 activity, altering systemic drug pharmacokinetics. This disruption is further exacerbated by individual genetic polymorphisms, polypharmacy, and hepatic or renal dysfunction, collectively disturbing metabolic homeostasis.164 These factors modulate drug exposure and the generation of active metabolites, ultimately fostering the emergence of therapeutic resistance.

Tissue distribution also influences therapeutic penetration; for instance, limited blood‒brain barrier permeability hampers glioblastoma treatment.165 Biotransformation pathways may generate active metabolites that enhance or reduce efficacy or cause off-target toxicity.166 Cyclophosphamide, for example, requires hepatic activation, but excessive metabolism may cause marrow suppression.167 Personalized dosing, PK monitoring, and targeted modulation of metabolic pathways are thus critical to optimizing cancer treatment and overcoming resistance.

Therapeutic targeting of transport-mediated resistance

Given the central role of efflux transporters in mediating MDR, extensive efforts have been dedicated to the development of pharmacological strategies aimed at overcoming transporter-driven drug efflux.168 Over the past few decades, inhibitors targeting key transporters such as P-gp, MRPs, and BCRP have evolved through three major generations.169 First-generation agents, including verapamil and cyclosporin A, showed in vitro efficacy but were hampered by off-target toxicity and limited clinical applicability. Second-generation inhibitors such as valspodar offered improved potency but interfered with CYP450 enzymes (e.g., CYP3A4), leading to problematic drug–drug interactions.170 More recently, third-generation compounds such as tariquidar and elacridar demonstrated enhanced specificity and pharmacokinetic profiles, showing promise in preclinical models when combined with agents such as paclitaxel and irinotecan.171 However, their clinical translation has been modest, underscoring the complexity of transporter-targeted therapy.

To circumvent the limitations of direct transporter inhibition, alternative approaches have emerged. Nanoparticle-based delivery systems, including liposomes, polymeric micelles, PEGylated constructs, and PLGA nanoparticles, can bypass efflux recognition and enhance tumor-selective drug accumulation, thereby restoring therapeutic efficacy.172 Natural compounds such as curcumin, quercetin, and salvianolic acid B have also demonstrated transporter-inhibitory properties with relatively low toxicity, although issues with solubility and bioavailability have limited their clinical utility and prompted formulation optimization.173 At the molecular level, gene modulation techniques, including siRNA- and shRNA-mediated silencing of efflux transporter genes (e.g., ABCB1, ABCG2), as well as CRISPR/Cas9-based gene editing, have successfully resensitized tumor cells to chemotherapy in preclinical models.174 Similarly, endogenous microRNAs (e.g., miR-451 and miR-326) have been shown to negatively regulate MDR1 expression and restore drug sensitivity in breast and gastric cancers.175,176 In parallel, novel therapeutic strategies are being explored to target functional domains of efflux transporters.143 These include inhibitors that bind ABCs, transmembrane domain mimetics that disrupt substrate recognition, and competitive peptide antagonists.177 One particularly promising avenue involves metabolic disruption: depletion of intracellular ATP, which powers transporter function, has been shown to impair drug efflux.178 For example, hybrid nanodrugs (HREDs) derived from citrus extracellular vesicles reduce ATP levels and suppress efflux activity, demonstrating potent antitumor effects in drug-resistant ovarian cancer models.172

Efflux-mediated resistance rarely occurs in isolation and often coexists with other resistance mechanisms, such as enhanced DNA repair, apoptosis evasion, or immune suppression.179,180,181,182 This has led to the development of rational combination strategies aimed at targeting multiple resistance nodes simultaneously.181 Notably, the combination of MDR1 inhibitors with PARPis has been shown to restore olaparib sensitivity in resistant ovarian cancer.108 Similarly, combined inhibition of ABCB1 (MDR1) and the use of PROTACs targeting the KRAS and MAPK signaling pathways enhances the treatment response in KRAS-mutant colorectal cancer xenograft models.153 Despite challenges such as compensatory upregulation of alternative transporters and feedback activation of resistance pathways, the transportome remains a tractable and druggable vulnerability.183 Moving forward, the integration of transporter profiling, nanotechnology-based delivery platforms and immunomodulatory interventions holds promise for overcoming transporter-mediated drug resistance and achieving more durable responses in refractory cancers.

Alterations in DNA damage repair (DDR)

Molecular mechanisms in DDR

DDR safeguards genomic stability under genotoxic stress, and its deficiency confers pronounced sensitivity to genotoxic therapies and PARP inhibitors while also driving resistance through repair restoration or pathway bypass.184 The most prevalent DNA lesions include single-strand breaks (SSBs) and double-strand breaks (DSBs), which are sensed by key damage sensors such as ataxia telangiectasia mutated (ATM), ATM and Rad3-related (ATR), and poly (ADP-ribose) polymerase 1 (PARP1). Activation of these sensors initiates checkpoint cascades, most notably ATM–Chk2 and ATR–Chk1, which coordinate cell cycle arrest, DNA repair pathway selection and apoptosis or senescence when repair fails.184,185 The downstream repair machineries comprise homologous recombination repair (HRR), nonhomologous end joining (NHEJ), base excision repair (BER), nucleotide excision repair (NER), and mismatch repair (MMR).185

In normal cells, DDR is indispensable for maintaining genomic fidelity and preventing malignant transformation. In cancer, however, DDR exerts a paradoxical influence: while repair deficiencies promote mutagenesis and tumorigenesis, restoration or hyperactivation of DDR pathways in established tumors fosters resistance by enabling efficient repair of therapy-induced DNA damage.186 These alterations underlie resistance not only to cytotoxic chemotherapy and radiotherapy but also to molecularly targeted agents and immunotherapies.187,188 Deciphering the context-specific regulation and plasticity of DDR, as well as its interplay with oncogenic signaling and tumor evolution, is critical for the development of rational therapeutic interventions (Fig. 2b).

Tumors with inherited or somatic deficiencies in HRR genes, such as BRCA1, BRCA2, PALB2, and RAD51, exhibit synthetic lethality to PARPis, including olaparib, rucaparib, niraparib, and talazoparib, which have shown durable efficacy in BRCA-mutant breast, ovarian, and prostate cancers.187,188 Nevertheless, clinical benefit is often limited by intrinsic and acquired resistance. For example, in pancreatic cancer, the inflammasome component NLRP4 mediates PARPi resistance by promoting NOXO1 expression, which inhibits nuclear translocation of SIRT7, thereby enhancing ROS-induced autophagy and reactivating DDR via reduced γH2AX accumulation and impaired BRCA1–RAD51 complex formation.189 In parallel, error-prone DNA damage tolerance mechanisms, such as translesion synthesis (TLS), contribute to therapy evasion.190 TLSs allow replicative bypass of alkylated or crosslinked lesions and prevent replication fork collapse. Upregulation of TLS has been implicated in resistance to combined olaparib and temozolomide in SCLC.190 These insights highlight the importance of identifying predictive biomarkers and vulnerabilities associated with repair pathway rewiring.

Beyond PARPis, multiple DDR kinases, including ATM, ATR, CHK1/2, WEE1, and DNA-dependent protein kinase catalytic subunit (DNA-PKcs), have emerged as therapeutic targets.191 For instance, WEE1 inhibition (e.g., with AZD1775) abrogates G2/M checkpoints, thereby potentiating the cytotoxicity of DNA-damaging agents such as cisplatin.192 ATR inhibitors (e.g., BAY1895344) demonstrate promising activity in DDR-deficient tumors and are undergoing clinical evaluation across solid tumor types.193 Furthermore, combining DDR inhibitors with ICB enhances antitumor immunity by promoting neoantigen exposure, micronuclei formation, and activation of the cGAS–STING pathway.194 Conversely, restoration or upregulation of DDR components can drive resistance. Intriguingly, PD-L1, a key immunoregulatory molecule, can act as an RNA-binding protein to stabilize transcripts encoding DDR proteins such as BRCA1, MRE11, and RAD50, thereby enhancing DNA repair and promoting resistance to radiotherapy and chemotherapy.50 D-mannose, by activating AMPK and impairing PD-L1 glycosylation, induces PD-L1 degradation and disrupts HRR, sensitizing tumors to ionizing radiation.195

Epigenetic and chromatin remodeling regulators modulate DDR efficiency and replication fork stability. In BRCA2-deficient cells, EZH2-mediated H3K27 trimethylation at stalled forks facilitates MUS81 recruitment and fork restart. Loss of EZH2 impairs this mechanism, stabilizing forks and attenuating PARPi efficacy.102 Similarly, GRB2 stabilizes RAD51 at reversed forks by inhibiting its ATPase activity; GRB2 depletion leads to fork collapse, cytosolic DNA accumulation, cGAS–STING activation, and increased PARPi sensitivity.196 Complex crosstalk between DDR and oncogenic survival pathways further complicates therapy. In RAS- or PI3K-driven tumors, elevated reactive oxygen species (ROS) levels induce oxidative DNA damage.197 Tumor cells adapt by upregulating BER components (e.g., Polβ, APE1, FEN1) and scaffolding proteins such as CUX1/2 and SATB1 to promote repair and evade senescence.198 Conversely, DNA-PK and ATM activate AKT in response to DNA damage, reinforcing DDR capacity and suppressing apoptosis via p53 inhibition.199 Radiation-induced exosomes in esophageal squamous cell carcinoma deliver HMGB1, which activates PI3K–AKT–FOXO3A signaling and elevates γH2AX expression in recipient cells, promoting radioresistance.200 Genomic amplifications of DDR genes also contribute to broad-spectrum resistance.199 Amplification of NBN, RAD51, or PARP1 has been associated with reduced sensitivity to more than 30 targeted agents across cancer types.29 Despite these insights, DDR-targeted therapies remain challenged by nonselective toxicity, resistance heterogeneity, limited biomarker availability and modest clinical durability.

Combating strategies in DDR

To address DDR-mediated therapeutic resistance, multiple strategies have been proposed that exploit vulnerabilities in DNA repair pathways (Fig. 2b).188 The synthetic lethality paradigm remains central, exemplified by the success of PARP inhibitors in HRR-deficient tumors.185 To circumvent resistance and expand the scope of DDR targeting, next-generation agents such as ATR, CHK1, WEE1, and DNA-PK inhibitors are being investigated, both as monotherapies and in combination with DNA-damaging agents.184,185,199 Rational combinations, such as PARPis plus ATR or WEE1 inhibitors, aim to exacerbate replication stress and collapse replication fork stability, particularly in tumors with partial or context-specific DDR competence.188,191

Combination approaches that integrate DDR inhibition with immunotherapy are of increasing interest.201 DDR-targeted agents promote immunogenic cell death by inducing micronuclei formation, enhancing TMB, and activating innate immune pathways such as cGAS–STING, thereby augmenting ICB efficacy.185,188,202 Early-phase trials of PARPis combined with PD-1/PD-L1 inhibitors have shown promising responses, particularly in tumors refractory to ICB alone.201 Targeting metabolic and chromatin remodeling pathways represents an additional strategy to sensitize DDR-proficient tumors. Modulating NAD⁺ metabolism, histone modifiers (e.g., EZH2), or ATP-dependent chromatin remodelers (e.g., BRG1, CHD4) may shift the balance of repair pathway utilization, destabilize replication forks, or impair lesion recognition.102 Furthermore, inhibiting DDR-related posttranslational modifications, such as ATM/ATR-dependent phosphorylation or ubiquitination cascades, can selectively impair tumor cell repair fidelity without disrupting normal cells.199

Advances in precision oncology have also enabled real-time monitoring and individualized DDR targeting. Functional genomic screens, single-cell profiling, and liquid biopsy-based analyses of DDR mutations or gene expression signatures offer tools for patient stratification and adaptive treatment modulation.12,13,203 These technologies are expected to refine predictive biomarker discovery and uncover resistance trajectories. Looking forward, a comprehensive understanding of DDR pathway rewiring, coupled with integrated omics-based profiling and network-level vulnerability mapping, will be pivotal.12 Combinatorial approaches involving DDR inhibitors, epigenetic modulators, metabolic disruptors and immunotherapeutics hold promise for overcoming resistance and achieving durable clinical responses across malignancies.

Altered signaling pathways

At the systems level, diverse oncogenic signaling pathways intersect to drive common downstream programs that sustain tumor survival, plasticity, metabolic fitness, DNA repair capacity, and immune suppression, forming the mechanistic basis of therapeutic resistance (Fig. 2c).80,179,204,205

PI3K/AKT and mTOR signaling

The PI3K-AKT-mTOR axis plays a central role in orchestrating tumor cell growth, survival, metabolic reprogramming, immune evasion, and apoptosis resistance.204,205 Aberrant activation of this pathway is a well-established mechanism of resistance to targeted therapies, chemotherapy, and endocrine therapy.206 Activation is typically initiated by upstream receptor tyrosine kinases (RTKs) or G protein–coupled receptors (GPCRs), which trigger PI3K to convert PIP2 into PIP3, thereby recruiting and activating AKT.207 Activated AKT subsequently stimulates mTOR complexes (mTORC1/2), modulating a wide array of oncogenic processes.208,209

This pathway is normally restrained by the tumor suppressor PTEN, which dephosphorylates PIP3 and prevents AKT overactivation.210 In hormone receptor–positive/HER2-negative breast cancers, PI3K-AKT-mTOR is among the most frequently activated signaling axes.211 Hyperactivation commonly arises from mutations in PIK3CA (detected in ~35-40% of ER+/HER2− cases), AKT1 mutations, or PTEN loss.211,212 HER2 amplification further potentiates PI3K signaling.213,214 Activation of this pathway also shapes the TME. For instance, tumor-associated macrophage (TAM)-derived CCL2 activates PI3K-AKT-mTOR signaling, promoting tamoxifen resistance in breast cancer via a prosurvival feedback loop.215 In NSCLC, PIK3CA mutations are associated with acquired resistance to EGFR TKIs.27 In HCC, loss of EVA1A leads to PI3K/AKT/MDM2 axis activation, resulting in destabilization of p53 and resistance to lenvatinib.99

MAPK signaling pathway

The mitogen-activated protein kinase (MAPK) pathway is a highly conserved signaling module regulating cellular proliferation, differentiation, apoptosis, inflammation, and stress responses.216 It comprises four primary branches: ERK, p38 MAPK, JNK, and ERK5. The canonical MAPK pathway involves the RAS–RAF–MEK–ERK cascade, typically activated by RTKs such as EGFR, FGFR and HER2. Sequential phosphorylation through this cascade culminates in the activation of nuclear transcription factors such as ELK-1, FOS, and MYC.216,217

Acquired mutations within MAPK pathway components represent a major mechanism of resistance to targeted therapy.218 Secondary mutations in BRAF, KRAS, NRAS, and MEK1/2 have been widely observed in patients treated with BRAF and MEK inhibitors, restoring ERK signaling and driving therapeutic failure.219 These mutations enable tumor cells to escape pharmacologic inhibition while maintaining MAPK pathway dependency.

MAPK signaling contributes to therapeutic resistance by enhancing the expression of drug efflux transporters such as MDR1 and P-gp and by upregulating antiapoptotic genes such as Bcl-2.220 In melanoma, resistance to BRAF inhibitors frequently arises from reactivation of MAPK signaling or activation of alternative oncogenic pathways.221 In colorectal cancer, elevated EGFR ligand expression (e.g., AREG, EREG) sustains EGFR–MAPK signaling and underlies resistance to EGFR-targeted therapies.222 In breast cancer, NF1 loss drives resistance to PI3Kα inhibitors by activating RAS-MAPK signaling and promoting metabolic rewiring, including increased glycolysis and decreased ROS.223 In gastric cancer, downregulation of circMAPK1 decreases its encoded tumor-suppressive micropeptide MAPK1-109aa, disrupting competitive inhibition of the MEK1–MAPK1 interaction and resulting in sustained MAPK activation and immune evasion.224 The S100A8/A9–TLR4–p38 MAPK–NF-κB axis also contributes to immune resistance. This signaling cascade induces CXCL1 secretion by gastric cancer cells, driving recruitment of polymorphonuclear myeloid-derived suppressor cells (PMN-MDSCs), CD8⁺ T-cell exhaustion, and resistance to ICIs.225

NF-κB signaling pathway

NF-κB (nuclear factor kappa-light-chain-enhancer of activated B cells) represents a master transcription factor family governing immune and inflammatory responses, cell survival, DNA repair, metabolism, and stemness.226 It is activated through two major branches, the canonical (IκB-dependent) and noncanonical (NIK-dependent) pathways, both of which are frequently dysregulated in tumors and their microenvironments. In the canonical pathway, inflammatory cues activate the IκB kinase (IKK) complex, particularly IKKβ, which phosphorylates IκB proteins.227 This leads to their degradation and nuclear translocation of NF-κB dimers (typically p50/RelA), where they regulate gene transcription. The noncanonical pathway is stimulated by cytokines such as CD40L or BAFF, involving NIK-mediated processing of p100 to p52 and formation of RelB/p52 dimers that translocate into the nucleus.228

NF-κB confers resistance by upregulating antiapoptotic proteins (e.g., Bcl-2, Bcl-xL, XIAP, c-FLIP), stemness regulators, drug efflux transporters, and DNA repair enzymes.100 In ER+ breast cancer, Dll1-expressing quiescent tumor stem cells activate Notch–NF-κB signaling to promote survival and resistance to doxorubicin.229,230 The heat shock protein HSPB1 induces IκB-α ubiquitination and degradation, sustaining NF-κB activation and blocking ferroptosis. Nude mouse xenograft and lung metastasis models further confirmed the in vivo functional role of HSPB1.231 In cisplatin-resistant bladder cancer, constitutive NF-κB activity upregulates EMT and stemness markers, as well as ABCB1, driving resistance and progression.179 In mantle cell lymphoma, compensatory activation of noncanonical NF-κB supports survival pathways and mediates resistance to Bruton tyrosine kinase (BTK) inhibitors such as ibrutinib.232

In HCC, overexpression of EIF5B enhances IκB phosphorylation and activates NF-κB, contributing to EMT, stemness, and 5-FU resistance.100 RelB, a key transcription factor of the noncanonical pathway, directly binds the CD274 promoter to upregulate PD-L1, promoting immune escape in prostate cancer.233 Moreover, IFN-γ stimulation induces RIPK1 expression, which sustains NF-κB activity. This enhances the transcription of antiapoptotic genes (e.g., CFLAR and TNFAIP3) and promotes the secretion of immunosuppressive cytokines (e.g., CCL2, CXCL1, and IL-10), recruiting ARG1⁺TREM2⁺-suppressive myeloid cells. Collectively, these events reduce T/NK cell infiltration and cytotoxicity, contributing to ICB resistance.234

TGF-β signaling pathway

The transforming growth factor-β (TGF-β) superfamily, including TGF-β1/2/3, bone morphogenetic proteins (BMPs), activins, and nodal, exerts pleiotropic effects on cancer biology, with context-dependent roles as both a tumor suppressor and promoter.235 In early stages, TGF-β suppresses tumorigenesis by inducing cell cycle arrest and apoptosis; however, in advanced cancers, it drives EMT, immune evasion, stemness, and therapy resistance.

TGF-β signaling operates through canonical (Smad-dependent) and noncanonical (Smad-independent) pathways.236 Upon ligand binding, TGF-β receptor II (TβRII) recruits and phosphorylates TβRI, which activates Smad2/3. The Smad2/3–Smad4 complex then translocates into the nucleus to regulate transcription. Alternatively, TGF-β can activate the PI3K/AKT, MAPK, Rho-GTPases, and JNK/p38 pathways via noncanonical signaling.235 A notable positive feedback loop amplifies TGF-β signaling: TGF-β-induced Smad2/3 activation upregulates TGFBRAP1, which competitively binds TβRI and prevents its degradation by Smurf1/2-mediated ubiquitination. Stabilization of TβRI sustains pathway activity, promotes CSC-like phenotypes, and confers resistance to TKIs such as regorafenib in HCC.237

Chemotherapy can also reinforce TGF-β–driven resistance. CXCL1 and CXCL5, secreted in response to therapy, recruit neutrophils that release neutrophil extracellular traps (NETs). These NETs bind latent TGF-β via integrin αvβ1 and activate it through matrix metalloproteinase 9 (MMP9). Active TGF-β subsequently phosphorylates Smad2, promoting EMT, CSC traits, and chemoresistance.136 In BRAFV600E-mutant cancers, loss of the aryl hydrocarbon receptor (AhR) reduces expression of its repressor AhRR, allowing ARNT to accumulate in the nucleus. ARNT then interacts with Smad2/3, hyperactivating TGF-β/Smad signaling. This compensatory mechanism supports MAPK inhibitor resistance and promotes lineage plasticity and tumor progression.238 Platinum-based chemotherapy can induce tumor cell senescence, a state that is increasingly recognized as a contributor to acquired resistance. Senescent tumor cells secrete a TGF-β-enriched senescence-associated secretory phenotype (SASP), which activates AKT-mTOR signaling, reshapes the TME, and promotes malignant progression under therapeutic pressure.

Wnt signaling pathway

The Wnt signaling network is a master regulator of embryonic development, tissue regeneration, stem cell maintenance, metabolism, and immune homeostasis.80 Dysregulation of this pathway is a hallmark of many cancers, contributing to tumor progression, metastasis, and therapeutic resistance. Wnt signaling operates through canonical (Wnt/β-catenin) and noncanonical branches (e.g., Wnt/PCP and Wnt/Ca²⁺ pathways).60

In the canonical pathway, Wnt ligands bind Frizzled (FZD) receptors and LRP5/6 coreceptors, activating Dishevelled (DVL) and inhibiting the β-catenin destruction complex (Axin/APC/GSK-3β).129 Stabilized β-catenin translocates to the nucleus and partners with TCF/LEF transcription factors to activate oncogenic targets, including MYC, Cyclin D1, LGR5, CD44, and ABCB1, genes that regulate proliferation, drug efflux, and stemness.129 Wnt/β-catenin signaling is a key driver of EMT and CSC maintenance.129 In melanoma, the transmembrane glycoprotein podoplanin (PDPN) activates β-catenin signaling via CLEC-2–mediated platelet activation.239 This cascade promotes the secretion of immunosuppressive cytokines such as TGF-β, recruitment of Tregs and M2 macrophages, and suppression of CD8⁺ T and NK cell cytotoxicity, ultimately facilitating metastasis and immune resistance.80,239

Cross-talk with other oncogenic pathways further augments resistance.240 In glioblastoma, hepatocyte growth factor (HGF)/c-Met signaling enhances β-catenin nuclear localization and LEF1-dependent transcription of MDR–associated genes such as MRP-1, inducing CSC traits, endothelial–mesenchymal transition (EndMT), and temozolomide resistance.241 In lenvatinib-resistant HCC, CDK6-mediated phosphorylation of GSK3β at Ser9 stabilizes β-catenin and promotes its nuclear translocation, reinforcing CSC phenotypes and immune evasion.79 Similarly, in pancreatic cancer, β-catenin/TCF4/Pygo2 transcriptionally activates the lncRNA PVT1, which sponges miR-619-5p to derepress Pygo2 and ATG14. This positive feedback loop promotes Wnt target gene expression, autophagy activation, drug efflux, and gemcitabine resistance.242

JAK/STAT signaling pathway

The Janus kinase–signal transducer and activator of transcription (JAK/STAT) pathway mediates cellular responses to cytokines and growth factors, governing proliferation, apoptosis, differentiation, inflammation, and immune regulation.243 Upon ligand engagement, receptor dimerization triggers JAK autophosphorylation, followed by STAT recruitment and activation.88 Phosphorylated STATs dimerize and translocate into the nucleus to regulate target gene expression.243

Persistent activation of the JAK/STAT axis is a hallmark of therapy resistance in multiple cancers.244 In high-grade serous ovarian cancer (HGSOC), single-cell transcriptomics reveals sustained JAK/STAT activity in both malignant epithelial cells and CAFs, driven by ascitic IL-6 and CAF-secreted cytokines, promoting platinum resistance via paracrine and autocrine loops.245 JAK2/STAT3 signaling also plays a pivotal role in CD8⁺ T-cell exhaustion.88 STAT3 forms complexes with TOX, directly binding promoters of inhibitory receptors such as PD-1, TIM-3, and LAG-3, increasing chromatin accessibility and enforcing an exhausted phenotype.88 This signaling axis simultaneously represses TCR signaling and interferon responses, dampening cytotoxic T-cell function.88 Tumor-intrinsic PD-L1 amplifies JAK2/STAT3 signaling by sequestering PTP1B, a phosphatase that normally deactivates JAK2. Nuclear PD-L1 further complexes with pSTAT3, transcriptionally upregulating IL-6 and CXCL1 and enhancing MDSC recruitment and resistance to ICBs.137 In metastatic CRPC, coloss of TP53/RB1 and overexpression of SOX2 activate JAK1/STAT1, promoting lineage plasticity and transition to a stem-like, multilineage-resistant state. This transition is reinforced by a SOX2–JAK–STAT feedback loop, which sustains chromatin accessibility and resistance to AR-targeted therapies such as enzalutamide.246

Other contexts include IL-11–mediated activation of JAK1/STAT4 in prostate cancer, where nuclear pSTAT4 enhances c-MYC transcription, conferring docetaxel resistance.247 In gastric cancer, defects in IFNγ-driven JAK/STAT signaling disrupt PD-1 expression, impairing responsiveness to PD-1 inhibitors.248 In CML, mitochondrial and nuclear forms of STAT3 mediate TKI resistance through metabolic rewiring.249 Nuclear STAT3-Y705 activates glycolysis and fatty acid oxidation (FAO) genes, while mitochondrial STAT3-S727 and acetylated STAT3-K685 impair oxidative phosphorylation by destabilizing electron transport chain (ETC) complexes, supporting leukemia stem cell dormancy and persistence.249 Furthermore, 5-FU/cisplatin–induced interferon responses upregulate ADAR1 via JAK/STAT, promoting A-to-I RNA editing that stabilizes SCD1 mRNA, reprograms lipid metabolism, activates Wnt/β-catenin signaling, and sustains stemness and chemoresistance in gastric cancer.250

Notch signaling pathway

The Notch signaling pathway is a highly conserved cell–cell communication system essential for cell fate determination, differentiation, and tissue homeostasis.251 In cancer, Notch signaling exhibits context-dependent and often paradoxical roles, contributing to tumor progression, cancer stemness, immune evasion, and therapy resistance. The pathway operates through both canonical (RBP-Jκ/CBF-1–dependent) and noncanonical mechanisms.251,252 In the canonical cascade, ligand binding (e.g., Jagged1/2, DLL1/3/4) to Notch receptors (Notch1–4) induces a two-step proteolytic cleavage, culminating in the release of the Notch intracellular domain (NICD), a cleaved cytoplasmic signaling domain that mediates intracellular signal transduction, by γ-secretase.252 The NICD then translocates into the nucleus, where it forms a transcriptional complex with RBP-Jκ and Mastermind-like (MAML) coactivators, activating downstream targets such as Hes, Hey, c-Myc, and Bcl-2.252 Noncanonical Notch signaling, in contrast, can function independently of ligand stimulation or involve nontraditional intracellular mediators.252

Aberrant Notch activation drives multiple resistance-related processes, including EMT, angiogenesis, metabolic rewiring, and maintenance of cancer stem-like cells.251,252 In pancreatic cancer, for example, the E3 ubiquitin ligase TRIM59 stabilizes RBP-Jκ via site-specific ubiquitination. RBP-Jκ then transcriptionally enhances TRIM59 expression, forming a feedforward loop that drives gemcitabine resistance.253 In gastric cancer, 5-FU resistance is mediated by PRMT1-dependent arginine methylation of NUSAP1, promoting its interaction with the PEST domain of Notch2. This impairs Notch2 degradation and sustains oncogenic Notch2 signaling, which upregulates c-Myc and Cyclin D3 expression.254 This study established cell line–derived xenograft (CDX) models to evaluate the effects of NUSAP1 and related gene regulation on tumor growth. Mechanical cues also activate Notch signaling in drug-resistant tumors. Actomyosin tension transmitted via E-cadherin–α-catenin complexes facilitates Notch receptor cleavage, leading to NICD translocation and induction of MVP, a mediator of multidrug efflux.255 Conversely, in gliomas, suppression of the Notch1/2–RBP-Jκ axis impairs interferon-γ (IFN-γ) signaling and derepresses oncogenes such as MYC. This Notch downregulation reduces MHC-I expression and chemokine secretion, hindering T-cell infiltration and promoting immune escape.256 The concurrent expansion of glioma stem cells and remodeling of the TME further dampens the efficacy of IFN-γ–based therapies.256 Collectively, the Notch pathway undergoes dynamic rewiring in response to therapeutic pressure, reinforcing its role in resistance biology and validating its potential as a target for rational combinatorial interventions.

Hippo signaling pathway

The Hippo pathway is a conserved regulatory cascade that controls tissue size, cell proliferation, apoptosis, stemness, and regeneration by modulating the subcellular localization of Yes-associated protein (YAP) and transcriptional coactivator with PDZ-binding motif (TAZ).257,258 The Hippo pathway also modulates apoptosis, as MST1/2 signaling can activate proapoptotic programs, whereas oncogenic RAS, PI3K/AKT, and RAF signaling suppress MST2 activity and promote cancer cell survival.258 In addition, ATR–RASSF1A-mediated mechanotransduction and YAP1–STAT1-dependent inflammatory regulation further support the concept that Hippo signaling integrates mechanical stress, immune remodeling, and apoptosis-related cell fate decisions during therapeutic resistance.259,260 The core kinases MST1/2 and LATS1/2 phosphorylate YAP/TAZ, sequestering them in the cytoplasm or promoting their degradation. Inactivation of Hippo signaling leads to YAP/TAZ nuclear translocation, where they interact with TEAD family transcription factors to drive transcriptional programs linked to tumor growth and resistance.257

Persistent YAP/TAZ activation is frequently observed in cancers such as HCC, breast cancer, and NSCLC.261 It promotes EMT, enhances DNA repair, maintains CSC phenotypes, and upregulates ABC transporters, collectively contributing to drug resistance.257 YAP/TAZ also serve as central integrators of upstream oncogenic signals (e.g., Wnt, TGF-β, and Notch) and mechanical cues from the TME, solidifying their role as resistance nodes.262 In pancreatic ductal adenocarcinoma (PDAC), the deubiquitinase VCPIP1 prevents K48-linked polyubiquitination of YAP, thereby stabilizing its nuclear pool. Nuclear YAP transcriptionally activates VCPIP1, forming a positive feedback loop that reinforces the expression of prosurvival and multidrug resistance genes.263 Similarly, in HCC, the oncofetal protein CLDN6 competes with TJP2 for YAP1 binding via its PDZ domain, displacing YAP1 from tight junctions and facilitating its nuclear localization. Activated YAP1 induces a cholangiocyte-like lineage program characterized by dedifferentiation and resistance.264 In solid tumors, proteasome inhibitors can induce YAP/TAZ activation by inactivating the Hippo pathway, thereby promoting tumor cell proliferation and resistance to apoptosis and ultimately driving therapeutic resistance.265 YAP/TAZ also regulate immune evasion. In melanoma and breast cancers, they induce PD-L1 expression, attenuating T-cell-mediated cytotoxicity.266 These findings highlight the Hippo–YAP/TAZ axis as a pivotal regulator of therapeutic failure and a promising target for combined treatment strategies.

GAS6/AXL signaling pathway

The GAS6/AXL axis, a key member of the TAM (TYRO3, AXL, MERTK) receptor tyrosine kinase family, is frequently overactivated in solid tumors and is strongly associated with therapy resistance.267 GAS6, secreted by stromal cells such as CAFs and macrophages, binds to AXL, promoting its dimerization, autophosphorylation, and activation of downstream survival pathways, including the PI3K/AKT, MAPK/ERK, and NF-κB pathways. These cascades enhance tumor cell proliferation, migration, EMT, and stemness maintenance.268

AXL activation mediates both intrinsic and acquired resistance to targeted therapies (e.g., EGFR-TKIs in NSCLC, HER2 inhibitors in breast cancer), chemotherapy (e.g., cisplatin, gemcitabine), and antiangiogenic agents (e.g., bevacizumab).269 In EGFR-mutant NSCLC, AXL activation by GAS6 stabilizes the E3 ligase RAD18 via ubiquitin-like modification, promoting monoubiquitination of PCNA and facilitating error-prone translesion DNA synthesis, thus accelerating mutagenesis and resistance.270 AXL also drives MYC-dependent purine biosynthesis, creating nucleotide imbalance and genomic instability, further contributing to resistance.270 Additionally, AXL promotes immune evasion by upregulating PD-L1 and reducing T-cell cytotoxicity.271 In breast cancer, ligand-induced activation of the AXL receptor tyrosine kinase initiates downstream signaling, leading to the phosphorylation and activation of AKT.252 Activated AKT in turn phosphorylates and inactivates GSK3β. This cascade prevents β-catenin from being targeted for degradation, thereby stabilizing it and promoting its nuclear translocation. Nuclear β-catenin upregulates ZEB1, a key EMT transcription factor, which enhances invasiveness and suppresses DNA repair, thereby reducing chemosensitivity to agents such as doxorubicin.272 AXL overexpression is a negative prognostic marker in several cancers.273 Pharmacological inhibitors targeting AXL (e.g., bemcentinib and gilteritinib) have shown promise in reversing resistance and enhancing treatment efficacy.273,274 The GAS6/AXL pathway represents a critical driver of tumor progression and resistance and a valuable therapeutic target in combination strategies.

Aberrant activation of signaling pathways and therapeutic implications

Taken together, the aberrant activation of signaling pathways such as PI3K-AKT-mTOR, MAPK, NF-κB, TGF-β, Wnt/β-catenin, JAK/STAT, Notch, Hippo-YAP/TAZ, and GAS6/AXL contributes extensively to therapy resistance across cancer types (Fig. 2c). These networks orchestrate a wide array of resistance-enabling processes, including survival signaling, cell fate plasticity, immune evasion, metabolic rewiring, DNA repair, and maintenance of cancer stemness. Importantly, these pathways often engage in intricate crosstalk, exhibit functional redundancy, and display compensatory activation upon therapeutic inhibition, making monotherapies prone to failure.

This phenomenon underscores a critical, systems-level resistance mechanism: signaling network adaptation.275 Rather than functioning as isolated linear cascades, oncogenic pathways form dynamic, self-stabilizing systems capable of re-establishing essential survival outputs under therapeutic pressure. However, feedback loops alone are insufficient to fully restore signaling output. Kholodenko et al. demonstrated that complete signal recovery requires either a two‑pathway network architecture or drug‑induced target dimerization.276 Lauffenburger’s early modeling revealed how negative feedback quantitatively controls MAPK signal adaptation, and his concept of temporal collateral sensitivity shows that tumor evolution creates transient windows of drug susceptibility, supporting adaptive therapy.277,278 Complementing these cell‑intrinsic models, Farrell extended network adaptation to the tumor microenvironment, arguing that resistance is ecologically driven by crosstalk among cancer cells, CAFs, and macrophages via paracrine signals and exosomes, enabling non‑cell‑autonomous drug tolerance.279

In parallel, many tumors exploit endoplasmic reticulum stress adaptation as a complementary systems-level mechanism.280 The accumulation of unfolded or misfolded proteins triggers the unfolded protein response (UPR), an adaptive signaling network coordinated by the endoplasmic reticulum sensors IRE1α, PERK, and ATF6, which functions to restore proteostasis and maintain cellular homeostasis.281 In cancer cells, sustained or rewired UPR activation promotes survival under chemotherapy and targeted therapy by enhancing chaperone expression, attenuating global protein translation, limiting oxidative stress, and suppressing apoptosis through the ATF4–CHOP axis.281 Importantly, while acute or overwhelming endoplasmic reticulum stress can induce cell death, chronic UPR activation favors drug tolerance and persistence, positioning endoplasmic reticulum stress adaptation as a systems-level resistance mechanism complementary to oncogenic signaling network adaptation.

Beyond discrete pathway alterations, tumor cells dynamically rewire their intracellular signaling networks through feedback loops and pathway crosstalk to maintain essential survival outputs under therapeutic pressure.282 Experimentally, this is evidenced by rapid feedback reactivation and state switching.283 From a theoretical perspective, systems biology provides a quantitative framework to interpret these emergent behaviors. Computational approaches, including kinetic modeling and Boolean network simulations, demonstrate how robustness is intrinsically encoded within oncogenic signaling architectures, enabling networks to buffer perturbations and maintain functional stability.284,285 Importantly, these models can delineate minimal intervention sets—combinatorial target nodes whose simultaneous inhibition is predicted to destabilize the network attractor state, thereby precluding adaptive escape and restoring therapeutic vulnerability.286 Kholodenko’s Modular Response Analysis (MRA) and Boolean network simulations can identify minimal intervention sets—combinatorial targets whose simultaneous inhibition destabilizes the adaptive network, precluding escape and restoring vulnerability.287 This theoretical perspective shifts the focus from static oncogenic drivers to the dynamic stability and plasticity of the signaling network as a whole, explaining why monotherapies often fail and providing a rationale for combinatorial strategies that target network vulnerabilities.

Beyond the core pathways discussed above, several additional signaling axes have been increasingly implicated in resistance phenotypes. These include the Hedgehog–GLI pathway, which sustains tumor stemness and contributes to chemotherapy resistance;288 the NRF2–KEAP1 antioxidant response pathway, which reprograms redox metabolism and drives multidrug resistance;289 and RTKs such as FGFR and MET, whose overactivation confers resistance to targeted therapies and immunotherapies. This growing complexity highlights the need for a comprehensive understanding of pathway interconnectivity and feedback dynamics in the resistant tumor state.

Therapeutically, this complexity necessitates the deployment of multitargeted and adaptive strategies with clinical trials (Table 2). These include (i) rational drug combinations targeting parallel or converging signaling cascades, (ii) the use of allosteric inhibitors or degraders that disrupt key signaling hubs, (iii) vertical inhibition along a single pathway to prevent upstream feedback reactivation, and (iv) the application of systems biology and network modeling to predict synthetic lethal vulnerabilities. Furthermore, the integration of temporal and spatial omics profiling may enable dynamic monitoring of signaling rewiring, informing the design of context specific, resistance-preemptive regimens.12,13

Table 2 Summary of clinical trials targeting signaling pathways

Multiple clinical trials have been launched to therapeutically target key oncogenic signaling pathways in drug-resistant cancers, underscoring the translational relevance of this axis (Table 2). For instance, a number of ongoing or completed trials are evaluating inhibitors of the PI3K-AKT-mTOR cascade, such as gedatolisib (NCT03065062) in advanced solid tumors, capivasertib (NCT04305496) in hormone receptor-positive breast cancer, and alpelisib (NCT02437318), which has shown efficacy in advanced breast cancer and is already approved for PIK3CA-mutated cases. Similarly, dual inhibition strategies targeting both PI3K and mTOR are being explored in relapsed/refractory T/NK-cell lymphomas (NCT06530550). In the MAPK pathway, clinical evaluation includes agents such as LY3009120 (NCT02014116) and ulixertinib in combination with palbociclib (NCT03454035) for patients with advanced pancreatic and other refractory solid tumors. Meanwhile, targeted inhibition of the TGF-β signaling axis is under active investigation with agents such as AdAPT-001 (NCT04673942) and vactosertib (NCT03732274) in sarcomas and NSCLC. Wnt pathway inhibitors, including WNT974 (NCT02278133) and vantictumab (NCT01973309), have been evaluated in BRAF-mutant colorectal cancer and metastatic breast cancer, respectively. Additional ongoing studies target JAK/STAT signaling with SHR-0302 and SHR-2554 (NCT06519526), as well as agents modulating the Notch (e.g., MK-0752, NCT00106145), Hippo (e.g., IK-930, NCT05228015), and GAS6/AXL (e.g., bemcentinib, NCT02424617) pathways in a variety of advanced or resistant tumors. These trials collectively demonstrate the increasing clinical momentum in disrupting compensatory or aberrant pathway activity and represent a critical component of precision strategies to surmount resistance in treatment-refractory malignancies.

Epigenetic reprogramming in cancer drug resistance and combating strategies

Phenotypic and epigenetic reprogramming

Epigenetic regulation, which governs heritable yet reversible changes in gene expression without altering the underlying DNA sequence, has emerged as a pivotal driver of therapeutic resistance across cancer types (Fig. 3a).1 Major epigenetic mechanisms include DNA methylation, histone modifications (e.g., methylation, acetylation, lactylation), chromatin remodeling, and noncoding RNA-mediated regulation.30 Together, these processes reshape transcriptional landscapes, sustain CSC plasticity, rewire metabolic networks, and remodel the immune microenvironment, thereby enabling tumor cells to evade therapeutic pressure through multifactorial routes.75

Fig. 3

Molecular mechanisms and combating strategies in cancer drug resistance: cellular plasticity and the tumor microenvironment. a Epigenetic reprogramming and transcriptional adaptation that contribute to resistance and strategies targeting chromatin modifiers and transcriptional networks. b Phenotypic plasticity, including epithelial-mesenchymal transition (EMT), stemness acquisition, and dedifferentiation, and approaches to target plastic cell states. c Conceptual framework of drug-tolerant persister (DTP) states, depicting maintenance programs (epigenetic remodeling, stress signaling, metabolic rewiring), exit trajectories (resensitization versus mutation-driven stable resistance), and potential intervention windows to disrupt state stabilization or redirect evolutionary outcomes. d Tumor microenvironment (TME)-mediated resistance, involving stromal cells, immune modulation, and extracellular matrix remodeling, and corresponding therapeutic strategies

Epigenetic dysregulation influences the expression of drug transporters, metabolic enzymes, and apoptotic regulators, thereby altering drug uptake, biotransformation, and clearance.75 In breast and ovarian cancers, for instance, hypomethylation of the ABCB1 (MDR1) promoter correlates with its overexpression, leading to elevated P-gp levels and enhanced efflux of chemotherapeutic agents, culminating in MDR.180 Similar outcomes are achieved through histone acetylation or miRNA-mediated upregulation of ABC transporters.290 Additionally, histone methyltransferases such as G9a epigenetically silence CYP genes, impairing the bioactivation of prodrugs and reducing treatment efficacy.291 Cancer cells frequently leverage epigenetic mechanisms to suppress drug target genes or activate compensatory signaling pathways, thereby bypassing pharmacological blockade.75 For example, in prostate cancer, loss of the histone methyltransferase KMT2C represses ASPP2 via impaired enhancer activity.106 This derepresses ΔNp63 expression, promoting lineage plasticity and the emergence of double-negative prostate cancer (DNPC) under androgen deprivation therapy. KMT2C deficiency simultaneously enhances fatty acid biosynthesis and HRAS palmitoylation, activating the MAPK/ERK pathway and stabilizing resistance phenotypes.106 In PDAC, downregulation of miR-146a-5p leads to TRAF6 upregulation, activation of NF-κB signaling, and increased ABCB1 transcription by NF-κB p65. This drives gemcitabine efflux and chemoresistance.292 In HCC, intracellular lactate triggers histone H3K18 lactylation, promoting HECTD2 transcription. As an E3 ligase, HECTD2 degrades KEAP1, thereby activating NRF2 and upregulating antioxidant defense programs to confer lenvatinib resistance.293 Multiple miRNAs modulate cisplatin resistance in bladder cancer by targeting critical pathways such as AKT/mTOR, JAK/STAT, Wnt/β-catenin, and p53, thereby regulating proliferation, apoptosis, autophagy, and glutathione metabolism.294,295 Under treatment-induced stress, tumor cells activate survival responses, including antiapoptotic signaling, autophagy, and ferroptosis inhibition.296 Emerging evidence implicates other noncoding RNAs, including long noncoding RNAs (lncRNAs) and circular RNAs (circRNAs), in shaping platinum resistance by modulating RNA‒protein interactions, translational control, and downstream oncogenic signaling pathways.297 In particular, extracellular vesicle-mediated transfer of lncRNAs has been shown to activate MAPK signaling and reinforce chemoresistant states in HGSOC.

Epigenetic reprogramming also modulates DNA damage response pathways. For instance, platinum and radiation therapies induce DNA lesions, which are often counteracted by chromatin remodeling that enhances homologous recombination and nonhomologous end joining repair.185 In EGFR-mutant lung cancer, resistance to osimertinib is tightly linked to epigenetic regulation by the ATPase subunit SMARCA4 of the mSWI/SNF complex. SMARCA4 maintains chromatin accessibility and upregulates stress response genes, facilitating survival and resistance.298

Within the TME, metabolic-epigenetic crosstalk sustains phenotypic heterogeneity and immune evasion.299 Lactate secreted by differentiated cancer cells (CDCs) is metabolized by CSCs into acetyl-CoA, promoting histone H3K27 acetylation, MYC activation, and CSC maintenance. This reciprocal reprogramming of CDCs into CSCs supports continuous intratumoural plasticity and therapeutic resistance.300 Furthermore, loss of MLL3/MLL4 in the TME silences enhancers and components of the RISC complex, inducing endogenous dsRNA stress and GSDMD-mediated pyroptosis, which can be harnessed to boost CD8⁺ T-cell–mediated responses.301 Immune resistance is also epigenetically orchestrated through exosomal communication and metabolic rewiring. For example, exosomal circUSP7 from NSCLC cells inhibits miR-934 in CD8⁺ T cells, upregulates SHP2, suppresses effector cytokine secretion (e.g., TNF-α, IFN-γ), and induces T-cell exhaustion, thereby impairing anti-PD-1 efficacy.83 Concurrently, drug-resistant tumor cells upregulate Fabp7 and suppress Lpcat3 via altered H3K27ac/H3K9ac marks, leading to ferroptosis resistance, enhanced FAO, and disrupted circadian signaling in T cells, all of which contribute to immune evasion and therapy failure.302

Combating strategies

The reversibility and plasticity of epigenetic modifications offer a compelling therapeutic window to counteract drug resistance (Fig. 3a). A variety of strategies have been developed to exploit these vulnerabilities. Epigenetic modulators, such as DNA methyltransferase inhibitors (DNMTis; e.g., decitabine, azacitidine), histone deacetylase inhibitors (HDACis; e.g., vorinostat, romidepsin), and bromodomain and extraterminal domain (BET) inhibitors (e.g., JQ1), can reverse the silencing of tumor suppressor genes, suppress oncogenic transcriptional programs, and resensitize tumors to chemotherapy, targeted agents, or immunotherapy.303 These compounds also reduce CSC populations and remodel the TME to enhance immune cell infiltration and activity.183 In addition, rational combination regimens, such as HDACis with EGFR-TKIs, DNMTis with platinum agents, or BET inhibitors with anti–PD-1/PD-L1 antibodies, have demonstrated synergistic efficacy by simultaneously targeting multiple resistance pathways. For instance, BET inhibition downregulates PD-L1 and reverses T-cell exhaustion, thereby augmenting the immunotherapeutic response.303

Beyond pharmacological epigenetic inhibition, other innovative approaches have emerged. CRISPR-based functional genomic screens have uncovered synthetic lethal interactions involving epigenetic regulators such as KDM5A, EZH2, and SMARCA2 in resistant tumor cells, which can be therapeutically exploited with selective inhibitors.304 Moreover, targeting the metabolic and epigenetic axes by modulating cofactors such as acetyl-CoA, S-adenosylmethionine (SAM), or α-ketoglutarate (α-KG) offers a means to indirectly reprogram aberrant chromatin states.303 Inhibiting lactate production or FAO can disrupt histone acetylation patterns that sustain resistance.305 Advances in single-cell and spatial epigenomics now enable precise mapping of epigenetic heterogeneity across tumor ecosystems, informing adaptive treatment designs.12,13 Furthermore, disrupting TME-derived epigenetic cues, including CAF-derived exosomes and lactate-induced histone lactylation, may help dismantle pro-resistance niches and restore antitumor immunity.306 Collectively, these multifaceted strategies reflect a paradigm shift in understanding epigenetic plasticity, not only as a mechanism of resistance but also as a therapeutic opportunity. Integrating epigenetic-targeted interventions into personalized regimens holds considerable promise for overcoming resistance and improving long-term clinical outcomes.

Several epigenetic agents targeting these pathways have progressed into clinical development. DNMTis, including azacitidine and decitabine, are approved for myeloid malignancies and are being actively evaluated in combination with chemotherapy and ICBs in solid tumors to reverse epigenetically mediated drug tolerance.303 HDACis such as vorinostat and entinostat have entered phase I–III clinical trials across multiple cancer types, where they are used as epigenetic priming agents to enhance tumor immunogenicity and resensitize tumors to targeted and immune-based therapies.303 In parallel, EZH2 inhibitors (EZH2is), exemplified by tazemetostat, have shown clinical activity in biomarker-defined populations, particularly in lymphomas and selected solid tumors, and are being tested in combination regimens to overcome lineage plasticity and resistance associated with chromatin reprogramming.304,307

Cell state plasticity in cancer resistance and combating strategies

Cell state plasticity in cancer resistance

TCP endows cancer cells with the capacity to adapt dynamically to therapeutic pressures, evade treatment, and re-emerge after drug withdrawal, ultimately contributing to resistance and relapse (Fig. 3b).308 One prominent example of TCP is the ability of tumor cells to reversibly transition between proliferative and quiescent states, thereby avoiding the cytotoxic effects of chemotherapy or targeted therapies.309 Upon exposure to these treatments, a subset of cells enters a DTP state characterized by stem-like features, low proliferation, and heightened survival capacity.132,309 DTP cells represent a rare subpopulation of tumor cells that survive initial anticancer therapy through reversible, nongenetic adaptive programs, often adopting a slow-cycling or quiescent state that enables transient drug tolerance and seeds subsequent resistance.132

DTP cells constitute a transient, nongenetic adaptive state that enables a minor tumor cell subpopulation to survive otherwise lethal anticancer therapies and acts as a critical reservoir for resistance evolution within a dynamic balance between state maintenance and exit trajectories (Fig. 3c).308 Rather than harboring stable resistance mutations, DTP cells adopt a slow-cycling or quasiquiescent phenotype driven by extensive epigenetic remodeling, transcriptional plasticity and metabolic reprogramming, which collectively constitute core maintenance programs that stabilize the DTP state under therapeutic pressure.310 Key mechanisms supporting DTP survival include chromatin reconfiguration mediated by histone-modifying enzymes, activation of stress-response and bypass signaling pathways such as IGF-1R, AXL and YAP/TAZ, and a shift toward oxidative or alternative nutrient metabolism, often coupled with enhanced mitochondrial ETC dependency, selective mitophagy and resistance to lipid peroxidation, which together mitigate therapy-induced apoptosis.308 Although this tolerant state is initially reversible upon drug withdrawal, representing a resensitization exit route, prolonged persistence under treatment pressure increases the probability of acquiring irreversible genetic alterations, driving an alternative exit toward stable, mutation-driven resistance and tumor relapse. DTP cells survive under chemotherapeutic pressure by actively engaging nongenetic adaptive mechanisms, such as CYP3A-mediated drug detoxification, thereby driving adaptive resistance and serving as a key cellular source of treatment failure and tumor recurrence in PDAC.311 Collectively, DTP cells represent an early, targetable node in resistance evolution and minimal residual disease, providing multiple intervention windows to disrupt state maintenance or bias exit trajectories toward therapeutic vulnerability.

A canonical manifestation of TCP is EMT, wherein epithelial tumor cells lose cell polarity and adhesion while gaining mesenchymal traits, including motility and resistance to apoptosis.309 EMT enhances DNA repair, alters drug metabolism, and facilitates immune evasion.5 For example, EMT-associated tumor cells upregulate RHOJ, a small GTPase that promotes DDR through nuclear actin polymerization, thus contributing to resistance against genotoxic agents.54 EMT is frequently detected in therapy-resistant tumors across cancer types.5 In NSCLC, resistance is often driven by HGF/c-MET–induced EMT, which activates PI3K/AKT/mTOR signaling to enhance stem-like properties and immune escape.312 Similarly, EMT contributes to oxaliplatin and cisplatin resistance in gastric and colorectal cancers, mediated by factors such as Rab31 (via the Stat3/MUC-1/Twist1 axis) and THBS2⁺ CAFs (via COL8A1-driven PI3K/AKT signaling).313,314 Notably, many tumors adopt a partial or hybrid EMT phenotype, retaining epithelial markers while acquiring mesenchymal traits, thereby enhancing adaptability, metastatic potential, and multidrug resistance.5 For instance, Rab31 promotes EMT and cisplatin resistance in stomach adenocarcinoma via the Stat3/MUC-1/Twist1 axis.314 Likewise, THBS2⁺ CAFs mediate oxaliplatin resistance in colorectal cancer by activating COL8A1-driven PI3K/AKT signaling and EMT.313 In NSCLC, hybrid EMT phenotypes in tumor-initiating cells correlate with immune escape via suppression of chemokines and increased expression of B7-H3, which resists NK cell-mediated killing.315 These microenvironment-derived signals act primarily by reinforcing tumor cell intrinsic stemness, plasticity, and survival programs.

Lineage plasticity is another critical form of TCP, allowing tumor cells to undergo transdifferentiation under therapeutic stress.316 In KRAS/LKB1-mutant NSCLC, resistance to KRAS inhibitors such as adagrasib involves adeno-to-squamous transdifferentiation (AST), driven by ΔNp63 and characterized by KRT6A expression.107 In prostate cancer, anti-androgen therapies such as enzalutamide induce the histone reader ZMYND8, which cooperates with FOXM1 to activate neuroendocrine transcriptional programs (e.g., ASCL1), facilitating transdifferentiation into neuroendocrine prostate cancer (NEPC).105 Similarly, loss of KMT2C promotes a transition to DNPC, further contributing to AR therapy resistance.106

CSCs, known for their self-renewal and multipotent capabilities, are central players in intratumoral heterogeneity and treatment resistance.317 CSCs may arise through dedifferentiation of non-stem-like tumor cells in response to therapeutic stress.309 They often express high levels of ABC transporters (e.g., ABCG2), ALDH activity, and robust DNA repair machinery, making them inherently resistant to chemotherapy and radiotherapy.317,318 Additionally, resistant CSCs can secrete small extracellular vesicles (sEVs) carrying phosphorylated PKM2 (pY105-PKM2), which reprogram recipient cells to acquire stem-like traits and chemoresistance.55 In esophageal squamous cell carcinoma (ESCC), QSOX2 promotes disulfide bond formation in TSC2, enhancing its phosphorylation by Akt and activating the mTOR/4E-BP1/c-Myc axis, thereby upregulating CSC markers (e.g., CD44, Notch1) and promoting platinum resistance.319 Furthermore, CAF-derived IGF-1 activates the IGF1R/Akt/mTOR/c-Myc pathway to upregulate QSOX2, reinforcing CSC phenotypes and therapy resistance.319

DTP cells are a transient, nongenetically distinct subpopulation of cancer cells that evade therapy by entering a quiescent or slow-cycling state.308 Their persistence relies on epigenetic remodeling, metabolic reprogramming, and altered signaling rather than stable genetic mutations.308 In EGFR-TKI–treated NSCLC, DTPs upregulate DPP4, activating the DPP4–CPT1A axis to increase FAO and mitochondrial respiration. Concurrently, NRF2 is engaged to mitigate oxidative stress and control cell cycle progression, enabling minimal residual disease and eventual relapse.320 Pharmacologic inhibition of DPP4 (e.g., with sitagliptin) restores EGFR-TKI sensitivity by disrupting this metabolic adaptation.320,321 DTPs are also characterized by increased autophagy and altered redox metabolism. PINK1-mediated mitophagy maintains mitochondrial function and redox balance; blocking mitophagy with agents such as chloroquine sensitizes DTPs to MAPK inhibitors and delays recurrence.322 Notably, DTPs can revert to a proliferative, drug-sensitive state upon treatment cessation, further complicating long-term disease control.308

Importantly, phenotypic plasticity and DTP-mediated resistance do not occur in isolation but intersect with other resistance mechanisms, including target mutations, bypass signaling, efflux transporters, and antiapoptotic pathways.308,309 EMT, CSCs, and DTPs are interconnected via regulatory networks involving transcription factors (e.g., SNAIL, ZEB1),318 signaling cascades (e.g., TGF-β), and cues from the TME (e.g., CAFs, hypoxia), collectively sustaining tumor heterogeneity and adaptive resistance.132,323,324,325

Combating strategies

Given the central role of phenotypic plasticity and DTPs in therapeutic resistance, targeted strategies have been devised to disrupt these adaptive states and restore treatment sensitivity (Fig. 3b).308,316 Suppressing EMT and lineage plasticity is a promising approach. For example, inhibition of epigenetic regulators such as ZMYND8 can prevent neuroendocrine transdifferentiation in prostate cancer, while restoration of KMT2C function suppresses the emergence of therapy-resistant DNPC phenotypes.105,106,326 Targeting key signaling pathways, such as TGF-β, Wnt, and Notch, and EMT-related transcription factors (e.g., ZEB1, TWIST1) is another strategy under active investigation.252,327 Moreover, certain natural compounds, including those from traditional Chinese medicine, exhibit potential in modulating EMT and suppressing plasticity-associated signaling, opening novel therapeutic avenues.328

Efforts to eliminate CSCs have focused on disrupting self-renewal and differentiation programs, such as those governed by the Hedgehog, Wnt, and Notch pathways.55 Argeting CSC-specific markers (e.g., ALDH) and disrupting feedback loops (e.g., QSOX2–mTOR) can reduce stemness and hinder recurrence.319 The metabolic dependencies of EMT-like cells and DTPs offer additional vulnerabilities. Therapeutic approaches include the inhibition of FAO, ROS detoxification pathways, and autophagy. For instance, DPP4 inhibition impairs oxidative metabolism and sensitizes DTPs to EGFR inhibition.322 Likewise, blocking mitophagy through agents such as chloroquine compromises mitochondrial function, enhancing the efficacy of targeted therapies and preventing relapse321,322 Recognizing the inherent heterogeneity and adaptability of plastic tumor cells, combination therapies are increasingly emphasized to achieve durable responses. Rationally designed regimens that integrate targeted inhibitors, epigenetic modulators, metabolic drugs and immunotherapies are being tested in preclinical models and clinical trials. Together, these multidimensional strategies hold promise in dismantling the plastic, drug-tolerant tumor cell states that underlie therapy resistance and disease progression.

TME-mediated cancer resistance and combating strategies

The TME in cancer resistance

The TME constitutes a critical layer of therapeutic resistance in which immune and stromal cells, extracellular matrix remodeling, and vascular–metabolic constraints jointly restrict drug and immune efficacy (Fig. 3d). Increasing evidence underscores the multifaceted roles of TME-resident stromal and immune components in fostering tumor survival, immune evasion, and therapeutic failure.37

CAFs are key regulators within the TME that promote resistance through ECM remodeling, metabolic crosstalk, and paracrine signaling.329 In breast cancer, TSPAN8⁺ myCAFs secrete IL-6 and IL-8 through the SASP, enhancing chemoresistance. Moreover, they activate the MAPK11–RBBP6–SIRT6 axis, which upregulates GLS1 and PYCR1, reprogramming tumor metabolism and creating a prosurvival microenvironment through aspartate and proline secretion.62

TAMs, especially those polarized toward the M2 phenotype, play an equally critical role in resistance.330 CAF-derived cytokines (e.g., IL-10, IL-6, CCL2) recruit and polarize macrophages into immunosuppressive M2-TAMs, which secrete TGF-β and IL-10, suppressing cytotoxic T-cell responses and facilitating immune escape.330,331 Increased glucose uptake by TAMs triggers the hexosamine biosynthetic pathway (HBP), enhancing O-GlcNAcylation of Cathepsin B, which promotes lysosomal secretion and fosters metastasis and chemoresistance.332

Bidirectional crosstalk between CAFs and TAMs amplifies immune suppression.8 For example, in NSCLC, COL11A1⁺ CAFs accumulate at tumor margins, deposit dense ECM components (COL1A1, COL3A1), and physically restrict CD8⁺ T-cell infiltration by interacting with tumor DDR1.78 These CAFs often colocalize with SPP1⁺ TAMs, enhancing fibrosis and immune exclusion. In gastric cancer peritoneal metastasis, SPP1⁺ TAMs and THBS2⁺ matrix CAFs (mCAFs) jointly construct a spatially dense immunosuppressive niche, further limiting T-cell access to tumor cores.329

T-cell dysfunction and exhaustion are additional hallmarks of TME-driven resistance.333 Tumor-derived extracellular vesicles carrying PD-L1 induce T-cell senescence by activating ATM/H2AX–CREB/STAT signaling, reprogramming lipid metabolism and suppressing effector function.334 TAMs deprived of TNFα signaling retain high expression of hematopoietic PGD2 synthase (HPGDS), continuously secreting prostaglandin D2 (PGD2), which reinforces macrophage immunosuppressive identity and directly inhibits CD8⁺ T-cell cytotoxicity.335 Additionally, lactate–HCAR1 signaling in tumor cells activates the 14-3-3ζ–STAT3 axis, promoting CCL2/CCL7 production and recruitment of CCR2⁺ PMN-MDSCs, which suppress T cells via ARG1 and ROS, thereby limiting PD-1 blockade efficacy.306 Intrinsic nuclear PD-L1 can also cooperate with p-STAT3 to upregulate IL-6, activating MDSCs through the IL-6/JAK/STAT3 axis in a PD-1–independent manner.137 Elevated IL-6 levels are predictive of poor response to immunotherapy in PD-L1high NSCLC patients.137

The ECM not only provides physical scaffolding but also functions as a biochemical regulator of resistance.181 Overproduction of collagen and hyaluronic acid creates a dense ECM that impedes drug diffusion and immune infiltration.181 ECM components interact with integrins to activate FAK, DDR, and Rho/MRTF pathways, fostering apoptosis resistance, CSC enrichment, and metabolic rewiring.336,337 ECM stiffness further modulates ABC transporter activity, affecting intracellular drug accumulation and compromising the efficacy of chemotherapeutics, targeted agents and ICIs.181,182

Metabolic reprogramming within the TME is a key determinant of immune resistance.338 In cholangiocarcinoma, CXCL6–CXCR1/2–JAK/STAT/PI3K-AKT signaling promotes tumor growth, gemcitabine resistance, and lipid metabolism reprogramming while inducing NETs that impair CD8⁺ T-cell cytotoxicity via ROS.81 Additionally, DLST-mediated succinylation of PDHA1 at K83 enhances PDH activity and α-KG accumulation, which activates OXGR1–MAPK/ERK signaling in TAMs, suppressing MHC-II expression and T-cell priming.339 Hypoxia-induced HIF activation augments drug efflux, suppresses apoptosis, and enhances DNA repair mechanisms. HIF also promotes EMT, autophagy, and CSC phenotypes. For instance, USP9X-mediated stabilization of HIF-2α facilitates CSC maintenance and platinum resistance.340 Collectively, the TME orchestrates resistance through immune suppression, metabolic rewiring, altered signaling, and physical exclusion. CAFs, TAMs, and MDSCs form an interdependent network that reinforces CSC maintenance, impairs drug efficacy, and hinders durable responses (Fig. 3d).

Combating TME-mediated resistance

To counteract TME-driven resistance, a multipronged therapeutic approach is needed, one that combines tumor-intrinsic targeting with strategies that reprogram or neutralize the suppressive TME. Targeting CAFs and ECM remodeling is a promising strategy (Fig. 3d).181,183 Inhibition of NOX4 in CAFs reduces ECM stiffness and enhances CD8⁺ T-cell infiltration, restoring immune surveillance and sensitizing tumors to immunotherapy.64 Enzymatic degradation of ECM components (e.g., hyaluronidase) or blockade of ECM–integrin interactions (e.g., FAK inhibitors) can also improve drug penetration and reduce stemness-supportive niches.341 Disrupting TAM and MDSC recruitment and reprogramming their polarization is another effective strategy.330 Blocking CSF1R, CCR2, or CXCR2 pathways can deplete or re-educate TAMs and MDSCs.330 For example, CCR2 inhibitors can prevent monocyte-derived TAM accumulation, enhancing the ICB response.342 Simultaneously, targeting lactate signaling (e.g., HCAR1 antagonists) may prevent myeloid cell recruitment and immune evasion.306

Targeting immunometabolic adaptations is gaining traction. Inhibiting key metabolic nodes such as FAO, HBP, or α-KG signaling in TAMs can restore antigen presentation and enhance T-cell-mediated cytotoxicity.332,339 Similarly, agents that reverse HIF stabilization or inhibit mitochondrial metabolism in CAFs and CSCs are being explored to disrupt metabolic dependencies that underlie resistance.340 Combination therapies incorporating ICIs, epigenetic drugs, metabolic inhibitors, and TME modulators hold particular promise. For example, cotargeting IL-6/JAK/STAT3 signaling and the PD-1/PD-L1 axis may overcome immune resistance in PD-L1high tumors with elevated IL-6.137 Nanoparticle-based delivery systems are also under investigation to codeliver anticancer agents and TME-targeted molecules in a spatiotemporally controlled manner.172

In conclusion, tackling TME-mediated resistance necessitates integrated therapeutic strategies that dismantle the immunosuppressive, fibrotic, and metabolically reprogrammed tumor niche. Rationally designed combination regimens that simultaneously target tumor cells and the TME offer a transformative opportunity to improve outcomes in patients with therapy-resistant malignancies.

Microbiome in cancer resistance and combating strategies

Microbiome in cancer resistance

The tumor microbiome, encompassing bacteria, fungi, viruses, and mycoplasma, has emerged as a key modulator of tumor progression and therapeutic response (Fig. 4a). Increasing evidence suggests that microbial communities residing within tumors or at distant mucosal sites can drive resistance to anticancer therapies through diverse mechanisms, including modulation of drug metabolism and transport, induction of ROS, impairment of DDR, activation of oncogenic signaling, and suppression of antitumor immunity.324,343

Fig. 4

Molecular mechanisms and combating strategies in cancer drug resistance. a The role of the tumor-associated microbiome in modulating drug efficacy and resistance, with potential microbiota-targeted interventions. b Impairments in cell death pathways, including apoptosis, necroptosis, pyroptosis, and ferroptosis, and strategies to restore death sensitivity

In pancreatic and colorectal cancers, intratumoral γ-proteobacteria express a long isoform of cytidine deaminase (CDD-L) that catalyzes the deamination of gemcitabine into its inactive metabolite 2’,2’-difluorodeoxyuridine (dFdU), thereby conferring chemoresistance.344,345 In cervical cancer, colonization by Lactobacillus iners promotes gemcitabine resistance by secreting L-lactate, which activates lactate signaling in tumor cells, triggering glycolytic reprogramming and enhancing nucleotide biosynthesis. Concurrently, L-lactate induces HIF-1α and ROS accumulation, disrupts the G2/M checkpoint, and impairs DDR mechanisms. Tumor-adapted L. iners strains also acquire lacG gene mutations that augment galactose metabolism, further driving glucose flux and lactate buildup.346

Microbial metabolites can also modulate therapeutic outcomes. For example, gut microbiota-derived indole-3-acetic acid (3-IAA), a tryptophan metabolite, accumulates in the TME and is oxidized by neutrophil myeloperoxidase (MPO), generating a burst of ROS. Simultaneously, 3-IAA downregulates the antioxidant enzymes GPX3 and GPX7 in tumor cells, enhancing ROS accumulation and inhibiting autophagy, ultimately sensitizing tumors to chemotherapy.347 In breast cancer, Pseudomonas aeruginosa secretes the quorum-sensing molecule N-(3-oxo-dodecanoyl)-L-homoserine lactone (3OC), which induces ligand-independent dimerization of TβRII, aberrantly activating TGF-β signaling. This cascade crosstalks with the ErbB2, PI3K/Akt, and MAPK pathways, thereby circumventing trastuzumab-mediated HER2 inhibition and promoting drug resistance.348 In colorectal cancer, Bacteroides fragilis interacts with tumor cells via the outer membrane proteins SusD and RagB, directly binding to Notch1 and activating its signaling. This engagement suppresses apoptosis induced by 5-FU and oxaliplatin while enhancing proliferative signaling, contributing to chemoresistance. Notably, the bacteriophage VA7, which targets B. fragilis, restores chemosensitivity in murine models.349 Similarly, Fusobacterium nucleatum activates TLR4/NF-κB signaling and upregulates the antiapoptotic protein BIRC3, conferring resistance to 5-FU.350 In breast cancer, enterotoxigenic B. fragilis (ETBF) secretes BFT-1, relieving the repression of Notch signaling and promoting the self-renewal and survival of breast cancer stem cells, thereby leading to taxane resistance.351

Immunotherapy resistance is also influenced by the microbiome. In colorectal cancer, Porphyromonas gingivalis impairs cytotoxic T-cell and NK cell function, fostering immune escape.352 Peptostreptococcus anaerobius binds integrin α2β1 on tumor cells, activating NF-κB and inducing CXCL1, which recruits MDSCs via CXCR2. Additionally, the bacterial lysozyme-like protein LytC_22 binds to Slamf4 on MDSCs, enhancing their immunosuppressive phenotype (increased Arg1 and iNOS), thereby suppressing CD8⁺ T-cell activation and resistance to ICB.353 In oral cancers, P. gingivalis activates the Akt–STAT3 pathway in dendritic cells through gingipain proteases, upregulating PD-L1 expression and suppressing CD8⁺ T-cell function. Clearance of P. gingivalis via antibiotics or knockout of the Kgp gene reverses ICB resistance.354

Combating strategies

Overcoming microbiome-mediated therapeutic resistance necessitates a multifaceted approach integrating microbial profiling, precision modulation, and host–microbiota–immune interplay (Fig. 4b).324 Targeted microbial clearance using selective antibiotics has demonstrated efficacy in restoring drug sensitivity; for example, depletion of P. gingivalis or F. nucleatum reverses resistance to ICB and chemotherapy, respectively.351,354 However, nonselective antibiotic administration risks disrupting the commensal microbiota and weakening systemic immune responses. Precision antimicrobials such as bacteriophages (e.g., VA7 targeting B. fragilis) represent a promising alternative, allowing strain-specific depletion while preserving microbial diversity.349,351

Another strategic axis involves microbiome-responsive drug design. Engineering drugs that resist microbial enzymatic degradation, such as CDD-L and resistant gemcitabine analogs, can circumvent intratumoral drug inactivation.344,345 Moreover, prodrug conjugates with microbially cleavable linkers may enable site-specific drug release in tumor regions devoid of resistance-conferring microbes.346 In parallel, modulation of microbial metabolites offers therapeutic leverage: promoting beneficial compounds such as 3-IAA, which enhances ROS and chemosensitivity, or suppressing lactate-secreting strains such as Lactobacillus iners may reverse resistance-associated metabolic reprogramming.346,347

Reprogramming the immune microenvironment is also critical.352 Disrupting microbe–host immunosuppressive circuits, such as integrin α2β1–CXCL1–MDSC or Slamf4–Arg1/iNOS axes, restores antitumor T-cell activity and improves response to immunotherapy.353,354 Microbial engineering approaches, including probiotic strains secreting immunostimulatory cytokines or locally delivering checkpoint inhibitors, are under active development. Finally, integrating metagenomic, metabolomic, and spatial transcriptomic analyses enables the identification of resistance-associated microbial signatures and host–microbiota interactions.12,13,355 Collectively, these strategies underscore the microbiome not merely as a passive bystander but also as an active modulator of therapeutic outcomes. Therapeutically targeting the microbiome through eradication, modulation, or functional rewiring holds promise to overcome drug resistance, reinvigorate antitumor immunity, and enhance the durability of cancer therapies across diverse tumor contexts.

Cell death mechanism in cancer resistance and combating strategies

Cell death mechanism in cancer resistance

Programmed cell death is a fundamental mechanism for maintaining tissue homeostasis in multicellular organisms.356 One of the hallmarks of cancer is resistance to cell death, which contributes to tumor progression and therapeutic resistance.3 Dysregulated forms of cell death, including apoptosis, necroptosis, pyroptosis, ferroptosis, and cuproptosis, play distinct roles in shaping the drug response through unique signaling pathways.356

In DNA damage–induced conditions, frequent inactivation of the SLFN11 gene in tumor cells leads to the loss of its tRNAse activity, causing ribosome stalling and inhibition of protein translation. This disrupts activation of the ZAKα–MAPK–JNK apoptotic cascade and weakens GCN2-mediated global translation suppression, thereby abolishing p53-independent apoptosis and contributing to chemoresistance against DNA-damaging agents.53 In pancreatic cancer, overexpression of MLKL triggers necroptosis, recruiting macrophages that form macrophage extracellular traps (METs).357 METs are web-like DNA–protein structures released by activated macrophages that can remodel the TME, dampen antitumor immunity, and thereby contribute to therapeutic resistance. METs cleave CXCL8 into active monomers to promote EMT and tumor–endothelial adhesion and release matrix metalloproteinases (MMPs) to degrade ECM, facilitating metastasis. Necroptosis also induces macrophage IL-6 production, which upregulates CD47 on tumor cells, allowing immune evasion and driving liver metastasis and therapeutic resistance.357,358 In bladder cancer, gemcitabine induces caspase-1–dependent pyroptosis, releasing inflammatory mediators that activate the CCR6 signaling pathway in the TME. This reprograms αSMA⁺ CAFs into collagen-III⁺ inflammatory CAFs (iCAFs), forming a fibrotic niche that supports CD44⁺ CSCs, thereby fueling chemoresistance.358

In colorectal cancer, ferroptosis suppression via the CBX3/NRF2/GPX2 axis promotes multidrug resistance. CBX3 represses CUL3 transcription, leading to reduced NRF2 ubiquitination and degradation. Stabilized NRF2 translocates to the nucleus and upregulates antioxidant enzymes such as GPX2, enhancing lipid peroxide detoxification and preventing ferroptosis induced by irinotecan and oxaliplatin.359 Another study revealed that tumor acidosis and elevated LDHA activity promote lactate accumulation, which leads to histone H4K12 lactylation (H4K12la) via p300. This epigenetic modification activates GCLC transcription, enhances glutathione synthesis, and protects against lipid peroxidation and ferroptosis, thereby driving chemoresistance in colorectal CSCs.360 USP18 promotes resistance to sorafenib in HCC by removing ISGylation from nuclear receptor coactivator 4 (NCOA4), leading to its degradation and suppression of NCOA4-mediated ferritinophagy.101 This reduces iron-dependent lipid peroxidation and ferroptosis. Targeting USP18 with hypericin (HYP) restores NCOA4 stability and ferroptotic sensitivity, overcoming acquired resistance.101,361

Cuproptosis, a recently discovered copper-dependent form of programmed cell death, is triggered by copper accumulation in mitochondria and preferentially occurs in cells with active tricarboxylic acid (TCA) cycles.362 Excess copper binds PDK1 and enhances its interaction with AKT, activating the AKT/GSK3β/β-catenin cascade. This signaling promotes CSC traits, while the activated β-catenin/TCF4 complex transcriptionally upregulates ATP7B, a copper efflux transporter. Increased ATP7B expression facilitates copper export and reduces intracellular copper stress, thereby enabling CSCs to evade cuproptosis and acquire resistance.363 In the hypoxic TME, HIF-1α activation suppresses cuproptosis by inducing PDK1/3, which inhibits the expression of DLAT, a key cuproptosis mediator. Simultaneously, HIF-1α upregulates metallothionein MT2A, which chelates and sequesters mitochondrial copper, preventing copper accumulation beyond the cytotoxic threshold. Moreover, excess copper stabilizes HIF-1α by inhibiting its ubiquitination and degradation, forming a positive feedback loop that reinforces cuproptosis resistance.362

Autophagy mediates resistance to chemotherapeutic agents by promoting tumor cell survival and adaptation to stress.364 One study showed that circSEC24B induces oxaliplatin resistance in colorectal cancer by enhancing autophagic activity and thereby stabilizing the SRPX2 protein.365 METTL3 downregulates DCP2 expression through m6A modification, thereby enhancing Pink1-Parkin pathway-mediated mitophagy, alleviating mitochondrial damage, and ultimately conferring chemoresistance in SCLC.366 Reticulophagy is a receptor-mediated form of selective autophagy that promotes cell survival, tumor progression, and chemoresistance across multiple cancers by maintaining endoplasmic reticulum homeostasis and buffering therapy-induced stress.367 In bladder cancer, the highly expressed receptor CCPG1 drives reticulophagy to facilitate tumor progression and mediate cisplatin resistance, and inhibition of this pathway represents a potential therapeutic strategy to reverse resistance. Mitophagy constitutes a critical adaptive survival mechanism for tumor cells under therapeutic pressure by eliminating treatment-induced damaged mitochondria, limiting reactive oxygen species accumulation, and maintaining mitochondrial homeostasis, thereby providing a buffering capacity for the development of resistance.368 Recent studies further reveal that the mitophagy receptor NLRX1 is directly regulated by the metabolic signal cytosolic acetyl-coenzyme A (AcCoA) and mediates resistance to KRAS inhibitors, offering a novel molecular framework and actionable vulnerability for overcoming targeted therapy resistance.

Combating strategies

Overcoming cancer resistance mediated by dysregulated cell death mechanisms requires tailored strategies that restore or exploit specific forms of programmed cell death (Fig. 4b).356 For tumors deficient in apoptosis, such as those with SLFN11 inactivation or impaired p53-independent pathways, strategies to restore translational stalling (e.g., via tRNAse mimetics) or activate alternative stress responses may sensitize cells to DNA-damaging agents.53 In the context of necroptosis, therapeutic modulation must be approached with caution. Although MLKL-mediated necroptosis can trigger immune activation, it may also promote metastasis and immune evasion via MET formation and CD47 upregulation.357,358 Thus, combinatorial strategies that block downstream pro-metastatic cytokines (e.g., IL-6 or CXCL8) or macrophage reprogramming may uncouple necroptosis from its deleterious consequences.357,358

In pyroptosis-mediated resistance, interventions targeting inflammasome components (e.g., caspase-1 inhibitors) or downstream fibroblast reprogramming (e.g., CCR6 antagonists) may limit fibrotic niche formation and CSC expansion.358 For ferroptosis, which represents a therapeutically actionable vulnerability, restoring iron-dependent lipid peroxidation is key. This may involve targeting the CBX3/NRF2/GPX2 axis with CBX3 or NRF2 inhibitors or impairing antioxidant buffering systems such as glutathione synthesis (e.g., via GCLC suppression).359 Epigenetic modulators that reverse histone lactylation, such as p300 inhibitors, may also resensitize CSCs to ferroptosis by limiting metabolic adaptation.360 In HCC, stabilizing ferritinophagy mediators such as NCOA4 using deISGylation inhibitors such as hypericin can restore ferroptotic sensitivity and overcome resistance to agents such as sorafenib.101,264 Targeting cuproptosis presents a novel frontier. Strategies include inhibition of copper efflux transporters such as ATP7B or blockade of upstream β-catenin signaling to prevent metabolic escape in CSCs.363 In hypoxic tumors, antagonizing HIF-1α or its transcriptional targets (e.g., PDK1/3, MT2A) may prevent mitochondrial copper sequestration and promote lethal copper accumulation.362 Additionally, copper ionophores or copper-ligand complexes (e.g., elesclomol) are being explored to selectively induce cuproptosis in tumor cells with active mitochondrial metabolism.369

Ultimately, combining cell death pathway modulators with standard therapies, ICIs, or epigenetic agents offers synergistic potential. Precision medicine approaches, guided by biomarkers such as GPX2, ATP7B, or H4K12la, may enable the stratification of patients for ferroptosis- or cuproptosis-inducing treatments. These integrative strategies hold promise to overcome resistance rooted in impaired cell death and improve clinical outcomes across malignancies.