Persister cells hiding in minimal residual disease drive cancer relapse

Even when a tumor appears to vanish on a scan, the war against cancer is rarely over. A new review published in Holistic Integrative Oncology argues that the invisible enemy behind most relapses is a hidden reservoir of residual disease, and that the most dangerous cells within it are neither dormant bystanders nor hardwired mutants. They are drug-tolerant persister cells, a transiently resistant population that survives chemotherapy, targeted therapy and immunotherapy through reversible, non-genetic adaptations, and then quietly evolves into fully resistant clones that seed recurrence. The review, led by researchers at Tianjin Medical University Cancer Institute and Hospital, maps the biology of these cells, the technologies that can now track them, and the therapeutic strategies that may finally erase them.

Minimal residual disease, or MRD, refers to the small population of cancer cells that persists after curative-intent treatment. These cells are typically undetectable by conventional imaging but can be identified through sensitive molecular methods such as next-generation sequencing, quantitative polymerase chain reaction and circulating tumor DNA analysis. In hematologic malignancies such as acute lymphoblastic leukemia, MRD has long been established as a robust prognostic indicator, and its relevance in solid tumors is increasingly recognized. The clinical data are striking. In one study of 299 patients with stage I to III colorectal cancer, patients whose ctDNA tested positive for any one of six methylation markers one month after surgery were 17.5 times more likely to experience recurrence than those with negative results. In non-small cell lung cancer, ctDNA was detected before treatment in 24 percent of stage I patients, 77 percent of stage II patients and 87 percent of stage III patients, and post-treatment detection of ctDNA was associated with unfavorable clinical outcomes.

Within this reservoir, drug-tolerant persister cells occupy a pivotal and paradoxical position. The concept originates from microbiology, where persister describes bacterial cells that survive antibiotic exposure through non-genetic mechanisms. In 2010, researchers extended this analogy to human cancer when they identified DTP cells in EGFR-mutant lung cancer cells treated with the EGFR inhibitor erlotinib. Despite lethal drug concentrations, a small fraction of cells persisted in a reversible drug-tolerant state characterized by quiescence and epigenetic reprogramming, distinguishing them from genetically resistant mutants. Three core functional assays now define bona fide DTP populations. In a reversibility assay, DTP cells regain full drug sensitivity and proliferative capacity after drug withdrawal for seven to fourteen days, whereas permanently resistant clones maintain stable insensitivity driven by fixed genetic alterations such as EGFR T790M or BRAF V600E secondary mutations. Single-cell sequencing confirms that DTP cells carry no stable driver resistance mutations, relying purely on epigenetic and metabolic adaptive plasticity. Clonal fluctuation testing shows that DTP populations do not produce stable resistant sublines upon continuous passaging without drug pressure.

The review proposes a hierarchical model that clarifies why these cells matter so much. MRD consists of all heterogeneous residual cancer cells that persist after therapy, covering three distinct subpopulations: therapy-sensitive dormant tumor cells, genetically stable permanent resistant clones, and transient drug-tolerant DTP cells. DTP cells exclusively embody the plastic, non-genetic tolerant faction within MRD, surviving initial cytotoxic treatments through reversible epigenetic, metabolic and cell-cycle adaptive mechanisms, and serving as the critical intermediate reservoir en route to stable acquired resistance. This positioning explains why DTP cells, rather than other MRD components, are the primary initiators of tumor recurrence. In acute myeloid leukemia, MRD identified by flow cytometry frequently includes quiescent cells with persister-like characteristics, indicating a functional connection between the two concepts.

The biological toolkit that DTP cells deploy is remarkably diverse. A prominent feature is cell cycle arrest in the G0/G1 phase, rendering them quiescent and less susceptible to therapies targeting proliferating cells. In HER2-positive breast cancer, HER2 inhibitor treatment induces DTP cells with either luminal epithelial-like or mesenchymal-like transcriptional profiles, and tumor cells stochastically and cyclically enter a G0-like pre-DTP state enriched for dormancy and diapause-associated genes. Metabolic reprogramming represents another adaptation. Under MAPK inhibitor treatment, a subset of lung adenocarcinoma cells shifts from glycolysis to mitochondrial respiration, rendering them highly dependent on antioxidant pathways to mitigate elevated reactive oxygen species. DTP cells also bolster anti-apoptotic mechanisms by upregulating proteins such as MCL-1, and during DTP formation, downregulation of MYC relieves transcriptional repression of PINK1, activating mitophagy that eliminates damaged mitochondria and maintains metabolic homeostasis under therapeutic stress.

The tumor microenvironment plays a decisive role in fostering these cells. Hypoxia, a hallmark of solid tumors, promotes DTP survival by stabilizing hypoxia-inducible factor-1 alpha, which upregulates glycolytic enzymes and anti-apoptotic genes. Under hypoxic or nutrient-deprived conditions, melanoma cells acquire a DTP state conferring resistance to BRAF inhibitors and platinum-based chemotherapies, accompanied by extensive chromatin remodeling. Cancer-associated fibroblasts contribute to DTP induction through balanced regulation of TGF-beta and NF-kappaB signaling. During EGFR inhibitor treatment, fibroblasts transition from a myofibroblastic phenotype to a novel state marked by activation of NF-kappaB and IL-6/JAK/STAT3 signaling, further enhancing DTP drug tolerance. Notably, substantial infiltration of Ccr2-positive macrophages occurs when tumor volume reaches its nadir and enters the DTP phase, coinciding with the transition of tumor cells from a reversible drug-tolerant state to an acquired resistant state.

Metabolic and redox adaptations offer some of the most exploitable vulnerabilities. In BRAF V600E-mutant melanoma, DTP cells develop tolerance to BRAF and MEK inhibitors by shifting from glycolysis to peroxisomal fatty acid oxidation, a process transcriptionally regulated by the PPAR alpha-ACOX1 axis. DTP cells also upregulate Lipin1, a fatty acid esterification enzyme, promoting lipid droplet formation to mitigate lipotoxicity. In obesity-associated colorectal cancer, the FABP4/UCP2 axis drives cetuximab resistance when DTP cells are co-cultured with adipocytes. Across multiple treatment contexts, including BRAF, MEK, ALK and androgen receptor inhibitor-treated tumors, DTP cells show reduced glycolysis but increased oxidative phosphorylation and redox regulation. Persister cells that survive treatment tend to adopt a high-mesenchymal state and become reliant on glutathione peroxidase 4 to detoxify lipid peroxides, thereby evading ferroptosis, an iron-dependent form of cell death. In ALK-positive lung cancer, DTP cells surviving ALK inhibitor treatment upregulate GPX4 to evade ROS-induced cytotoxicity.

Epigenetic reprogramming is a frequent feature of DTP biology. In melanoma under hypoxic or nutrient-deprived conditions, DTP cells acquire resistance through chromatin remodeling characterized by the loss and gain of epigenetic marks such as H3K9me3. Upregulation of O-GlcNAc transferase, in synergy with TET1, promotes H3K4me3 deposition at CpG islands via the hexosamine biosynthesis pathway, driving the transition from a dormant DTP state to a proliferative drug-tolerant persister-proliferative state that manifests as acquired resistance. In BRAF-mutant melanoma treated with combined RAF and MEK inhibition, MRD harbors co-existing DTP populations with pronounced transcriptional and spatial heterogeneity, including a key subpopulation displaying a neural crest stem cell-like program driven by RXRG signaling. Cells that survive lethal drug pressure also enhance methylation of histone H3K9 and H3K27 at LINE-1 repetitive elements, suppressing drug-induced activation of repetitive elements and interferon-stimulated genes.

On the therapeutic front, the review highlights several mechanism-based strategies. The Notch signaling pathway has emerged as an actionable target in lung cancer, where Notch1 and its target genes are upregulated in osimertinib-treated DTP cells, and gamma-secretase inhibitors significantly suppress DTP survival. Combining osimertinib with these inhibitors markedly downregulates phosphorylated ERK and enhances DUSP1 expression, and clinical tissue samples corroborate Notch1/HES1 upregulation following EGFR inhibitor treatment in patients. Epigenetic regulation serves as a cornerstone for DTP-targeted therapies. In melanoma, ALDH1A3 cooperates with ACSS2 in the nucleus to convert glucose metabolic flux into acetyl-CoA, promoting histone H3 acetylation and activating genes associated with the neural crest stem cell-like state. Pharmacological inhibition of ALDH1 delays or prevents relapse after BRAF inhibitor therapy. AMPK activators such as aspirin downregulate OGT expression, preventing DTPP formation and delaying acquired resistance. Autophagy offers a third avenue, as blocking autophagy with chloroquine in combination with chemotherapy eliminates DTP survival in colorectal cancer, and inhibiting PINK1 or mitophagy effectively eliminates DTP cells and enhances sensitivity to targeted therapies.

Translating these insights into clinical practice faces real hurdles. The heterogeneity of DTP cells across cancer types and treatment contexts necessitates robust biomarkers to identify and monitor these populations, and the dynamic plasticity of DTP cells complicates therapeutic strategies as they transition between drug-tolerant and drug-sensitive states. Toxicity associated with combination therapies must be carefully managed, and a gap persists between preclinical models and human tumors, where heterogeneity, off-target effects and resistance mechanisms often diminish therapeutic efficacy. Consensus on MRD thresholds and survival correlates remains unresolved, and aggressive DTP-targeting regimens may increase toxicity, raising concerns about quality of life versus survival gains. Yet emerging technologies offer reason for optimism. Single-cell omics, spatial transcriptomics, digital PCR, live-cell imaging and multiplexed ion beam imaging are pushing detection limits toward ultra-rare DTP cells, while artificial intelligence and machine learning are being deployed to identify DTP signatures, predict relapse and optimize therapies. Adaptive therapy approaches that modulate treatment intensity based on tumor response are being tested to prevent the emergence of DTP populations, and liquid biopsy technologies are being developed to detect circulating DTP cells and DTP-derived ctDNA for real-time MRD monitoring. If these threads converge, the review concludes, targeting DTP cells within MRD holds transformative potential to dismantle the persister niche, prevent relapse and reshape long-term cancer outcomes.

Subject of Research: Cancer drug-tolerant persister cells and minimal residual disease

Article Title: Erasing the invisible: targeting persister cells to cure minimal residual disease

Article References: Wang, Y., Shi, Z., Xu, F., Zhu, Y., Liu, C., Wang, B., Ji, N., Wang, Z., Wang, S., Zhou, X., & Ren, Y. (2026). Erasing the invisible: targeting persister cells to cure minimal residual disease. Holistic Integrative Oncology, 5(1), 81. https://doi.org/10.1007/s44178-026-00307-3

Image Credits: AI Generated

DOI: 10.1007/s44178-026-00307-3

Keywords: minimal residual disease, drug-tolerant persister cells, cancer relapse, epigenetic reprogramming, metabolic reprogramming, tumor microenvironment, ferroptosis, autophagy, liquid biopsy, single-cell sequencing, targeted therapy, drug resistance