Title Page
Title:
Authors:
Xiaotong Qiu1†, Li Zhao2, Yongji Jiang1†, Simin Liu1†, Zhongwei Lv1,3, Chuanzi Zuo1, Yanlei Huo1, Ru Wang1, Yichuan Pang1* and Chao Ma1*
Affiliations:
1 Department of Nuclear Medicine, Shanghai Tenth People’s Hospital, Tongji University School of Medicine, Shanghai, China
2 The Affiliated Qingdao Central Hospital, Qingdao University, Nuclear Medicine Imaging Department, Shandong Qingdao, China
3 Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
† These authors share first authorship.
Corresponding Author:
Dr. Chao Ma
Department of Nuclear Medicine,
Shanghai Tenth People’s Hospital,
Tongji University School of Medicine,
301 Yanchang Road,
Shanghai, China, 200072
Email: mc_7419@hotmail.com.
https://orcid.org/0000-0002-1105-6793
.
Tel.: +86-187-2128-8964
Fax: +86-21-6598-3358
Reprint requests should be directed to Dr. Chao Ma.
Abstract
Background
Radioiodine (RAI) resistance is a major barrier in the treatment of differentiated thyroid cancer (DTC), especially in tumors that retain iodine uptake but fail to respond. The role of DNA repair mechanisms, particularly ataxia-telangiectasia mutated (ATM) kinase, in this resistance remains unclear.
Methods
Single-cell RNA sequencing (scRNA-seq) was performed on 28 thyroid cancer (TC)/adjacent normal tissues to trace ATM expression during tumor dedifferentiation using publicly available datasets. Tissue microarrays from 89 TC/adjacent normal tissues cases, including RAI-avid and RAI-refractory (RAIR) tumors, validated ATM expression patterns. Therapeutic synergy between the ATM inhibitor AZD1390 and RAI was evaluated in xenograft models and K1 thyroid cancer cells. Mechanistic studies included RNA sequencing, comet assays, cell cycle profiling, and apurinic/apyrimidinic (AP) site quantification.
Results
scRNA-seq revealed stepwise ATM upregulation during TC progression, accompanied by cell cycle dysregulation. TMA analysis confirmed significantly higher ATM expression in anaplastic thyroid cancer and RAIR tumors (median score: 21.82 vs. 4.85 in RAI-sensitive; P < 0.0001). AZD1390 combined with RAI significantly suppressed tumor growth and enhanced apoptosis (P < 0.001). Mechanistically, radioiodine exposure was associated with prominent oxidative base damage–related DNA lesions, including AP sites, whereas canonical markers of extensive and persistent double-strand break accumulation were not prominently detected under these experimental conditions. ATM inhibition did not markedly increase the initial burden of radioiodine-induced DNA lesions but impaired cell cycle checkpoint control, promoting the conversion of sublethal AP site–associated damage into lethal genomic instability.
Conclusion
ATM promotes RAI resistance by enabling repair of AP sites and enforcing cell cycle arrest. Its inhibition converts sublethal lesions into cytotoxic damage and restores RAI sensitivity, highlighting ATM as a promising therapeutic target in RAI-refractory DTC.
Keywords:
Thyroid cancer
radioiodine resistance
ATM
targeted therapy
base excision repair
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Introduction
Differentiated thyroid cancer (DTC), accounting for 90–95% of thyroid malignancies [1], typically carries a favorable prognosis following standard therapies, including surgery, radioactive iodine (RAI), and thyroid-stimulating hormone suppression [2]. However, 5–20% of patients experience recurrence or metastasis within 20–25 years, and 10–15% develop distant metastases [3, 4]. For these metastatic cases, RAI remains a cornerstone treatment. Yet its efficacy is hampered by two intertwined challenges: dose-limiting toxicity and RAI resistance, particularly in metastases that retain iodine uptake capacity (e.g., bone metastases) but evade apoptosis, a phenomenon termed RAI-refractory (RAI-R) DTC [3]. RAIR-DTC patients face dismal outcomes, with a median survival of 3–5 years [5], underscoring the urgent need to unravel resistance mechanisms. The 2016 ATA guidelines 3 define four RAI-R categories, from lesions with no uptake to those that retain uptake but do not respond [3]. In this study we focus specifically on the ATA category characterized by measurable 131I uptake but failure to achieve a clinical response (i.e., lesions that take up radioiodine yet remain refractory), because the therapeutic strategy of impairing DNA repair to potentiate 131I cytotoxicity is most relevant to tumors that receive radioactive iodide but fail to undergo cell death.
RAI exerts cytotoxicity primarily through ionizing radiation–induced DNA damage, classically attributed to DNA double-strand breaks (DSBs) [6]. Unlike external beam radiotherapy, RAI efficacy relies on functional sodium/iodide symporter (NIS)–mediated uptake, a process frequently impaired in advanced disease [7]. Nevertheless, approximately 47% of metastatic DTCs retain NIS expression but remain RAI-resistant [4], suggesting that resistance involves factors beyond iodine transport.
One critical, yet underexplored, contributor is the DNA damage response (DDR). RAI-induced DSBs activate the apical DDR kinase ataxia-telangiectasia mutated (ATM), which regulates cell cycle arrest, DNA repair, and apoptosis [8–10]. Paradoxically, excessive DDR activation may promote tumor survival by enabling DSB repair and disrupting apoptosis [11]. This duality is mirrored in clinical observations: cells from Ataxia Telangiectasia (A-T) patients (lacking functional ATM) exhibit radiosensitivity due to defective DSB repair [12], and ATM inhibition in thyroid cancer cells has been shown to restore NIS function and enhance RAI uptake and cytotoxicity [13].
While NIS downregulation remains the primary focus in RAI-R research, the role of DDR, particularly ATM signaling, is less understood. Notably, ATM not only orchestrates DSB repair but also influences NIS expression [13], linking DDR directly to RAI responsiveness. Although ATM inhibitors have been evaluated in combination with external radiation across various tumor types [14, 15], their interaction with internal radiation modalities like RAI has not been systematically studied.
Here, we investigate the role of ATM in DTC progression and RAI resistance. We assess ATM expression across thyroid cancer stages and evaluate whether ATM inhibition can sensitize DTC cells to RAI both in vitro and in vivo. Our study aims to provide mechanistic insights into how ATM activity may promote resistance to RAI and to explore its potential as a therapeutic target in RAIR-DTC.
Materials and Methods
Single-Cell RNA Sequencing Analysis
The GSE193581 dataset was analyzed with R/Seurat, including SCTransform normalization, UMAP, and clustering. Following the workflow described by Lu et al. [16], quality control and normalization were conducted using the Seurat package (v4.0.5). Low-quality cells with fewer than 200 genes, more than 6,000 genes, or mitochondrial gene expression exceeding 30% were excluded. Gene expression counts were normalized using Seurat’s SCTransform method, and highly variable genes were identified for downstream analysis. Dimensionality reduction was performed using UMAP, and clustering was conducted using the Louvain algorithm with a resolution of 0.5.
Cell clusters were annotated based on known marker genes, manual curation, and predictions from the modeling tool described in Lu et al [16]. Major cell types included: Epithelial cells (normal and malignant): EPCAM, KRT18, KRT8, TFF3, TPO, and SLC26A4. Fibroblasts: COL1A1, DCN, PDPN. Endothelial cells: PECAM1, VWF, CDH5. B cells: CD79A, MS4A1. T cells: CD3E, CD4, CD8A. NK cells: NKG7, GNLY, KLRD1. Myeloid cells: CD14, LYZ, ITGAM. Malignant epithelial cells were identified using the scTypeTC modeling tool described in Lu et al [16]. This tool integrates transcriptional signatures and machine learning to delineate tumor cell subtypes. The modeling predicted malignant cells based on the loss of thyroid differentiation markers (TPO, SLC26A4) and the expression of tumor-specific markers (EPCAM, KRT18, KRT8) in epithelial clusters. Both TPO and SLC26A4 were absent in malignant cells, consistent with dedifferentiation during tumor progression. Malignant epithelial cells were further classified into PTC and ATC subtypes: PTC cells: Expressed epithelial markers (KRT18, KRT8) with mild dedifferentiation. ATC cells: Exhibited mesenchymal and inflammatory phenotypes, with markers such as VCAN, ZEB2, and S100A9.
Pseudotime trajectory analysis was performed using Monocle3 to reconstruct the transcriptional progression from normal thyroid follicular cells (NORMs) to malignant subtypes, following the methodology outlined by Lu et al [16]. Epithelial cells (TFCs, PTC, iATC, and mATC) were selected for trajectory inference. Dimensionality reduction was performed using UMAP embeddings, and the "learn_graph" function in Monocle3 was used to infer developmental trajectories. The starting point of the trajectory was manually set to normal TFCs based on the expression of thyroid-specific markers (TFF3, TPO, SLC26A4). Pathway enrichment analysis was conducted using KEGG to identify pathways enriched along the pseudotime trajectory. Differentially expressed genes (DEGs) associated with cell cycle regulation were identified using Seurat’s "FindMarkers" function, with a Wilcoxon rank-sum test applied to compare malignant and normal epithelial cells. Gene expression values were log2-transformed and z-score normalized across samples. The heatmap was generated using the ComplexHeatmap package in R, with hierarchical clustering used to group genes and cell types.
Tissue Microarray and Immunohistochemistry
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An 89-sample tissue microarray from Shanghai Tenth People's Hospital, comprising normal, cancerous, and metastatic thyroid tissues, was used. All samples were obtained with patient consent.
Human sample information
Human samples (normal thyroid, TC, paraneoplastic, and metastatic tissues specimens) were obtained with the patient's consent through the Shanghai Tenth People's Hospital. This study was approved by the Institutional Review Board of Shanghai Tenth People's Hospital (approval number: 24KN265). To identify the expression of ATM in TCs, a tissue microarray (TMA) was constructed, including 89 samples, including normal thyroid tissues, thyroid cancer (TC) tissues, paraneoplastic tissues, and metastatic lymph nodes (2 mm tissue core per sample). All tissue samples were fixed in formalin and embedded in paraffin for IHC. Samples were dewaxed with xylene and then rehydrated in anhydrous ethanol solution. Sections were then incubated overnight at 4°C with an anti-ATM antibody (1:100; #2873T, CST) and followed by incubation with the secondary antibody. Two independent pathologists assessed the positivity and staining intensity of the tissue sections blindly.
The expression levels were assessed based on the staining intensity (0 for no staining, 1 for weak staining, 2 for moderate staining, and 3 for strong staining) and the positive cell ratio (0 for < 10%, 1 for 10 to < 50%, and 2 for ≥ 50% cell). The histochemistry score (H-SCORE) was calculated as follows: H-SCORE = (percentage of cells with weak staining × 1) + (percentage of cells with medium staining × 2) + (percentage of cells with strong staining × 3).
TIMER2.0 Database Analysis
To enhance the understanding of the role of ATM in thyroid cancer, the Cancer exploration module from the TIMER2.0 database was utilized to investigate the correlation between ATM expression and the expression levels of genes associated with thyroid cancer dedifferentiation. The Gene_Corr module analyzes the relationship between ATM expression and the BRAF, KRAS, MTOR, and PIK3CA gene expression. A correlation coefficient of 0.1 ≤ ρ ≤ 1.0 indicates a significant correlation between ATM and thyroid cancer dedifferentiation genes, while a p < 0.05 denotes statistical significance.
Cell Culture and Treatments
The K1 (RRID: CVCL_2537), BCPAP (RRID: CVCL_0153), and TPC-1 (RRID༚CVCL_6298) cell lines were procured from the American Type Culture Collection (ATCC, Manassas, VA, USA). K1 cells were incubated in medium DMEM (Gibco) supplemented with 1% Penicillin-Streptomycin solution (100x Gibco) and 10% FBS (Avantor). The cells were maintained at 37°C in 5% CO2. BCPAP and TPC-1 cells were incubated in medium RPMI-1640 (Gibco) supplemented with 1% Penicillin-Streptomycin solution (100x Gibco), and 10% FBS (Avantor). The cells were maintained at 37°C in 5% CO2. Treatments included AZD1390 (5–50 nM) and ¹³¹I (0.74–4.6 MBq/mL), alone or combined.
Radioiodine Uptake Assay
K1, BCBAP, and TPC-1 cells were seeded into 12-well plates at a density of 5 × 105 cells per well separately, with three replicate wells prepared for each cell line. Each well was supplemented with 1 mL of complete medium and incubated at 37°C in a 5% CO2 atmosphere for 24 hours. Subsequently, the three replicate wells were incubated with 1 mL of serum-free medium containing 5 µM potassium iodide (KI) and 0.74 MBq 131I for 1 hour at 37°C in a 5% CO2 atmosphere. Subsequently, the radioactive medium was aspirated from the supernatants of 12-well plates. To wash the cells, 400 µL of pre-cooled phosphate-buffered saline (PBS) at 4°C was added and repeated twice. The aspirated medium and PBS were collected. Cells in each well were then digested with 200 µL of 0.25% trypsin at room temperature. The digestion was terminated by adding 500 µL of NaOH containing 1% SDS (0.33 M) to lyse the cells, which were collected upon completion of the lysis process. Following collection, the cells were rinsed twice by adding phosphate-buffered saline (PBS) to the wells. The rinsed PBS was subsequently collected. The radioactivity in the supernatant and the lysed cells was measured using a γ-counter (GC-1200).
In Vivo Tumor Models
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SPF nude BALB/c female mice (4–6 weeks old, weighing approximately 20 g) were purchased from Shanghai SLAC Laboratory Animal Co., Ltd., China, and placed in the SPF facility of the Tenth People's Hospital, Tongji University School of Medicine. To improve RAI uptake in mouse tumors, thyroid tissues in mice were removed by electroacupuncture before tumor cell injection. Postoperatively, they were given a normal diet of 0.1% calcium gluconate (to prevent calcium deficiency due to intra-operative parathyroid damage) to feed. Levothyroxine was also supplemented, and L-T4 at a dose of 14ug/Kg BW was given daily by gavage to prevent hypothyroidism until 7 days before treatment with RAI. Shanghai Tenth People Hospital's Animal Ethics Committee approved these experiments according to the Guidelines for the Care and Use of Laboratory Animals (approval number: SHDSYY-2024-4456).
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Xenograft tumors in nude mice: K1 cells (1×10
6) were implanted into mice through hypodermic injection, the mice were randomized into four groups (n = 7): vehicle (intraperitoneal injection of 100uL saline), RAI (a single intraperitoneal injection of 37 MBq of
131I solution per mice once), iATM (per mice was injected intraperitoneally with 5mg/kg AZD1390 QD for 12 days), RAI + iATM (a single intraperitoneal injection of 37 MBq of
131I solution once and intraperitoneal 5mg/Kg AZD1390 QD per mice for 12 days). These mice were housed in a clean barrier system at 20–25°C and 50–60% humidity, with free access to food and water. Tumor growth was monitored by digital calipers every 3 days, and tumor volumes were recorded using the following formula: Volume = (longer diameter × shorter diameter
2)/2. All mice were executed on day 12.
Histological analyses of the mice's tumors: Tissues were fixed in 10% formalin at room temperature, treated with anhydrous ethanol and xylene, and embedded in paraffin. The thickness of paraffin-embedded tissue sections was 5 µm and was stained with H&E, Ki-67, and TUNEL, respectively. Immunohistochemical staining was performed using anti-γH2AX (1:200, #NB100-638, Novus Biologicals), and the slides were scanned with a digital pathology slide scanner (KFBIO). The scanning results were statistically positive ratio using ImageJ software.
Functional Assays
CCK-8: Cell viability was examined using the Cell Counting Kit-8 (CCK-8) (#GK10001, GLPBIO) assay. The cells were plated in 96-well plates (about 5×103 cells/well in 100 µL culture medium) and incubated for 48h. Then we replaced the medium with 0-1500uCi/mL concentration of 131I (adding 5nM KI per well) or 0-300uM AZD1390 2.3 MBq/mL 131I + 0-300nM AZD1390 (adding 5nM KI per well). After maintaining 48h or 96h, the CCK-8 working solutions were added. Then the cells were incubated continuously for 2h at 37℃. Next, a microplate reader (Tecan, Infinite 200Pro) was used to detect each group's light absorption values at 450nm. Cell survival could be displayed by the ratio of absorption values, with the calculation formula of: (dosing-blank) / (control-blank).
The synergistic effect of RAI and ATM inhibitor was demonstrated through isohologram analysis. The CompuSyn software generates a CI value to quantify the interactions between drugs [17]. This CI value was calculated following the methodology outlined by Chou et al. [18, 19]. A CI value approaching 1 suggests additive effects of the drug combinations, while values less than 1 indicate synergy, and values greater than 1 indicate antagonism.
Immunofluorescence staining of dsDNA and ssDNA: Cells were collected at the indicated times to detect cytosolic DNA in K1 cells after RAI irradiation. K1 cells were fixed with 4% PFA and permeated with 5% Triton X-100. Then blocked with 1% BSA in PBS, and incubated with anti-dsDNA (1:400; #MAB1293, AE2, Millipore) or anti-ssDNA (1:400, # MAB3299, F7-26, Millipore) primary antibody overnight at 4℃. After 3 washes with PBS, the cells were incubated with donkey anti-mouse-Alexa Fluor 555 (#A-31570, Thermo Fisher) for 1h at room temperature. Subsequently, DAPI staining was performed at room temperature for 10 min. Confocal microscopy was conducted using a Zeiss LSM900 microscope with a 60x oil-immersion lens following standard protocol, and images were analyzed using Image J software.
Molecular Analyses
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Western Blot: Cells were seeded in six-well plates at a density of 50% and incubated at 37°C for 24 hours. Cells were divided into four groups: Control, RAI (treated with 2.3 MBq/mL
131I), iATM (treated with 50nM AZD1390),
131I + iATM (treated with 2.3 MBq/mL
131I + 50nM AZD1390). Proteins were harvested after 24 hours of the above treatment by scraping the cells in radioimmunoprecipitation assay (RIPA) lysis buffer supplemented with a protease inhibitor cocktail (#K1007, APExBIO). Protein content was quantified using the BCA Protein Assay Kit according to the manufacturer's instructions (#T9300A, Takara). Standard methods of Western blot have been used to analyze each protein expression. Primary antibodies used were anti-ATM (#A19650, ABclonal), anti-Phospho-ATM-S1981 (#AP1030, ABclonal), anti-CDK1 A17 (#ab18, Abcam), anti-Phospho-CDC2 Tyr15 (#9117, CST), and anti-GAPDH (#2118, CST).
Statistical Analysis
Statistics were analyzed using GraphPad Prism 9.0 and IBM SPSS Statistics 20 software. Results were presented as mean ± SD as indicated in the figure legends. Unpaired samples t-test, one-way or two-way ANOVA, Tukey's multiple comparison tests, ns > 0.05, *p < 0.05, **p < 0.01, ***p < 0.001, **** p < 0.0001.
Results
Single-Cell Analysis Indicates ATM as a Driver of Thyroid Cancer Progression.
Single-cell RNA sequencing (scRNA-seq) of 28 thyroid tissue samples, including 15 anaplastic thyroid cancers (ATC), 7 papillary thyroid cancers (PTC), and 6 normal thyroid follicular epithelial cell samples delineated the trajectory of malignant progression [26]. Uniform Manifold Approximation and Projection (UMAP) revealed eight distinct cell populations [26], including epithelial, immune subsets, fibroblasts, endothelial cells (Fig. 1A, S1A-B), validated by marker gene profiling (KRT18 for epithelium, PECAM1 for endothelium) (Fig. 1B).
To visualize the dynamic transcriptional evolution of epithelial cells, we reconstructed a pseudotime developmental trajectory using Monocle3 (Fig. 1C & Fig. S1C). This trajectory clearly revealed a gradual transition from normal thyroid follicular cells (NORM) through PTC to ATC, indicating a continuous dedifferentiation process during tumor evolution. KEGG pathway enrichment along this trajectory revealed a stepwise activation of metabolic (e.g., ribosome biogenesis, oxidative phosphorylation) and oncogenic signaling pathways (e.g., PI3K-Akt, relaxin) (Fig. S1D). A comparative analysis highlighted the ATC-specific upregulation of cell cycle (adjusted P < 0.05) and chromosomal instability genes (BUB1, MCM2) compared to NORM (Fig. 1D-E). Critically, among cell cycle-associated genes, ATM was identified as progressively upregulated during dedifferentiation (Fig. 1F), implicating it as a potential driver of genomic instability and aggressive tumor progression.
Clinical Validation of ATM Overexpression in Advanced and RAI-Resistant Thyroid Cancer.
We validated ATM's clinical relevance via immunohistochemistry on 89 thyroid samples, including normal thyroid tissues, primary tumors, adjacent tissues, and metastatic lymph nodes (Fig. S2A-B and Supplemental Table 1). Consistent with scRNA-seq data, ATM protein levels were significantly elevated in thyroid cancer tissues compared to adjacent normal tissues (p < 0.05) (Fig. 2A). ATM expression was highest in ATC tissues, significantly exceeding levels in PTC and follicular thyroid carcinoma (FTC) samples (P < 0.0001) (Fig. 2B).
In RAI-refractory (RAI-R) PTC, ATM expression was substantially elevated, with a median score of 21.82 (95% CI: 12.59–29.20), compared to radioiodine-avid (RIA) PTC cases (median score 4.85, 95% CI: 3.17–12.99) and normal paraneoplastic tissues (median score 2.89, 95% CI: 1.31–8.44) (Fig. 2C). Metastatic lymph nodes from RAI-R PTC cases exhibited higher ATM scores (median 7.20, 95% CI: 5.60–16.60) compared to those from RIA cases (median 2.33, 95% CI: 0.73–13.84) (Fig. 2D). Correlation analysis using the TIMER2.0 database revealed positive associations between ATM and oncogenic drivers including BRAF (ρ = 0.546), KRAS (ρ = 0.636), MTOR (ρ = 0.546), and PIK3CA (ρ = 0.704) (Fig. 2E). Figure 2F presents representative images of ATM staining for different tissue types.
Targeting ATM Inhibition Synergizes with RAI to Suppress Tumor Growth In Vivo.
To evaluate ATM inhibition in vivo, we selected K1 cells for xenograft studies due to their selective ¹³¹I uptake (Fig. S3A), as baseline ATM expression did not differ significantly across tested cell lines (Fig. S3B). Having established this model, we next ensured that the ATM inhibitor AZD1390 itself did not interfere with the fundamental mechanism of RAI action. A radioactive uptake assay confirmed that AZD1390 treatment did not alter 131I accumulation in K1 cells compared to the control (Fig. S3C).
Tumor-bearing nude mice were treated with RAI (37 MBq, single dose), the ATM inhibitor AZD1390 (5 mg/kg, daily), or the combination for 12 days (Fig. 3A, B). Tumor volumes were significantly reduced in the combination group compared to monotherapies (P < 0.01, two-way ANOVA) (Fig. 3C). Final tumor weights were also significantly lower in the combination group.
Immunohistochemistry analysis of excised tumors showed decreased Ki-67 staining and increased TUNEL staining in the combination group (P < 0.001) (Fig. 3D). While 131I alone activated the DDR, evidenced by γH2AX foci accumulation, co-treatment with AZD1390 suppressed γH2AX levels, indicating compromised DDR signaling (Fig. 3D). These findings suggest that ATM inhibition potentiates RAI efficacy by impairing DNA repair and promoting apoptosis.
ATM Blockade Potentiates RAI-Induced Cytotoxicity and Suppresses Migration In Vitro.
In vitro, ATM inhibition radiosensitized K1 cells treated with 131I (0–55.5 MBq/mL) or AZD1390 (0–1200 nM) for 48–92 hours. CCK-8 assays revealed time- and dose-dependent inhibition of cell proliferation by 131I, while AZD1390 alone showed minimal cytotoxicity (Fig. 4A-B). Co-treatment with 131I (2.3 MBq/mL) and AZD1390 (1.2–75 nM) significantly reduced cell viability compared to monotherapies (Fig. 4C). CompuSyn analysis confirmed synergistic inhibition (combination index < 1) (Fig. 4D) [27, 28].Colony formation assays demonstrated reduced clonogenic survival with the combination therapy (P < 0.001), with fewer colonies observed at higher AZD1390 doses (Fig. 4E-F). Annexin V/PI staining showed activity-dependent increases in apoptosis upon 131I treatment (P < 0.001), which was significantly enhanced by combination therapy (P < 0.01) (Fig. 4G–J). We established stable ATM-knockdown K1 cells (shATM) to genetically validate on-target effects (Fig. 4K). We first assessed the impact of ATM depletion on cell migration. Wound-healing assays revealed that ATM knockdown significantly impaired the migratory capacity of K1 cells compared to the non-targeting control (shNC) (p < 0.05) (Fig. 4L-M). We next asked whether genetic ATM knockdown could recapitulate the chemosensitization effect observed with AZD1390. Flow cytometric analysis of Annexin V/PI staining demonstrated that ATM knockdown alone induced an increase in apoptosis (p < 0.01). Crucially, the combination of ATM knockdown and RAI treatment resulted in a synergistic enhancement of apoptotic cell death, significantly exceeding the effects of either single treatment (p < 0.0001) (Fig. S4A-B). This genetic evidence unequivocally confirms that the sensitization to RAI is an on-target effect of ATM ablation.
RAI Induces Genotoxic Stress with Limited Detectable Double-Strand Breaks in RAI-R DTC cells.
RNA-seq of RAI-treated K1 cells identified 1,144 differentially expressed genes (|log2FC| >1.3, FDR < 0.05) (Fig. S5A) [29–34]. GO and KEGG analyses revealed enrichment of DNA repair, cell cycle regulation, and G1/S transition pathways (Fig. 5A, Fig. S5C). GSEA demonstrated downregulation of mitosis- and G2/M checkpoint-related genes, alongside activation of DNA repair pathways (FDR < 0.05) (Fig. 5B).
Transcriptomic analysis revealed differential expression of numerous DNA repair genes in response to RAI. These included a modest upregulation of key components of the base excision repair (BER) pathway, such as POLB (Fig. 5C), which is consistent with a cellular response to RAI-induced oxidative base damage, a known source of apurinic/apyrimidinic (AP) sites. EdU staining confirmed a time-dependent decrease in proliferation after RAI (Fig. 5D, K), but TUNEL and dsDNA staining did not reveal a sustained increase in detectable double-strand breaks (Fig. 5F–I, K). Comet assays showed limited DNA fragmentation under these experimental conditions in 131I-treated cells compared to DNase I controls (Fig. 5G, K). Notably, RAI induced modest increases in single-stranded DNA (ssDNA) accumulation (P < 0.01) (Fig. 5H–J, K). These results suggest that in K1 cells with high ATM activity, RAI-induced double-strand breaks, if present, are rapidly resolved, whereas non-DSB lesions such as AP sites may persist and constitute a dominant source of unresolved genotoxic stress.
ATM Inhibition Exacerbates Genotoxic Stress and Induces Mitotic Catastrophe.
Flow cytometry revealed that 131I (2.3–4.6 MBq/mL) induced G2/M arrest in K1 cells, with dose-dependent enrichment (Fig. 6A–B, D). While 131I alone caused S-phase accumulation, co-treatment with AZD1390 (50 nM) further augmented G2/M arrest (Fig. 6C–E). Western blotting confirmed that ATM inhibition attenuated phosphorylation of checkpoint kinases (pChk2, pCDC2), suggesting dysregulated G2/M checkpoint control and premature mitotic entry. (Fig. 6F–G, Fig. S6A).
To assess DNA damage persistence, cells were irradiated with 131I (4.6 MBq/mL) for 24 hours, washed to remove residual RAI, and then incubated with or without AZD1390. Co-treatment of 131I-AZD1390 resulted in a time-dependent accumulation of AP sites compared with RAI alone. At the same time, cell survival was reduced, emphasizing the cytotoxic consequences of impaired DNA repair (Fig. 6H). These results support that ATM inhibition disables DDR checkpoints, driving cells with unresolved damage into mitosis, ultimately triggering mitotic catastrophe and apoptosis.
Discussion
RAI remains a cornerstone therapy for DTC [6], yet its efficacy is often limited by intrinsic or acquired resistance. Our study identifies ATM as a molecular determinant associated with disease progression and therapeutic resistance in thyroid cancer. By integrating single-cell transcriptomics, clinical TMAs, functional preclinical models and in vitro mechanistic explorations, we delineate a central role for ATM in promoting dedifferentiation, genomic instability, and escape from RAI-induced cytotoxicity.
Single-cell RNA-sequencing revealed a continuum from normal thyroid follicular cells through papillary thyroid carcinoma (PTC) to anaplastic thyroid carcinoma (ATC), with a stepwise upregulation of ATM along this dedifferentiation trajectory. Pseudotemporal analysis showed progressive ATM activation during tumor evolution, coinciding with cell cycle, DNA replication, and chromosomal instability programs. These findings were validated in clinical specimens, where RAI-R tumors exhibited significantly higher ATM levels than RAI-sensitive counterparts. ATM expression positively correlated with oncogenic drivers (BRAF, KRAS, PIK3CA [35]), suggesting its integration into pro-tumorigenic signaling networks. While these data strongly associate ATM upregulation with the dedifferentiated state, future studies manipulating ATM expression (e.g., knockdown/overexpression) in thyroid models are needed to definitively establish its causal role in driving dedifferentiation. These findings align with studies in breast and gastric cancers [36, 37], where ATM overexpression is linked to both oncogenic transformation and therapy resistance, underscoring its context-dependent roles in cancer biology [38]. Notably, in other cancer types, ATM has been implicated in epithelial-to-mesenchymal transition and loss of differentiation markers, supporting the concept that it may play a similar role in thyroid carcinogenesis [39].
In preclinical models, both pharmacologic and genetic ATM suppression synergized with RAI to inhibit tumor growth, induce apoptosis, and impair migration. This consistency confirms ATM's role in RAI resistance. Mechanistically, under the experimental conditions used, RAI treatment was associated with prominent accumulation of AP sites arising from oxidative base damage, while persistent or readily detectable double-strand breaks were limited. While γH2AX was observed post-RAI, comet assays confirmed no significant DSB induction. This observation aligns with the physical properties of 131I, which is primarily a low-LET β particle emitter. Unlike high-LET radiation, the sparse ionization events produced by electrons and β particles predominantly cause localized oxidative base damage and single-strand breaks, which are significantly more frequent than immediate DSBs [40]. These lesions often manifest as non-DSB clustered DNA damages, including a high density of AP sites [41]. Our findings suggest that in the context of high ATM expression, these pervasive sublethal lesions are the primary genotoxic stress managed by the cell's repair machinery. Instead, γH2AX likely reflects replication stress from unresolved AP sites, as persistent AP lesions stall replication forks, activating ATR and downstream DDR signaling [42]. ATM inhibition exacerbated this stress by abrogating G2/M checkpoint control (pChk and pCDC2 downregulation), forcing cells with unrepaired AP sites into mitosis, where replication errors culminated in mitotic catastrophe. While AP sites are canonically repaired via base excision repair (BER), the role of ATM in this context is uncharted. Intriguingly, ATM inhibition exacerbated AP site retention, suggesting its potential involvement in BER coordination. This corroborates earlier findings indicating that ATM or it’s signaling intermediates govern oxidative DNA damage responses [43, 44]. And researchers have shown that ATM directly participates in BER through phosphorylation of TDP1 at Ser81, a modification that enables XRCC1-dependent recruitment of TDP1 to sites of base lesions [45]. The limited detection of SSB intermediates suggests they are either transiently repaired or AP sites are processed via long-patch BER. This aligns with studies showing that oxidative agents, such as ionizing radiation, can directly generate AP sites without requiring SSB intermediates [46, 47]. Beyond its well-established role in DSB repair, our data suggest that ATM also contributes to the cellular response to RAI-induced AP site–associated genotoxic stress, potentially through coordination of BER and cell cycle checkpoints. Critically, ATM inhibition prolonged AP site retention, suggesting that ATM facilitates AP site resolution potentially through direct BER coordination or indirect checkpoint-mediated repair windows. This mechanism represents a distinct paradigm of synthetic lethality, diverging from PARP inhibitor strategies in BRCA-mutant cancers; here, it is the massive accumulation of 'hidden' sublethal AP sites, rather than a canonical deficiency in DSB repair, that drives genomic instability and cell death.
In addition to DNA-damage–related pathways, alterations in membrane transporters and ion-channel regulators have also been implicated in RAI refractoriness. A recent transcriptomic analysis identified ANO1 as a potential biomarker distinguishing RAI-avid from non-avid thyroid tumors [48]. Although ANO1 was not examined in the present study, its reported association underscores that multiple molecular mechanisms, including DNA damage response, oxidative stress, and altered ion transport, may collectively determine RAI uptake and treatment sensitivity.
The therapeutic implication is twofold: (1) ATM upregulation serves as a biomarker of aggressive, RAI-resistant thyroid cancer; and (2) pharmacologic inhibition of ATM may re-sensitize these tumors to RAI by dismantling DDR checkpoints and enhancing genotoxic burden. Importantly, our findings parallel similar observations in other solid tumors, where ATM deficiency or inhibition exacerbates therapeutic DNA damage, underscoring a broader applicability of ATM-targeted radiosensitization strategies.
Conclusions
A
In summary, this study establishes ATM as a key driver of thyroid cancer progression and a therapeutic vulnerability in RAI resistance. While its direct causal role in dedifferentiation requires further validation, our data position ATM as a critical contributor to the RAI-resistant phenotype. Our findings are most applicable to tumors that retain measurable radioiodine uptake but are clinically refractory (ATA category 4), and do not imply that ATM inhibition will restore radioiodine responsiveness in tumors that lack iodide uptake. These insights provide a strong mechanistic rationale for incorporating ATM inhibitors into treatment regimens for advanced or refractory thyroid cancers. Future clinical trials of ATM inhibition combined with RAI may offer a novel strategy to overcome radioiodine resistance and improve patient outcomes, and future work extending these findings to ATC and other dedifferentiated thyroid cancer models will further clarify the role of ATM in tumor progression and therapeutic resistance.
Acknowledgements
We thank the Department of Pathology of Shanghai Tenth People's Hospital for providing clinical samples to support this study.
A
Author contributions
X.T.Q.: Writing – original draft, Formal analysis, Visualization. L.Z.: Data curation, Resources, Methodology. Y.J.J.: Investigation, Validation, Writing – review & editing. S.M.L.: Software, Formal analysis, Visualization. Z.W.L.: Project administration, Resources. C.Z.Z.: Data curation, Software, Validation. Y.L.H.: Methodology, Investigation, Writing – review & editing. R.W.: Supervision, Conceptualization. Y.C.P.: Supervision, Funding acquisition, Writing – review & editing. C.M.: Conceptualization, Project administration, Writing – review & editing.
A
Data Availability
The data sets produced through the current study are available from the corresponding author on reasonable request.
The study adhered to the principles outlined in The Declaration of Helsinki. The study involving human participants, was approved by the Institutional Review Board of Shanghai Tenth People's Hospital (approval number: 24KN265). All of mouse experiments have been approved by Shanghai Tenth People Hospital's Animal Ethics Committee according to the Guidelines for the Care and Use of Laboratory Animals (approval number: SHDSYY-2024-4456).
Electronic Supplementary Material
Below is the link to the electronic supplementary material
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