Introduction

Genomic instability is a hallmark of cancer and is a driving force for the acquisition of other characteristics of cancer1. In hereditary cancers, mutations in DNA repair genes cause genomic instability that promotes cancer development. On the other hand, recent high-throughput sequencing studies have revealed that sporadic cancers have fewer defects in DNA repair genes2. Instead, more than half of the top 20 genes mutated in human cancers are associated with features of sustained proliferation, raising the possibility that genes driving cell proliferation, such as oncogenes, are embracing complex environmental changes that disrupt cellular processes and contribute to genomic instability3. Such cellular disruptions involve physiological dysregulation of DNA replication and are widely referred to as replication stress (RS). A large body of evidence indicates that during the early stages of tumorigenesis, oncogenes cause RS, leading to genomic instability4. While replication cannot be completed in most of these distressed cells, resulting in programmed cell death or senescence5, a limited number continue to proliferate and expand clonally in noncancer tissues6. These findings raise the question of how cells adapt to RS while driving genomic instability during early carcinogenic processes.

KRAS is one of the most frequently mutated oncogenes in human cancers and is considered to be an important early driver of many tumors7. KRAS mutations commonly lead to substitution of a single amino acid (G12) in the KRAS protein with another amino acid, which causes constitutive activation of the downstream RAS signaling cascade and induces oncogenic events8,9. For instance, such mutations cause loss of normal growth barriers and disruption of tissue homeostasis resulting in increased exposure of mutant KRAS cells to stress-inducing conditions such as RS10,11. Recent evidence suggests that strong overexpression of oncogenic Ras in normal fibroblasts increases RNA synthesis accompanied by R-loop accumulation, which interferes with replication fork progression and causes RS, whereas inhibition of origin firing failed to abrogate RAS-induced RS in the same system12. However, the obstacles to abrogating fork progression have not been fully addressed, and whether a similar mechanism is active in normal human epithelial cells expressing oncogenic KRAS mutants—a frequent situation in human carcinogenesis—remains elusive.

Ataxia Telangiectasia and Rad3-related kinase (ATR), a master regulator of RS, and its critical substrate, Checkpoint Kinase 1 (Chk1), regulate cell cycle checkpoints and facilitate DNA repair via their substrates13,14,15,16,17,18,19. Therefore, ATR and Chk1 have long been considered tumor suppressors20,21,22. However, recent studies have shown that ATR and Chk1 are required for cell survival in response to oncogenic RAS expression during tumorigenesis, suggesting that the ATR-Chk1 kinase pathway protects cells from deleterious and chronic RS induced by oncogenes, thus promoting RS tolerance (RST)23,24,25,26. As a mechanism of RST in human cells, repriming of DNA synthesis at stalled replication forks promotes discontinuous replication at leading strands with single-stranded DNA (ssDNA) gaps27,28. Human primase and DNA-directed polymerase (PrimPol) is a major factor that mediates the repriming process during the RS response29. PrimPol needs to be tightly regulated during DNA replication to prevent aberrant repriming, fork speeding, and chromosomal breakage, which increase the risk of genomic instability30,87 with the human genome (GRCh38) (https://gdc.cancer.gov/about-data/gdc-data-processing/gdc-reference-files) and transcriptome data (GENCODE version 3188) as reference datasets. Transcripts per million (TPM) values were calculated using the StringTie (2.0.4) program89. This study was approved by the Institutional Review Board of the National Cancer Center.

The samples were grouped depending on ATR expression, PrimPol expression, KRAS mutation status, and the previous/current smoking status of the patient. The low and high expression groups for each gene were defined as follows. The cohort was divided into two groups (High and Low) such that the average expression levels in the Low group (Av_Low) and High group (Av_High) met the following condition: the ratio of the average expression levels [(Av_High)/(Av_Low)] is minimized (typically ~2) or not <1.5. The OS of each group was analyzed by the Kaplan‒Meier method, with the log-rank (Mantel‒Cox) test.

Western blot analysis

Cells were lysed in sampling buffer (120 mM Tris-HCl (pH 6.8), 12% glycerol, 4% SDS, 200 mM DTT, 0.004% bromophenol blue) and denatured at 95 °C for 5 min. The protein concentration in the cell lysate was estimated by the Bradford assay (XL-Bradford, Apro Science, Cat# KY-1031). Equal amounts of protein were separated by SDS‒PAGE (10% SDS-polyacrylamide gel) at 120 V for 2 h and were then transferred to polyvinylidene difluoride (PVDF) membranes (Immobilon-P, Millipore, Cat# IPVH00010) at 150 mA for ~16 h at 4 °C. The membranes were blocked with 5% skim milk in TBST (25 mM Tris-HCl (pH 7.8), 140 mM NaCl, 0.1% Tween 20) for 20 min at room temperature (RT) and probed with the following primary antibodies diluted in 5% skim milk in TBST (supplemented with 0.02% of NaN3): anti-pan-RAS (1:1000, Santa Cruz, Cat# sc-166691), anti-αTubulin (1:5000, MBL, Cat# PM054), anti-phospho-ATR (Thr1989) (1:3000, Cell Signaling Technology, Cat# 30632), anti-ATR (1:3000, GeneTex, Cat# GTX128146), anti-phospho-Chk1 (Ser317) (1:500, Cell Signaling Technology, Cat# 12302), anti-phospho-Chk1 (Ser345) (1:500, Cell Signaling Technology, Cat# 2348), anti-Chk1 (1:100, Santa Cruz, Cat# sc-8408), anti-phospho-RB (Ser807/811) (1:1000, Cell Signaling Technology, Cat# 8516), anti-E-cadherin (1:1000, Cell Signaling Technology, Cat# 3195), anti-Vimentin (1:1000, Cell Signaling Technology, Cat# 5741), anti-PrimPol (1:3000, Proteintech, Cat# 29824-1-AP), anti-myc tag (1:1000, MBL, Cat# 192-3), anti-HistoneH1.4 (1:1000, Cell Signaling Technology, Cat# 41328), anti-GAPDH (1:1000, Wako, Cat# 010-25521), anti-phospho-Chk1 (Ser296) (1:500, Cell Signaling Technology, Cat# 90178), anti-RNaseH1 (1:1000, Abcam, Cat# ab56560), anti-HP1α (1:1000, Millipore, Cat# 05-689), anti-HP1β (1:1000, Cell Signaling Technology, Cat# 8676). After 3 washes with TBST, the membranes were incubated with Horseradish Peroxidase (HRP)-conjugated AffiniPure Goat Anti-Rabbit or Mouse IgG (H + L) (1:5000, Jackson ImmunoResearch, Cat# 111-035-003 or Cat# 115-035-003) in 5% skim milk for 1 h at RT and were then washed with TBST 5 times. The blots were developed with Western Lightning Plus ECL Reagent (PerkinElmer, Cat# NEL105001EA) according to the manufacturer’s instructions and imaged with an LAS 3000 luminescent image analyzer (Fujifilm).

Long-term time-to-progression (TTP) assay

A total of 2 × 105 cells were plated in 6-cm plates with or without 0.1 μM 4OHT. After 3 or 4 days of incubation, cells were collected and counted. This 2D culture process was repeated for ~30 days depending on the deleterious effects of 4OHT-induced KRASG12V. The daily growth rate (μ) was calculated according to the formula: μ = (ln N – ln N’)/t, where N is the number of cells at the current week, N’ is the number of cells plated at the previous week, and t is the culture days. Based on the daily growth rate (μ) calculated at every split time, the total current cell number (Nx) was estimated according to the formula ln Nx = ln N0 + μ * T, where N0 is the number of cells plated at the initial split point and T is the total number of incubation days.

Anchorage-independent growth assay

A total of 2 × 104 cells were suspended in 1 ml of 0.4% soft agar solution (SeaPlaque agarose, Lonza, SeaPlaqueTM, Cat# 50101) and then plated on 1.5 ml of 0.7% bottom agar. Top medium containing 0.1 μM of 4OHT was added every 3 ~ 4 days. After ~30 days of culture at 37 °C, cells were stained with 0.01% crystal violet dissolved in 20% MtOH for 1 h at RT and were then imaged using a LAS-3000 imager (Fujifilm).

RNA extraction and real-time PCR

A total of 1 × 105 cells were plated in 6-well plates. Following treatments, total RNA was purified using ISOGEN II (Nippon Gene, Cat# 311-07361) according to the manufacturer’s instructions. Extracted RNA was resuspended in TE buffer (pH 8.0, NipponGene, Cat# 314-90021).

To detect ATR, PrimPol and ActinB mRNA, reverse transcription of the mRNA library was carried out using a High-Capacity RNA-to-cDNA Kit (Applied Biosystems, Cat# 4387406) according to the manufacturer’s instructions. SYBR Green real-time PCR was performed using a KAPA SYBR FAST ABI Prism qPCR Kit (Kapa Biosystems, Cat# KK4604). The following primers were used at 500 nM: ATR-F, 5'-GGTATGCTCTCACTTCCATG-3'; ATR-R, 5'-GTCAGAAGAAACACACATCG-3'; PRIMPOL-F, 5'-TGTGGCTTTGGAGGTTACTGA-3'; PRIMPOL-R, 5'-TTCTACTGAAGTGCCGATACTGT-3'; Hs_ACTB_1_SG QuantiTect Primer Assay (QIAGEN, ID# QT00095431).

To detect miR185, reverse transcription was carried out using a TaqMan™ MicroRNA Reverse Transcription Kit (Applied Biosystems, Cat# 4366596) and TaqMan™ MicroRNA Assays (Applied Biosystems, RNU48: Assay ID# 001006, miR185: Assay ID# 002271) according to the manufacturer’s instructions. TaqMan real-time PCR was performed using TaqMan™ Fast Advanced Master Mix (Applied Biosystems, Cat# 4444556) according to the manufacturer’s instructions.

PCR was performed using a StepOnePlus thermocycler (Applied Biosystem). The comparative Ct (ΔΔCt) method was selected to validate the quantification of mRNA or miRNA expression.

Proliferation assay

A total of 2000 cells were seeded in 96-well plates and treated with 0.1 μM 4OHT. The numbers of proliferating cell were determined 7 days after 4OHT treatment using PrestoBlueTM. According to the manufacturer’s instructions, PrestoBlueTM Cell Viability Reagent (Invitrogen, Cat# A13262) was added directly to the cells and incubated for 1 h at 37 °C. The optical density (excitation: 560 nm, emission: 590 nm) was measured with a Biotek Epoch microplate reader and analyzed with Gen5 2.05 software (Biotek).

For HP1α KD effect validation, 1.5 ×105 cells were transfected with 1 nM siRNA for 2 days and then replated on 96-well plates with 0.1 μM 4OHT. After 5 days of incubation, cell proliferation was evaluated by Cell Titer-Glo 2.0 Assay (Promega, Cat# G9243) according to the manufacturer’s instructions. The luminescence was measured with a Biotek Epoch microplate reader and analyzed with Gen5 2.05 software (Biotek).

DNA fiber assay and S1 fiber assay

The standard DNA fiber assay was previously described53. A total of 1 ×105 cells were plated in 6-well plates. Following treatments, cells were sequentially labeled with 100 μM IdU (5-iodo-2’-deoxyuridine, Sigma–Aldrich, Cat# l7125-5G) for 20 min, washed with PBS 3 times, labeled with 100 μM CldU (5-chloro-2’-deoxyuridine, Sigma–Aldrich, Cat# C6891-100MG) for 40 min, and washed with PBS. The labeled cells were trypsinized and pelleted at 800 x g for 5 min at 4 °C and were then resuspended in 200 μl of PBS.

The S1 fiber assay was performed as previously described with modifications45. Labeled cells were permeabilized with CSK100 (10 mM MOPS (pH 7.0), 100 mM NaCl, 3 mM MgCl2, 300 mM sucrose, 0.5% Triton X-100) for 10 min at RT, gently washed twice with S1 buffer (30 mM sodium acetate (pH 4.6), 50 mM NaCl, 10 mM zinc acetate, 5% glycerol), treated with 10 U/ml S1 nuclease (Invitrogen, Cat# 18001-016) in S1 buffer for 30 min at 37 °C, and collected in 500 μl of PBS containing 1% BSA (Nacalai Tesque, Cat# 01860-07) with a cell scraper. Cell nuclei were pelleted at 4900 x g for 5 min at 4 °C, and 300 μl of the supernatant was then removed, leaving 200 µl. Cell nuclei were carefully resuspended by pipetting.

For both the standard DNA fiber assay and S1 fiber assay, 100 μl of fixative solution (3:1 MtOH:acetic acid) was added dropwise to 200 μl of cell suspension. This step was repeated 3 times, and 500 μl of fixative solution was then added; This step was repeated 2 times. Cells/nuclei were pelleted at 800 x g for 5 min at 4 °C and resuspended in fixative solution to a final concentration of ~1000 cells/μl.

Fifty microliters of fixed cells were spotted onto slides (Matsunami, Cat# S2112). After drying for 3 min, the slides were immersed in lysis solution (200 mM Tris-HCl (pH 7.5), 50 mM EDTA, 0.5% SDS) for ~20 min at 37 °C. The DNA fibers released from the cells were extended by tilting the slides in a high-humidity chamber for at least 30 min. The slides were immersed in fixative solution for 20 min and were then dried overnight (O/N) at 4 °C.

For immunostaining of DNA fibers, DNA fibers were rehydrated in PBS twice for 5 min each, immersed in 2.5 M HCl for 1 h to denature the DNA and washed with PBS 3 times for 5 min each. After blocking (5% BSA and 0.1% Tween 20 in PBS) for 1 h, the slides were incubated for ~2 h at 37 °C with anti-IdU (1:25, BD Biosciences, 347580) and anti-CldU (1:100, Abcam, ab6326) antibodies diluted in blocking solution to label the DNA, washed 3 times with PBST (PBS containing 0.1% Tween 20) and incubated for 1 h with Alexa Fluor 488-conjugated anti-rat IgG (1:500, Invitrogen, Cat# A11006) and Alexa Fluor 555-conjugated anti-mouse IgG (1:250, Invitrogen, Cat# A21422) in blocking solution. The stained slides were washed with PBST 3 times and mounted with ProLong Gold Antifade (Invitrogen, Cat# P36980).

Images were acquired with a fluorescence microscope (Celldiscoverer 7, Zeiss) and analyzed using ImageJ software (v2.0.0-rc-69, National Institutes of Health). Continuous red (IdU) and green (CldU) tracks were measured, and the distance in micrometers was converted to kilobase pairs (1 μm = 3.5 kb). Finally, the fork speed was calculated from the labeling time. A total of 200 ~ 500 fibers were measured in each sample, and 200 randomly selected fibers are shown in the figures.

Immunofluorescence staining

A total of 1 × 104 cells were plated in collagen-coated 8-well chamber dishes. Following treatments, cells were prefixed with ice-cold PBS for 5 min on ice, and a pre-extraction step was performed with pre-extraction buffer (20 mM MOPS (pH 7.0) and 0.05% Triton X-100 in PBS) for 5 min on ice. Cells were fixed with 4% paraformaldehyde (PFA) in PBS for 10 min prior to post-extraction with 0.25% Triton X-100 in PBS for 10 min. To detect incorporated native BrdU, cells were further fixed by ice-cold MtOH for 10 min. After blocking with wash buffer (3% BSA and 0.05% Tween 20 in PBS) for 1 h at 37 °C, the cells were incubated for 1 h at 37 °C or O/N at 4 °C with the following primary antibodies in wash buffer: anti-BrdU (1:1000, GE health, Cat# RPN20AB) anti-RPA32 (1:200, Abcam, Cat# ab2175), anti-phospho-RPA32 (Ser4/8) (1:200, Bethyl, # A300-245A), anti-phospho-RPA32 (Ser33) (1:200, Bethyl, # A300-246A), anti-γH2AX (1:500, Cell Signaling Technology, Cat# 9718), anti-H3K27me3 (1:500, Cell Signaling Technology, Cat# 9733), H3K9me3 (1:500, Abcam, Cat# ab8898), anti-PICH (1:250, Abnova, Cat# H00054821-B01P), and anti-phospho-HistoneH3 (Ser10) (1:500, Millipore, Cat# 06-570). The cells were washed with wash buffer 3 times and incubated with the following Alexa Fluor-conjugated secondary antibodies for 1 h at RT: Alexa 488 donkey anti-rabbit or anti-mouse IgG (H + L) (1:500, Jackson ImmunoResearch, Cat# 711-545-152 or Cat# 715-545-151) and Alexa 594 donkey anti-rabbit or anti-mouse IgG (H + L) (1:500, Jackson ImmunoResearch, Cat# 711-585-152 or Cat# 715-585-151). After 3 washes, the nuclei were stained with 1 μg/ml DAPI and mounted with VECTASHIELD. Immunofluorescence images were acquired with a fluorescence microscope (Celldiscoverer 7, Zeiss) for intensity analysis (Zen v2.6, Zeiss).

PrimPol phosphoproteomics assay

Following treatments, 1.5 × 107 cells were washed with PBS supplemented with PhosSTOP and were then lysed in 8 ml of lysis buffer (30 mM Tris-HCl (pH 7.5), 150 mM NaCl, 2.5 mM MgCl2, 0.5% NP40, PhosSTOP, cOmplete, 1 mM dithiothreitol (DTT)). After treatment with 100 U/ml benzonase for 1 h at 4 °C, the insoluble fraction was pelleted at 20000 × g for 10 min at 4 °C. The cell lysate was collected, and the protein concentration was estimated by the Bradford assay. Samples containing equal amounts of protein were incubated with an anti-myc tag antibody (15 μg/1.5 × 107 cells, MBL, Cat# M192-3) conjugated to Protein-G Sepharose beads (Cytiva, Cat# 17061802) for 4 h at 4 °C, and the beads were washed 3 times with lysis buffer. Immunoprecipitated proteins were denatured with sampling buffer and were then separated by SDS‒PAGE. Proteins were stained using SYPRO Ruby Protein Gel Stain (Invitrogen, Cat# S12000) according to the manufacturer’s instructions.

Protein bands were excised and subjected to in-gel tryptic digestion essentially as described previously90. In brief, the gel pieces were destained and washed, and after DTT reduction and iodoacetamide alkylation, the proteins were digested with trypsin O/N at 37 °C. The resulting tryptic peptides were extracted from the gel pieces by sequential treatment with 30% acetonitrile, 0.3% trifluoroacetic acid and 100% acetonitrile. The extracts were evaporated in a vacuum centrifuge to remove the organic solvent and were then desalted and concentrated with reversed-phase C18 StageTips as previously described91. Immobilized metal affinity chromatography (IMAC) enrichment of phosphopeptides was performed as previously described92.

LC‒MS/MS was performed by coupling an UltiMate 3000 Nano LC system (Thermo Fisher Scientific) and an HTC-PAL autosampler (CTC Analytics) to a Q Exactive hybrid quadrupole-Orbitrap mass spectrometer (Thermo Fisher Scientific). Peptides were delivered to an analytical column (75 μm × 30 cm, packed in-house with ReproSil-Pur C18-AQ, 1.9 μm resin, Dr. Maisch, Ammerbuch, Germany) and separated at a flow rate of 280 nl/min using an 85-min gradient from 5% to 30% of solvent B (solvent A, 0.1% formic acid (FA) and 2% acetonitrile; solvent B, 0.1% FA and 90% acetonitrile). The Q Exactive instrument was operated in data-dependent mode. Survey full-scan MS spectra (m/z 350 to 1800) were acquired in the Orbitrap at a resolution of 70,000 after ion accumulation to a target value of 3 × 106. The dynamic exclusion time was set to 20 s. The 12 most intense multiply charged ions (z ≥ 2) were sequentially accumulated to a target value of 1 × 105 and fragmented in the collision cell by higher-energy collisional dissociation (HCD) with a maximum injection time of 120 ms and a resolution of 35,000. Typical mass spectrometric conditions were as follows: spray voltage, 2 kV; heated capillary temperature, 250 °C; normalized HCD collision energy, 25%. The MS/MS ion selection threshold was set to 2.5 × 104 counts. A 2.0 Da isolation width was chosen.

Raw MS data were processed with MaxQuant (version 1.6.14.0) supported by the Andromeda search engine. The MS/MS spectra were searched against the UniProt human database (https://www.uniprot.org) with the following search parameters: full tryptic specificity, up to two missed cleavage sites, carbamidomethylation of cysteine residues as a fixed modification, and serine, threonine, and tyrosine phosphorylation, N-terminal protein acetylation and methionine oxidation as variable modifications. The false discovery rates (FDRs) of protein groups, peptides, and phosphosites were <0.01. The quantitative values of the phosphorylation sites across the fractions were automatically integrated and summarized in “Phospho (STY) Sites.txt” by MaxQuant. Peptides identified from the reversed database or identified as potential contaminants were not used subsequent analysis.

Chromatin fractionation

The fractionation method was previously described93. A total of 2 × 105 cells were plated in a 60 mm dish. Following treatments, cells were harvested with a scraper, pelleted at 800 × g for 5 min at 4 °C, and resuspended in 120 μl of PBS. Approximately 15% of the cells were collected as the input sample. The cells were pelleted again and were then resuspended in 50 μl of Solution A (10 mM HEPES-KOH (pH 7.9), 10 mM KCl, 1.5 mM MgCl2, 0.34 M sucrose, 10% glycerol, PhosSTOP, cOmplete, 1 mM DTT) supplemented with 0.2% Triton X-100. After incubation on ice for 5 min, the nuclear fraction was precipitated at 2500 x g for 5 min at 4 °C, and the supernatant was then collected as the cytosolic fraction. After washing with Solution A, the nuclear fraction was resuspended in 100 μl of Solution B (3 mM EDTA, 0.2 mM EGTA, 1 mM DTT) and incubated on ice for 20 min. The chromatin fraction was precipitated and washed with Solution B and finally pelleted at 20,000 × g for 5 min at 4 °C. The fraction samples were denatured with sampling buffer, and the protein concentration was estimated by the Bradford assay. Samples containing equal amounts of protein were resolved by SDS‒PAGE and analyzed by Western blotting.

EU incorporation assay

EU incorporation assays were performed with a Click-iT RNA Alexa Fluor 594 Imaging Kit (Invitrogen, Cat# C10330). Following treatments, cells were labeled with 1 mM EU for 1 h or 23 h and were then fixed with 4% PFA in PBS for 15 min. Fixed cells were permeabilized with 0.5% Triton X-100 for 15 min. The Click-iT reaction was performed according to the manufacturer’s instructions. Nuclei were stained with 1 µg/ml DAPI, and slides were mounted with VECTASHIELD (Vector Laboratories, Cat# H-1000). Images were acquired with a fluorescence microscope (Celldiscoverer 7, Zeiss) for intensity analysis (Zen v2.6, Zeiss).

Slot blot assay

The DNA‒RNA hybrid detection method was previously described (Matos et al., 2020). A total of 1 × 105 cells were plated in 6-well plates. Following treatments, cells were trypsinized, pelleted at 800 × g for 5 min at 4 °C, and resuspended in 200 μl of PBS. Total DNA and RNA were purified using a QIAamp DNA Mini Kit (QIAGEN, Cat# 51106) according to the manufacturer’s instructions and were then resuspended in 10 mM TE buffer (pH 8.0). To digest DNA‒RNA hybrids, the nucleic acid solution was treated with 50 mU/μl RNaseH1 (NEB, Cat# M0297) for 1 h at 37 °C, and the reaction was then terminated with 5 mM EDTA. The DNA concentration was estimated using a NanoDrop 1000 spectrophotometer (Thermo Scientific). A total of 125 ng of nucleic acids was spotted on nylon membranes (Amersham Hybond-N, GE Healthcare, Cat# RPN303N) using a BIO-DOT SF apparatus (Bio-Rad) according to the manufacturer’s instructions, and the membrane was subjected to UV crosslinking (120 mJ/cm2). As mentioned in the Western blot method, the membrane was blocked and probed with S9.6 (1:500, Millipore, Cat# MABE1095) and anti-dsDNA (1:5000, Abcam, Cat# ab27156) primary antibodies diluted in Block Ace (DS Pharma Biomedical) prior to incubation with HRP-conjugated secondary antibodies and blot development with Western Lightning Plus ECL reagent. The S9.6 signals were normalized based on the dsDNA signals to determine the relative amount of DNA:RNA hybrids.

MNase sensitivity assay

Cells (8 × 104) were plated on a collagen-coated 35 mm dish. Following treatments, cells were permeabilized with CSK100 for 10 min at RT, gently washed with MNase buffer (50 mM Tris-HCl pH 8.0, 5 mM NaCl, 5 mM CaCl2), and then treated with the 75 gelU/ml of MNase (New England Biolab, Cat# M0247S) in MNase buffer for 5 ~ 20 min at 25 °C. The MNase-treated cells were lysed in 250 μl of TES buffer (10 mM Tris-HCl pH 7.5, 10 mM EDTA, 0.5% SDS). The cell lysates were sequentially treated with 1 mg/ml RNaseA (NipponGene, Cat# 318-06391) for 45 min and with 200 μg/ml Proteinase K (QIAGEN, Cat# 19133) for 90 min at 50 °C, after which an equal volume of phenol/chloroform (NipponGene, Cat# 311-90151) was added. The insoluble fraction was pelleted at 20,000 x g, the supernatant was mixed with 0.5 M of NaCl, and an EtOH wash was performed. The extracted DNA was resuspended in TE buffer (pH 8.0), resolved by 1.2% agarose gel (Fast Gene, Cat# NE-AG02) electrophoresis at 1 μg per lane, and stained with EtBr (NipponGene, Cat# 315-90051). Images were captured with a LAS 3000 luminescent image analyzer (FujiFilm) for intensity analysis with ImageJ.

PLA

A total of 1 × 104 cells were plated in collagen-coated 8-well chamber dishes. To monitor the proximity between ssDNA gaps and H3K27me3, the cells were cultured with 10 μM BrdU (Sigma–Aldrich, Cat# B5002-1G) for 48 h and then incubated without BrdU for 24 h. S-phase cells were pulse labeled with 10 μM EdU for 30 min. As mentioned in the immunofluorescence method, cells were pre-extracted, fixed and processed with the Click-iT Plus EdU Alexa Fluor 488 Imaging Kit (Invitrogen, Cat# C10337) according to the manufacturer’s instructions prior to blocking and primary antibody incubation O/N at 4 °C. PLA was performed using Duolink In Situ PLA kits according to the manufacturer’s instructions (Sigma–Aldrich, Cat# DUO92001, Cat# DUO92005 and Cat# DUO92008) with the following primary antibodies: anti-BrdU (1:1000, GE Healthcare, Cat# RPN202) and anti-H3K27me3 (1:1600, Cell Signaling Technology, Cat# 9733) or anti-PCNA (1:500, Santa Cruz, Cat# sc-56) and anti-phospho-POLII (Ser2) (1:10000, Novus, Cat# NB100-1805). Nuclei were stained with 1 μg/ml DAPI, and slides were mounted with VECTASHIELD. Images were acquired with a fluorescence microscope (Celldiscoverer 7, Zeiss) for PLA focus counting (Zen v2.6, Zeiss) or a confocal laser scanning microscope for representative nucleus imaging (TCS SP8, Leica).

Whole-transcriptome RNA-seq

Following treatments, 1 × 106 cells were washed with PBS, and total RNA was then purified using an RNeasy Plus Mini Kit (QIAGEN, Cat# 74134) according to the manufacturer’s instructions. Paired-end sequencing with a read length of 150 bases was performed on the DNBSEQ-G400 (MGI tech) platform following the manufacturer’s instructions. Raw sequence data quality was checked with FastQC software (ver. 0.11.9). Alignment and TPM calculations were performed using Kallisto with a human cDNA reference. Output files of Kallisto (ver. 0.46.0) were converted to an expression matrix with the ‘tximport (ver. 1.18.0)’ package in R software (ver. 3.6.3). Scaled TPM counts were used for further analysis. The distributions of H3K27me3 ChIP-seq signals within gene loci were visualized with the scale-regions function of deepTools94. H3K27me3 ChIP-seq data of SAECs were provided by Suzuki, A., et al. (2014)49.

Micronucleus assay

Following treatments, cells were fixed with 4% PFA in PBS and stained with an anti-phospho-HistoneH3 (Ser10) antibody (1:500, Millipore, Cat# 06-570) as described above. After imaging with a fluorescence microscope (Celldiscoverer 7, Zeiss), the number of cells with MN or blebs was determined. Phospho-HistoneH3 (Ser10)-positive cells were omitted because of nuclear membrane disappearance. At least 200 cells were analyzed per sample (Zen v3.1, Zeiss).

Plate colony-forming efficiency assay

A total of 1 × 104 cells were plated in 6-well plates and treated with 4OHT and/or berzosertib for 6 days. The medium was changed 3 days after cell seeding. Cells were then stained with 0.5% crystal violet dissolved in 20% MtOH for 30 min and rinsed 3 times with distilled water. After drying, images of each whole 6-well plate were acquired using a LAS-3000 imager (Fujifilm). The mean gray value of each well was quantified using ImageJ.

WGS

Following treatments, ~2 × 105 cells were lysed in 250 μl of TES buffer (10 mM Tris-HCl (pH 7.5), 10 mM EDTA, 0.5% SDS). Cell lysates were sequentially treated with 1 mg/ml RNaseA (NipponGene, Cat# 318-06391) for 45 min and 200 μg/ml proteinase K (QIAGEN, Cat# 19133) for 90 min at 50 °C prior to the addition of 260 μl phenol/chloroform (NipponGene, Cat# 311-90151). The insoluble fraction was pelleted at 20,000 x g, and the supernatant was mixed with 0.5 M NaCl and washed with EtOH 2 times. Extracted DNA was resuspended in 50 μl of TE buffer (pH 8.0).

Genome library preparation was performed with a TruSeq DNA PCR-Free Library Prep Kit (Illumina). Sequencing with 150 bp paired-end reads was performed on the NovaSeq 6000 system (Illumina) at a sequencing depth of ~120x, and the sequence reads were aligned to the human reference genome (hg38) with BWA-MEM (version 0.7.17)95 according to the GATK Best Practices workflow. SAEC cells were defined as the normal-equivalent specimen, and Control-ER-Kras-G12V, RSTC#2, RSTC#5 and RSTC#7 cells were defined as tumor-equivalent specimens. Somatic SNVs and small insertions and deletions (INDELs) were called with Mutect2 (gatk version 4.1.2.0)96 with tumor-normal mode, subtracting variants in normal specimens from those in tumor specimens. These variants were filtered with FilterMutectCalls and FilterAlignmentArtifacts, and those with a variant allele frequency (VAF) of <0.1 were removed.

Structural variations were detected by the Manta program (version 1.6.0)97, which identified the break-end junction by discordant paired and split reads. To identify high-confidence rearrangements, we selected them with the following criteria: PASS in the FILTER field, VAF > 0.1 and split read >0. Circos plots were generated with the shinyCircos program (ver 1)98. Allele-specific copy numbers, tumor purity and ploidy were estimated with FACETS (version 0.6.2)99 with the recommended parameter “cval = 400”.

Single-base substitutions, excluding repeat regions, were categorized into trinucleotide contexts with SigprofilerMatrixGenerator (version 1.2.12)100, and de novo signatures were extracted with SigprofilerExtracter (version 1.1.2)101,102 using nonnegative matrix factorization (NMF) with default parameters. These signatures were decomposed to COSMIC signatures (version 3.3) using cosine similarity and assigned to each sample.

Statistical analysis

Boxplot data are presented as the biological means ± SEM for biological repetition or ± SD for technical repetition. For two-group experiments, statistical significance was determined by a t-test (see the figure legends). For multiple-group experiments, statistical significance was determined by multiple comparison test (see the figure legends). All statistical analysis were performed using Prism 9 software, with p < 0.05 considered statistically significant.

Reporting summary

Further information on research design is available in the Nature Portfolio Reporting Summary linked to this article.