ENCODE Project at UCSC -

U2OS (ATCC; HTB-96), Saos-2 (ATCC; HTB-85) and HOS (ATCC; CRL-1543) cell lines were obtained from ATCC. The HeLa (LT, long telomere) cell line was validated using short-tandem-repeat profiling by ATCC’s cell line authentication services. The LM216J/T cells (described initially by J. P. Murnane) were provided by R. Greenberg. U2OS cells with a doxycycline-inducible ATRX allele were provided by D. Clynes26. SV40 large T-antigen immortalized IMR90 control and ATRX-KO ALT IMR90 cells were previously described and provided by H. Zheng and J. Paik8. U2OS cells stably expressing SNAP-tagged CENP-A were provided by G. Almouzni13,29. All of the cell lines were cultured in GlutaMax-DMEM supplemented with 10% bovine growth serum or fetal calf serum, non-essential amino acids and penicillin–streptomycin under 20% O2 and 7.5% CO2 at 37 °C. Cell lines were routinely tested for mycoplasma contamination. Plasmids Y. Dalal previously described and provided the GFP-tagged HJURP WT plasmid51. The GFP-tagged HJURP deletion mutants, Δ1-80aa and ΔTLTY box42, were generated as variants of this plasmid in this study. D. R. Foltz provided GFP-tagged Mis18BP1 (ref. 52) and YFP-H3CATD (ref. 30). pBabe-SNAP-CENP-A-HA were previously described and provided by L. Jansen13. Flag-tagged TRF1-FokI WT and D450A plasmids were gifts from R. Greenberg37,38. pINDUCER dCas9-TET1-CD plasmids53...

Human embryonic lung MRC5 fibroblasts (ATCC) and IMR90 fibroblasts (ATCC) were cultured in Dulbecco’s modified Eagle’s medium (Sigma Aldrich, D5796) supplemented with 10% heat-inactivated fetal bovine serum (FBS), 100 U ml−1 penicillin, 100 μg ml−1 streptomycin and 2 mM l-glutamine. The cultures were maintained at 37 °C in an atmosphere of 5% CO2. MRC5 fibroblasts were grown under atmospheric oxygen conditions, and IMR90 fibroblasts were cultured under low-oxygen (3%) conditions. Cells were tested regularly for mycoplasma contamination. For lentiviral transduction HEK293T cells (ATCC) were used, cultured in DMEM without antibiotic and supplemented with 10% heat-inactivated fetal bovine serum (FBS) and 2 mM l-glutamine. Stress-induced senescence was triggered by exposing cells to 20 Gy of X-ray irradiation and collected between 10 and 12 days post-irradiation. Chemotherapy-induced senescence was performed by treated cells with 250 nM of doxorubicin (MedChemExpress, HY-15142) for 24 h and collected 12 days after treatment. Replicative senescence was performed through serially passaging until the cells reached their replicative limit. Senescence was verified through the presence of p16 and p21, lack of proliferation and the expression of SASP genes. For chronic acetate treatment, MRC5 or Parkin IMR90 cells were treated with 20 mM of sodium acetate solution (Sigma, S7899)...

To identify vulnerabilities of senescent cells, we took advantage of a library of electrophilic compounds (Methods) to conduct a senolytic screen (Fig. 1a and Extended Data Fig. 1a). We screened IMR90 primary human lung fibroblasts expressing an ER:RAS fusion protein, a model of oncogene-induced senescence (OIS)19,21,33. Treatment with 4-hydroxytamoxifen (4-OHT) activates ER:RAS, inducing senescence (Supplementary Fig. 1). Senolytic drugs such as the BCL2 family inhibitors ABT-263 and ABT-73723,24,34 selectively killed senescent IMR90 ER:RAS cells when compared with non-senescent controls (Extended Data Fig. 1b). The library comprised 10,480 electrophilic compounds with diverse warheads that target cysteines (for example, acrylamides and chloroacetamides) or other nucleophilic residues (for example, aldehydes and boronic acids) (Extended Data Fig. 1a). In the screen, we compared the effect that electrophiles (at 10 μM) had on the viability of senescence and normal cells, identifying 72 candidates with senolytic activity (Fig. 1b,c and Supplementary Table 1). We retested these compounds in IMR90 ER:RAS cells, and in a melanoma cell line, SK-MEL-103, in which we induced senescence by treatment with the chemotherapeutic agent etoposide or the Aurora kinase inhibitor tozasertib (Supplementary Fig. 2). We calculated the half maximal effective concentration (EC50) across dose–response series in control and senescent cells. The...

Human embryonic lung MRC5 fibroblasts and IMR90 fibroblasts were grown in Dulbecco’s Modified Eagle’s Medium (Sigma, D5796) supplemented with 10% heat-inactivated fetal bovine serum (FBS), 100 units/ml penicillin, 100 μg/ml streptomycin, and 2 mM L-glutamine and maintained at 37 °C...

MEFs and HeLa cells were maintained in DMEM-GlutaMAX (Thermo Fisher Scientific) containing 4.5 g l−1 of glucose supplemented with 1 mM sodium pyruvate (Gibco), 100 μM non-essential amino acids (Gibco) and 10% FBS (Biochrom). IMR90 cells were maintained in MEM-GlutaMAX...

We downloaded Hi-C matrices for HCT116 (ref. 26), mESC27, K562, and IMR90 cell lines from the 4DN portal and the Gene Expression Omnibus (Table 1). We binned the Hi-C matrix for HCT116, K562, and IMR90 cells at 30-kb resolution and...

Purpose: This study aims to investigate the FLASH irradiation effect on lung tumor (A549) and health

Purpose: This study aims to investigate the FLASH irradiation effect on lung tumor (A549) and health