Pt-seq unveils the genomic binding pattern of platinum-based drugs [Target-seq]
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ABSTRACT:
PROVIDER: PRJNA1223323 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR32329205_1.fastq.gz | Fastqsanger.gz | |||
| SRR32329205_2.fastq.gz | Fastqsanger.gz | |||
| SRR32329206_1.fastq.gz | Fastqsanger.gz | |||
| SRR32329206_2.fastq.gz | Fastqsanger.gz | |||
| SRR32329207_1.fastq.gz | Fastqsanger.gz |
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Project description:Platinum-based drugs (Pt drugs) are widely used in cancer chemotherapy, yet their genome-wide DNA binding patterns remain incompletely understood. Here, we present Pt-seq, an antibody-assisted, genome-wide method for mapping Pt-DNA adducts at single-base resolution. By employing exo- and endo- nucleases to remove background DNA, Pt-seq enables highly robust and sensitive profiling of binding sites for cisplatin, oxaliplatin, lobaplatin, and a Pt(IV) complex. Using Pt-seq, we identified hundreds to a few thousand binding clusters that are 10-20 kb in length and highly consistent among different Pt drugs. Notably, these binding clusters predominantly localize to centromeric and rDNA regions. In cisplatin-resistant cells, we found significantly reduced binding within these regions, suggesting a potential role in drug resistance. Moreover, we found that de novo mutations in cancer cells can create novel binding sites for Pt drugs. Based on this, we demonstrated that ICR-191, an acridine orange compound capable of inducing G insertions, enhances cisplatin-DNA crosslinking and sensitizes cells to Pt drugs. Collectively, Pt-seq sensitively profiles Pt drug-DNA interactions and deepens our understanding of the genome-wide effect of chemotherapeutic drugs.
2025-02-13 | GSE289501 | GEO
Project description:Pt-seq unveils the genomic binding pattern of platinum-based drugs [Pt-seq]
| PRJNA1223326 | ENA
Project description:Platinum-based drugs (Pt drugs) are widely used in cancer chemotherapy, yet their genome-wide DNA binding patterns remain incompletely understood. Here, we present Pt-seq, an antibody-assisted, genome-wide method for mapping Pt-DNA adducts at single-base resolution. By employing exo- and endo- nucleases to remove background DNA, Pt-seq enables highly robust and sensitive profiling of binding sites for cisplatin, oxaliplatin, lobaplatin, and a Pt(IV) complex. Using Pt-seq, we identified hundreds to a few thousand binding clusters that are 10-20 kb in length and highly consistent among different Pt drugs. Notably, these binding clusters predominantly localize to centromeric and rDNA regions. In cisplatin-resistant cells, we found significantly reduced binding within these regions, suggesting a potential role in drug resistance. Moreover, we found that de novo mutations in cancer cells can create novel binding sites for Pt drugs. Based on this, we demonstrated that ICR-191, an acridine orange compound capable of inducing G insertions, enhances cisplatin-DNA crosslinking and sensitizes cells to Pt drugs. Collectively, Pt-seq sensitively profiles Pt drug-DNA interactions and deepens our understanding of the genome-wide effect of chemotherapeutic drugs.
2025-02-13 | GSE289502 | GEO
Project description:Non Small Cell Lung Cancer (NSCLC) causes the premature death of over 1 million people worldwide each year, but remains inadequately understood at the molecular level. To provide new insights for NSCLC treatment we performed a molecular characterisation of wild type and platinum drugs resistance in A549 cells. Transcriptome profiling revealed contrasting patterns of gene expression in sensitive and resistant cells and identified genes whose expression was highly correlated with the platinum drugs. Our results revealed a gene set of 15 transcripts whose expression was highly correlated with platinum-resistance in NSCLC A549 cell lines.
2012-02-24 | E-MEXP-3123 | biostudies-arrayexpress
Project description:PPARγ is a member of the nuclear receptor family for which agonist ligands have anti-growth effects. However, clinical studies using PPARγ ligands as a monotherapy failed to show a beneficial effect. Here we have studied the effects of PPARγ activation with chemotherapeutic agents in current use for specific cancers. We observed a striking synergy between rosiglitazone and platinum-based drugs in several different cancers both in vitro and using transplantable and chemically induced “spontaneous” tumor models. The effect appears to be due in part to PPARγ-mediated downregulation of metallothioneins, proteins that have been shown to be involved in resistance to platinum-based therapy. These data strongly suggest combining PPARγ agonists and platinum-based drugs for the treatment of certain human cancers Keywords: Gene expression, change, synergy of interaction
2007-04-19 | GSE7035 | GEO
Project description:Pt based drugs play a very important role in current cancer treatment; yet their cellular and mechanistic aspects are not fully understood. NMR metabolomics provides a powerful tool to investigate the metabolic perturbations induced by Pt drugs in cancer cells and decipher their meaning in relation to the presumed molecular mechanisms. We have carried out a systematic and comparative NMR metabolomics study to analyze the responses of A2780 human ovarian cancer cells to the main clinically established Pt drugs, i.e. cisplatin, carboplatin and oxaliplatin, with a particular attention for the oxaliplatin/cisplatin comparison in view of recently described mechanistic differences. Notably, NMR analysis revealed some moderate and consistent changes in the metabolomic profiles of A2780 cells treated with the 3 Pt drugs with respect to controls but only very small differences among them. Beyond the expected alterations at the level of the nucleic acids the observed changes highlight in all cases induction of a significant ER stress. Owing to the clinical relevance of platinum resistance the behavior of a cisplatin resistant A2780 cancer cell line upon cisplatin treatment was also evaluated.
2022-03-22 | ST002116 | MetabolomicsWorkbench
Project description:Resistance to platinum-based chemotherapy is a clinical challenge in the treatment of ovarian cancer (OC) and limits survival. Therefore, innovative drugs against platinum-resistance are urgently needed. Our therapeutic concept is based on the conjugation of two chemotherapeutic compounds to a monotherapeutic pro-drug, which is taken up by cancer cells and cleaved into active cytostatic metabolites. Here, we explore the activity of the duplex-prodrug 5-FdU-ECyd, covalently linking 2'-deoxy-5-fluorouridine (5-FdU) and 3'-C-ethynylcytidine (ECyd), on platinum-resistant OC cells. RNA-Sequencing was used for characterization of 5-FdU-ECyd treated platinum-sensitive A2780 and isogenic platinum-resistant A2780cis.
2018-02-22 | GSE98230 | GEO
Project description:PPARγ is a member of the nuclear receptor family for which agonist ligands have anti-growth effects. However, clinical studies using PPARγ ligands as a monotherapy failed to show a beneficial effect. Here we have studied the effects of PPARγ activation with chemotherapeutic agents in current use for specific cancers. We observed a striking synergy between rosiglitazone and platinum-based drugs in several different cancers both in vitro and using transplantable and chemically induced âspontaneousâ tumor models. The effect appears to be due in part to PPARγ-mediated downregulation of metallothioneins, proteins that have been shown to be involved in resistance to platinum-based therapy. These data strongly suggest combining PPARγ agonists and platinum-based drugs for the treatment of certain human cancers Experiment Overall Design: Cells were treated with either DMSO/control, rosiglitazone, carboplatin or combination or rosiglitazone and carboplatin in duplicate for 24 hr. RNA was isolated and microarray analysis carried out by the Dana-Farber Cancer Institute Microarray Core.
2009-04-30 | E-GEOD-7035 | biostudies-arrayexpress
Project description:Pt-ttpy (tolyl terpyridin-Pt complex) covalently binds to G-quadruplex (G4) structures in vitro and to telomeres in cellulo via its Pt moiety. Here, we identified its targets in the human genome, in comparison to Pt-tpy, its derivative without G4 affinity, and cisplatin. Pt-ttpy, but not Pt-tpy, induces the release of the shelterin protein TRF2 from telomeres concomitantly to the formation of DNA damage foci at telomeres but also at other chromosomal locations. -H2AX chromatin immunoprecipitation (ChIP-seq) after treatment with Pt-ttpy or cisplatin revealed accumulation in G- and A-rich tandemly repeated sequences, but not particularly in potential G4 forming sequences. Collectively, Pt-ttpy presents dual targeting efficiency on DNA, by inducing telomere dysfunction and genomic DNA damage at specific loci.
2021-05-04 | GSE171450 | GEO
Project description:G-quadruplex DNA (G4) is a non-canonical structure forming in guanine-rich regions, which play a vital role in cancer biology and are now being acknowledged in both nuclear and mitochondrial (mt) genome. However, the impact of G4-based targeted therapy on both nuclear and mt genome, affecting mt function and its underlying mechanisms remain largely unexplored. Here, we demonstrated that the G4-binding platinum(II) complex, Pt-ttpy, shows a highest accumulation in the mitochondria of A2780 cancer cells as compared with two other platinum(II) complexes with no/weak G4-binding properties, Pt-tpy and cisplatin. Pt-ttpy induces mtDNA deletion, copy reduction and transcription inhibition, hindering mt protein translation. Functional analysis reveals potent mt dysfunction without reactive oxygen species (ROS) induction. Mechanistic study by RNA-seq, Chip- seq and CUT-RUN shows Pt-ttpy impairs most nuclear-encoded mt ribosome genes’ transcription initiation through dampening the recruiting of TAF1 and NELFB to their promoter with G4-enriched sequences. In vivo studies show Pt-ttpy's efficient anti-tumor effects, disrupting mt genome function with fewer side effects than cisplatin. This study underscores Pt-ttpy as a G4-binding platinum(II) complex, effectively targeting cancer mitochondria through dual action on mt and nuclear G4-enriched genomes without inducing ROS, offering promise for safer and effective platinum-based G4-targeted cancer therapy.
2024-06-01 | GSE249026 | GEO