DNA methylation and RNA-seq profiling of 2Rv1 prostate cancer cells exposed to repeated DNA damage
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA858764 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR20204114.fastq.gz | Fastqsanger.gz | |||
| SRR20204115.fastq.gz | Fastqsanger.gz | |||
| SRR20204116.fastq.gz | Fastqsanger.gz | |||
| SRR20204117.fastq.gz | Fastqsanger.gz | |||
| SRR20204118.fastq.gz | Fastqsanger.gz |
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Project description:DNA damage is frequently utilized as the basis for cancer therapies; however, resistance to DNA damage remains one of the biggest challenges facing cancer patients and their treating clinicians. Critically, the molecular drivers behind resistance are poorly understood. To address this question, we created an isogenic model of prostate cancer exhibiting more aggressive characteristics to better understand the molecular signatures associated with resistance and metastasis. 22Rv1 cells were repeatedly exposed to DNA damage daily for 6 weeks, similar to patient treatment regimes. Using Illumina MethylationEPIC arrays and RNA-seq, we compared the DNA methylation and transcriptional profiles between the parental 22Rv1 cell line and the lineage exposed to prolonged DNA damage. Here we show that repeated DNA damage drives the molecular evolution of cancer cells to a more aggressive phenotype and identify molecular candidates behind this process. Total DNA methylation was increased in cells exposed to repeated DNA damage. Further, RNA-seq demonstrated these cells had dysregulated expression of genes involved in metabolism and the unfolded protein response (UPR) with ASNS identified as central to this process. While limited overlap between RNA-seq and DNA methylation was evident, OGDHL was identified as altered in both data sets. Utilising a second approach we profiled the proteome in 22Rv1 cells following a single dose of radiotherapy. This analysis also highlighted the UPR in response to DNA damage. Together, these analyses identified dysregulation of metabolism and the UPR and identified ASNS and OGDHL as candidate genes for resistance to DNA damage. This work provides critical insight into molecular changes which may underpin treatment resistance and metastasis.
2023-04-27 | PXD033400 | Pride
Project description:RNA-seq profiling of 22Rv1 prostate cancer cells exposed to repeated DNA damage for 6 weeks.
| PRJNA858768 | ENA
Project description:DNA methylation profiling of prostate cancer cells exposed to daily DNA damage
| PRJNA858767 | ENA
Project description:RNA-seq profiling of 22Rv1 prostate cancer cell line either untreated, 6 weeks in culture (age matched) or treated daily for 6 weeks with 1 microgram per ml phleomycin to induce DNA damage (n=3 per sample).
2022-07-18 | GSE208190 | GEO
Project description:Illumina Infinium MethylationEPIC BeadChip profiling of 22Rv1 prostate cancer cell line either untreated, 6 weeks in culture (age matched) or treated daily for 6 weeks with 1 microgram per ml phleomycin to induce DNA damage (n=2 per sample).
2022-07-18 | GSE208189 | GEO
Project description:Acute damage to the intestinal epithelium can be repaired via de-differentiation of mature intestinal epithelial cells to a stem cell state, but there is a lack of knowledge on how these stem cells function after chronic injury, such as in inflammatory bowel disease (IBD). We developed a chronic injury model in human colonoid monolayers by repeated rounds of air-liquid interface and submerged growth. We used this model to understand how chronic intestinal damage affects the ability of IECs to respond to microbial stimulation, using the TLR5 agonist FliC; and to regenerate and protect the epithelium from further damage. Here, we profiled the effect of repeated rounds of damage on global DNA methylation levels of these human colonid monolayers. We observed a trend towards global demethylation with repeated damage, including in loci associated with genes implicated in DNA repair (NHEJ1) and colon hemostatsis and inflammation regulation (FAM3D).
2021-06-23 | GSE178700 | GEO
Project description:Targetted metabolomics in U2OS PRDX1 WT and PRDX1-/- While cellular metabolism impacts the DNA damage response, a systematic understanding of the metabolic requirements that are crucial for DNA damage repair has yet to be achieved. Here, we investigate the metabolic enzymes and processes that are essential when cells are exposed to DNA damage. By integrating functional genomics with chromatin proteomics and metabolomics, we provide a detailed description of the interplay between cellular metabolism and the DNA damage response. Subsequent analysis identified Peroxiredoxin 1, PRDX1, as fundamental for DNA damage repair. During the DNA damage response, PRDX1 translocates to the nucleus where it is required to reduce DNA damage-induced nuclear reactive oxygen species levels. Moreover, PRDX1 controls aspartate availability, which is required for the DNA damage repair-induced upregulation of de novo nucleotide synthesis. Loss of PRDX1 leads to an impairment in the clearance of γΗ2ΑΧ nuclear foci, accumulation of replicative stress and cell proliferation defects, thus revealing a crucial role for PRDX1 as a DNA damage surveillance factor.
2022-07-19 | ST002234 | MetabolomicsWorkbench
Project description:Heldt2018 - Proliferation-quiescence decision
in response to DNA damage
This model is described in the article:
A comprehensive model for
the proliferation-quiescence decision in response to endogenous
DNA damage in human cells.
Heldt FS, Barr AR, Cooper S, Bakal
C, Novák B.
Proc. Natl. Acad. Sci. U.S.A. 2018 Feb;
:
Abstract:
Human cells that suffer mild DNA damage can enter a
reversible state of growth arrest known as quiescence. This
decision to temporarily exit the cell cycle is essential to
prevent the propagation of mutations, and most cancer cells
harbor defects in the underlying control system. Here we
present a mechanistic mathematical model to study the
proliferation-quiescence decision in nontransformed human
cells. We show that two bistable switches, the restriction
point (RP) and the G1/S transition, mediate this decision by
integrating DNA damage and mitogen signals. In particular, our
data suggest that the cyclin-dependent kinase inhibitor p21
(Cip1/Waf1), which is expressed in response to DNA damage,
promotes quiescence by blocking positive feedback loops that
facilitate G1 progression downstream of serum stimulation.
Intriguingly, cells exploit bistability in the RP to convert
graded p21 and mitogen signals into an all-or-nothing
cell-cycle response. The same mechanism creates a window of
opportunity where G1 cells that have passed the RP can revert
to quiescence if exposed to DNA damage. We present experimental
evidence that cells gradually lose this ability to revert to
quiescence as they progress through G1 and that the onset of
rapid p21 degradation at the G1/S transition prevents this
response altogether, insulating S phase from mild, endogenous
DNA damage. Thus, two bistable switches conspire in the early
cell cycle to provide both sensitivity and robustness to
external stimuli.
This model is hosted on
BioModels Database
and identified by:
MODEL1703030000.
To cite BioModels Database, please use:
Chelliah V et al. BioModels: ten-year
anniversary. Nucl. Acids Res. 2015, 43(Database
issue):D542-8.
To the extent possible under law, all copyright and related or
neighbouring rights to this encoded model have been dedicated to
the public domain worldwide. Please refer to
CC0
Public Domain Dedication for more information.
2024-09-02 | BIOMD0000000700 | BioModels
Project description:The small heat shock protein Hsp27 has been long demonstrated as a major driver of Castration Resistant Prostate Cancer (CRPC) progression via an androgen receptor-independent pathway. In the light of identification of its molecular mechanisms, we found that the RNA helicase protein DDX5 was an interactor of Hsp27 and DDX5 expression was regulated by Hsp27 through its cytoprotective function. We showed that DDX5 was overexpressed in a large collection of human samples in aggressive PCs, especially CRPC. Here, we described the protein-protein interaction network of DDX5 which were identified in four human prostate cell lines (PNT1A, LNCaP, DU-145 and PC-3) representing different disease stages using immunoaffinity purification and quantitative mass spectrometry. The DDX5 interactome in CRPC cells was enriched in several functions (DNA damage response, translation, transcription, RNA stability, and DNA conformation changes) involved in disease progression. Furthermore, we found a new critical function of DDX5 in DNA damage repair in CRPC and validated the interaction of DDX5 with the DNA repair complex Ku70/Ku86 which plays a pivotal role in the NHEJ process. We also showed that DDX5 overexpression conferred resistance to DNA damage poisoners (such as irradiation and cisplatin) in CRPC, a feature that could lead to genome maintenance, tumor progression and treatment resistance.
2022-08-21 | PXD023252 | Pride
Project description:Prostate cancer is the second most occurring cancer in men worldwide, and with the advances made with screening for prostate-specific antigen, it has been prone to early diagnosis and over-treatment. To better understand the mechanisms of tumorigenesis and possible treatment responses, we developed a mathematical model of prostate cancer which considers the major signalling pathways known to be deregulated. The model includes pathways such as androgen receptor, MAPK, Wnt, NFkB, PI3K/AKT, MAPK, mTOR, SHH, the cell cycle, the epithelial-mesenchymal transition (EMT), apoptosis and DNA damage pathways. The final model accounts for 133 nodes and 449 edges. We applied a methodology to personalise this Boolean model to molecular data to reflect the heterogeneity and specific response to perturbations of cancer patients, using TCGA and GDSC datasets.
2022-06-22 | MODEL2106070001 | BioModels