Integrated transcriptome analysis of radioresistant cells revealed genes and pathways predictive of tumor response to radiotherapy and chemotherapy in breast cancer
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE210306 | GEO | 2022/08/09
REPOSITORIES: GEO
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Project description:Background: Radiotherapy plays an important role in the multimodal treatment of breast cancer. The response of a breast tumour to radiation depends not only on its innate radiosensitivity but also on tumour repopulation by cells that have developed radioresistance. Development of effective cancer treatments will require further molecular dissection of the processes that contribute to resistance. Methods: Radioresistant cell lines were established by exposing MDA-MB-231, MCF-7 and ZR-751 parental cells to increasing weekly doses of radiation. The development of radioresistance was evaluated through proliferation and colony formation assays. Phenotypic characterisation included migration and invasion assays and immunohistochemistry. Intrinsic differences and changes in response to radiation between parental and radioresistant cells were investigated by whole-transcriptome gene expression analysis. Gene enrichment and pathway-focused analyses identified signalling networks differentially activated in radioresistant cells, which were confirmed by western blotting. Results: Proliferation and colony formation assays confirmed radioresistance. Radioresistant cells exhibited enhanced migration and invasion, with evidence of epithelial-to-mesenchymal-transition, and limited activation of DNA damage and apoptotic pathways in response to 2 Gy ionising radiation. Significantly, acquisition of radioresistance in MCF-7 and ZR-751 cell lines resulted in a loss of expression of both ERα and PgR and an increase in EGFR expression; based on gene analysis they changed subtype classification from their parental luminal A to HER2-overexpressing (MCF-7 RR) and normal-like (ZR-751 RR) subtypes, indicating the extent of phenotypic changes and cellular plasticity involved in this process. Whole-transcriptome gene expression analysis identified down-regulation of ER signalling genes and up-regulation of genes associated with PI3K, MAPK and WNT pathway activity in radioresistant cell lines derived from ER+ cells; this was confirmed by western blot, which showed increased p-AKT and p-ERK expression following radiation. Conclusions: This is the first study to date that extensively describes the development and characterisation of three novel radioresistant breast cancer cell lines through both genetic and phenotypic analysis. More changes were identified between parental cells and their radioresistant derivatives in the ER+ (MCF-7 and ZR-751) compared with the ER- cell line (MDA-MB-231) model; however, multiple and likely interrelated mechanisms were identified that may contribute to the development of acquired resistance to radiotherapy.
2018-10-04 | GSE120798 | GEO
Project description:To provide preliminary insights into metabolic and lipidomic characteristics in radioresistant triple-negative breast cancer (TNBC) cells and suggest potential therapeutic targets, we performed a comprehensive metabolic and lipidomic profiling of radioresistant MDA-MB-231 (MDA-MB-231/RR) TNBC cells and their parental cells using gas chromatography-mass spectrometry and nano electrospray ionization-mass spectrometry, followed by multivariate statistical analysis. Buthionine sulfoximine (BSO) and radiation were co-treated to radioresistant TNBC cells. The level of glutathione (GSH) was significantly increased, and the levels of GSH synthesis-related metabolites, such as cysteine, glycine, and glutamine were also increased in MDA-MB-231/RR cells. In contrast, the level of lactic acid was significantly reduced. In addition, reactive oxygen species (ROS) level was decreased in MDA-MB-231/RR cells. In the lipidomic profiles of MDA-MB-231/RR cells, the levels of phosphatidylcholine (PC) and phosphatidylethanolamine (PE) were significantly increased, whereas those of most of the phosphatidylinositol species were significantly decreased. BSO sensitized MDA-MB-231/RR cells to radiotherapy, which resulted in decreased GSH level and increased ROS level and apoptosis. Radioresistant TNBC cells showed distinct metabolic and lipidomic characteristics compared to their parental cells. We suggested activated GSH, PC, and PE biosynthesis pathways as potential targets for treating radioresistant TNBC cells. Particularly, enhanced radiosensitivity was achieved by inhibition of GSH biosynthesis in MDA-MB-231/RR cells.
2021-09-22 | ST001920 | MetabolomicsWorkbench
Project description:Epitransciptomic reader, writer and eraser (RWE) proteins recognize, install, and remove modified nucleosides in RNA, which are known to play essential roles in RNA processing, splicing, and stability. Here, we established a liquid chromatography–parallel reaction monitoring (LC-PRM) method for high-throughput profiling of a total of 152 epitransciptomic RWE proteins, including 68 human epitranscriptomic RWE proteins deposited in the Modomics database. To our knowledge, this is the first report of quantifying a comprehensive list of epitranscriptomic RWE proteins using LC-PRM. To access the roles of epitranscriptomic RWE proteins in breast cancer radioresistance, we applied the LC-PRM method, in conjunction with stable isotope labelling by amino acids in cell culture (SILAC), to quantify these proteins in two pairs of matched parental/radioresistant breast cancer cells (i.e., MDA-MB-231 and MCF-7 cells, and their radioresistant counterparts, i.e., C5 and C6 cells). We found that eight epitranscriptomic RWE proteins were commonly altered by over 1.5-fold in the two pairs of matched breast cancer cells, from which TRMT1 (an m2,2G writer) may play a role in promoting breast cancer radioresistance due to its clinical relevance and correlation with DNA repair gene sets. Furthermore, we envision that the LC-PRM method is applicable for studying the roles of epitranscriptomic RWE proteins in the metastatic transformation of cancer and therapeutic resistance of other types of cancer.
2022-08-15 | PXD030387 | Pride
Project description:Radiotherapy is a commonly used treatment modality for the local control of breast cancer. However, the clinical signs of radiotherapy response are often not apparent for several weeks post-treatment. We currently lack tools to predict and/or monitor tumor responses during treatment. The aim of this study was to identify tumor secreted biomarkers of radiotherapy response. Estrogen receptor positive (ER+) MCF-7 cells were serum-starved for 2 h, and were then exposed to various doses of radiation (0, 2, 4, 6, 8 or 10 Gy). Conditioned media (CM) was harvested at 1, 2, 4, 8 and 24 h post-radiation for each radiation dose. Samples underwent processing for liquid chromatography-mass spectrometry (LC-MS) following collection. 33 proteins at the 24 h time point were found to have significantly increased secretion levels (up to 12-fold) at all radiation doses compared to untreated cells. To validate the secretomic results and to further investigate the potential use of these proteins as biomarkers of radiosensitivity, the secreted protein levels of candidate biomarkers were assessed through western blot (WB). WB analysis was performed using CM samples to assess the secretion levels from parental and radioresistant (RR) cell lines (developed within our lab) 24 h after the cells had received a single radiation dose of 2 Gy. Secretion levels of our candidate biomarkers were found to be significantly increased from the radiosensitive MCF-7 cells treated with 2 Gy of radiation at 24 h compared to 24 h untreated controls. In comparison, candidate biomarker levels in the CM samples from untreated and radiation-treated MCF-7 RR cells remained low. Currently there are no validated predictive biomarkers to monitor radiotherapy responses during treatment. These biomarkers could have a clinical role in personalising radiotherapy dosing schedules and durations for solid tumours in the neoadjuvant and palliative setting.
2021-08-13 | PXD027572 | Pride
Project description:Background: Research using in vitro canine mammary carcinoma cell lines and studies involving naturally occurring canine mammary tumours are not only fundamental models used to advance the understanding of cancer in veterinary patients but are also regarded as excellent translational models for human breast cancer. In human medicine, following disease classification and staging breast cancer is typically treated with multimodal therapies including radiotherapy. The response of a breast tumour to radiation depends not only on its innate radiosensitivity but also on tumour repopulation by cells that have developed radioresistance. Comparative canine and human studies investigating the molecular mechanisms of radioresistance may lead to the development of effective cancer treatments that benefit both species. Methods: Human (MDA-MB-231, MCF-7 and ZR-751) and canine (REM-134) radioresistant cell lines were established by exposing parental cells to increasing weekly doses of radiation. The development of radioresistance was evaluated through proliferation and colony formation assays. Phenotypic characterisation included migration and invasion assays and immunohistochemistry. Intrinsic differences between parental and radioresistant cells were investigated by whole-transcriptome gene expression analysis. Gene enrichment and pathway-focused analyses identified signalling networks differentially activated in radioresistant cells. Results: Colony formation assays identified a range of intrinsic radiosensitivities in the human and canine parental cell lines with the REM-134 cell line showing significantly greater radioresistance compared to the human cell lines. Colony formation and proliferation assays confirmed radioresistance in all developed radioresistant cell lines. Radioresistant cells exhibited enhanced migration and invasion, with evidence of epithelial-to-mesenchymal-transition. Gene analysis identified that following the acquisition of radioresistance in MCF-7 and ZR-751 cell lines the cell lines changed subtype classification from their parental luminal A to HER2-overexpressing (MCF-7 RR) and normal-like (ZR-751 RR) subtypes, indicating the extent of phenotypic changes and cellular plasticity involved in this process. MDA-MB-231 and MDA-MB-231 RR cell lines both classified as basal, whereas the REM-134 and REM-134 RR cell lines with enriched for HER2 overexpression. Whole-transcriptome gene expression analysis identified down-regulation of ER signalling genes and up-regulation of genes associated with PI3K, MAPK and WNT pathway activity in radioresistant cell lines derived from ER+ cells; this was confirmed by western blot, which showed increased p-AKT and p-ERK expression following radiation. Conclusions: To our knowledge, our study is the first to develop a canine radioresistant cell line and provide a comparative genetic and phenotypic analysis of the mechanisms of acquired radioresistance between canine and human cell lines. The cellular process that occur with the development of acquired radioresistance are similar between the human and canine cell lines; this suggests that not only is the canine model an appropriate model to study human disease but that treatment strategies used in human medicine may also be applicable to veterinary patients.
2020-07-08 | GSE149988 | GEO
Project description:For atypical meningiomas (AM), the combination of gross total resection (GTR) and adjuvant radiotherapy (ART) is still a controversial therapeutic strategy to improve prognosis. This study analysed the factors influencing the prognosis on AM patients treated with GTR+ART by investigating both clinical characteristics and the change in microRNA (miRNA) expression.Adult AM patients who were admitted to the Tiantan hospital from 2008 to 2015 and underwent GTR+ART were included. Patients who suffered recurrence within 3 years after operation were considered radioresistant, while the others were considered radiosensitive. Clinical characterizations were compared between these two groups. The miRNAs expression was detected via miRNA microarray in 10 patients, 5 from the radiosensitive group and 5 from the radioresistant group.No significant difference was found in the clinical characteristics. between radiosensitive and radioresistant patients. We found 7 significantly upregulated miRNAs and 7 significantly downregulated miRNAs in patients resistant to radiotherapy. The differentially expressed miRNAs were enriched mostly in the Fatty acid metabolic pathways (hsa00061, hsa01212) and TGF-β signalling pathway (hsa04350). For AM patients treated with GTR+ART, the changes in miRNA expression discovered in this study may be a potential predictor of individual sensitivity to adjuvant radiotherapy. Further research is needed regarding the predictive power and mechanism by which these miRNAs influence prognosis.
2020-01-23 | GSE144037 | GEO
Project description:We established radioresistant cell sublines, named as BxPC3/RR1 and BxPC3/RR2 which were derived from parental human pancreatic cancer cell line BxPC3. The miRNA expression profiles of the radioresistant pancreatic cancer cells were then compared with their parental cells. Three samples were analysed. miRNAs that were differentially expressed (increased or decreased in expression by M-bM-^IM-%1.5-fold) between the radioresistant and parental cells were identified.
2013-07-01 | E-GEOD-41249 | biostudies-arrayexpress
Project description:We established radioresistant cell sublines, named as BxPC3/RR1 and BxPC3/RR2 which were derived from parental human pancreatic cancer cell line BxPC3. The miRNA expression profiles of the radioresistant pancreatic cancer cells were then compared with their parental cells.
2013-07-01 | GSE41249 | GEO
Project description:SN-38 resistant breast cancer cell lies (MCF-7 and MDA-MB-231) were established by stepwise increasing the concentration of SN-38. Gene expression profiling was performed on parental (sensitive) MCF-7 and parental (sensitive) MDA-MB-231 cell lines and their respective SN-38 resistant cell lines. For each cell line we harvested RNA from three independent passages and conducted 3 arrays.
2016-01-05 | E-MTAB-3224 | biostudies-arrayexpress
Project description:Most of the NPC patients suffer from local recurrences and distant metastases within 1.5 years after radiotherapy due to radioresistance. Distinct patterns of gene expression and signatures were found in NPC, and have been used to associate them with cell proliferation, apoptosis, invasion and metastasis, but few gene expression profiling studies have been focused on the tumor radioresistance.We used gene expression microarray analyses to identify the difference of mRNA in radioresistant NPC CNE2-IR cells and radiosensitive CNE2 cells. Radioresistant subclone of nasopharyngeal carcinoma CNE2-IR cell line was cultured and produced according to the experienment schedule to undergo five rounds of sublethal dose of irradiation (11 Gy), and the parent cell line CNE2 cell line sensitive to radiotherapy as the control
2013-12-10 | E-GEOD-48501 | biostudies-arrayexpress