Expression profile of mouse primary and recurrent breast cancer cell lines
Ontology highlight
ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE124593 | GEO | 2020/10/10
REPOSITORIES: GEO
Similar Datasets
Project description:To understand to role of RIPK3 during tumor recurrence, we performed RNAseq to study the transcriptional response of mouse recurrent breast cancer cells to RIPK3 knockdown.
2020-01-27 | GSE124634 | GEO
Project description:Expression profile of mouse primary and recurrent breast cancer cell lines
| PRJNA512619 | ENA
Project description:Despite aggressive multi-modal treatment, advanced head and neck squamous cell carcinoma (HNSCC) patients are at high risk of recurrence. Matched pairs (n=38) of primary/recurrent tumors were subjected to whole exome and RNA sequencing. Mutational landscapes and genomic copy number alterations indicated diverging clonal origins in a subset of cases. Transcriptional subtyping (classical/CL, basal/BA, inflamed-mesenchymal/IMS) in primary and recurrent HNSCC (n=112) revealed more frequent CL and IMS in primary tumors with low recurrence rates and a prevalence of BA in recurrent tumors associated with p-EMT and early recurrence. 44% of matched cases underwent a subtype change from primary to recurrent tumors, preferably from IMS to BA or CL. In recurrences, HYPOXIA, P-EMT and RADIATION RESISTANCE signatures were up- and TUMOR INFLAMMATION down-regulated compared to index tumors. A therapy-induced selection of transcriptional subtypes demonstrates the importance of molecular characterization of recurrences for second-line therapy decisions to enable optimally tailored treatments.
2022-04-08 | GSE173855 | GEO
Project description:Well-differentiated liposarcoma (WDLPS) recurs in approximately one-third of the patients. The molecular relationship between primary tumor and recurrent tumors is barely studied, but is important to reveal potential drivers of recurrence. Here we investigated the biology of recurrent WDLPS using 27 paired primary and recurrent WDLPS samples. MicroRNA expression profiles were determined using TaqMan® Low Density Array (TLDA)-cards. In the supervised clustering analyses, no clear clustering separating the primary from the recurrent tumors, based on differentially expressed microRNAs was observed. The clustering was also not based on tumor localization, time to recurrence, age or status of the resection margins. Subgroup analysis for tumors localized in the extremity or retroperitoneum also did not yield a clear distinction between primary and recurrent WDLPS. In conclusion, microRNA expression profiles do not distinguish between primary and recurrent WDLPS and no putative common drivers for recurrence could be identified.
2019-09-20 | GSE137722 | GEO
Project description:Desmoplastic small round cell tumor (DSRCT) is a rare pediatric cancer caused by the EWSR1-WT1 fusion oncogene. Despite initial response to chemotherapy, DSRCT has a recurrence rate of over 80% leading to poor patient prognosis with a 5-year survival rate of only 15-25%. Owing to the rarity of DSRCT, sample scarcity is a barrier to understanding DSRCT biology and developing effective therapies. Here, we performed RNA-sequencing on a novel pair of primary and recurrent DSRCT tumors harvested from the same patient 5-years apart. To gain insights into gene expression alterations associated with recurrence, we performed pathway analysis on Gene Ontology Biological Processes and KEGG pathways. Upregulated pathways in the recurrent tumor included DNA repair and mRNA splicing related pathways, while downregulated pathways included immune system function and focal adhesion. We further examined the expression of previously identified EWSR1-WT1 regulated targets, a large number of which were enriched in the recurrent tumor. Overall, this study provides novel understanding of DSRCT biology and a new RNA-seq data set to advance future studies.
2023-07-19 | GSE230603 | GEO
Project description:Despite aggressive multi-modal treatment, advanced head and neck squamous cell carcinoma (HNSCC) patients are at high risk of recurrence. n=19 different selected areas of matched pairs (n=3) of primary/recurrent tumor specimens were subjected to RNA sequencing. Transcriptional subtyping (classical/CL, basal/BA, inflamed-mesenchymal/IMS) in matched primary and recurrent HNSCC specimens revealed heterogeneity.
2022-04-08 | GSE186461 | GEO
Project description:Molecular profiling of breast cancer has achieved great depth in defining the mutational landscapes and molecular profiles of primary tumors, though little is still known regarding cancer evolution into a recurrence. Proteogenomic workflows are particularly useful in defining the multi-layered biology of complex diseases by combining genomic, transcriptomic, and proteomic technologies so to inform not only on mutational processes, but also on their repercussion at the effector level, proteins. We employed our recently developed proteogenomic workflow to analyze a cohort of 27 primary breast cancers and their matched loco-regional recurrences by whole genome sequencing, RNA sequencing, and mass spectrometry.
2023-02-03 | PXD032266 | Pride
Project description:We performed RNAseq to study the transcriptional changes of human CAOV2 recurrent vs CAOV2 primary ovarian cancer cells to understand the genetic determinants of ferroptosis response
2019-10-02 | GSE133663 | GEO
Project description:Glioblastoma multiforme (GBM) is the most aggressive and frequent primary brain tumor with dismal prognosis which might be due to the resistance to the current standard chemotherapeutic regimens and high recurrence rate even after total resection of GBM mass. Here, to gain the mechanistic insights on the altered phenotypic acquisition of recurrent tumors compared to the corresponding primary tumors, we performed gene expression profiling on the 43 cases of GBM tumors including 15 paired recurrent and primary GBMs. Unsupervised and consensus clustering analyses revealed two subtypes of G1 and G2, which were enriched with proliferation, and neuron-like gene expression traits, respectively. Most of the primary tumors were classified into G1, while the recurrent tumors were classified into both G1 and G2 groups. The gene expression of recurrent GBMs in G2 group have changed from proliferation type to neuron-like type, while the other recurrent GBMs in the G1 group showed no significant subtype change. In addition, we observed that the recurrent tumors in G1 subtype were characterized with the expression of stemness-related genes and DNA-repair genes. Of the G1 subtype classifier genes, AURKA/B and HOX genes were identified as key hub regulators. On the other hand, the recurrent G2 tumors have acquired the expression of MGMT but suppression of MSH6 gene, which may lead to TMZ resistance. The consistency of these findings could be validated with independent data sets. In summary, our molecular classification of recurrent GBMs could suggest that the differential mechanisms of drug resistance be involved in the tumor recurrence. Targeting the subtype-specific mechanisms might be a beneficial strategy for the treatment of recurrent GBMs.
2015-10-20 | GSE62153 | GEO
Project description:Glioblastoma multiforme (GBM) is the most lethal brain malignant neoplasm, associated with poor prognosis and high recurrence. The mechanisms involved in GBM development and recurrent remains largely unknown. Hence, it’s considerably imperative to explore the potential targets and unravel the mechanism implicated in GBM tumorigenesis and recurrence. In our study, mass spectrometry-based label-free quantitative proteomics was employed to explore the proteomic profiling in non-paired samples of primary and recurrent GBM. Bioinformatic analysis of differentially expression proteins (DEPs) were applied to screen the hub genes. Subsequently, hub genes expression was verified by western blot and immunohistochemistry (IHC) in GBM tissues, followed by its biological effect on GBM at a cellular level determined. We contoured the divergent landscape of proteome between primary and recurrent GBM, with only ten overlapped DEPs included. The several hub genes screened (e.g., CKAP4 and CANX) and enriched pathways correlated with primary GBM such as post-translation, metabolism, energy pathways and cell growth were profiled. Furthermore, CKAP4 was implicated in proliferation, migration and invasion of A172 and T98G cell lines. However, UQCRC1, together with relative enriched pathways such as oxidative phosphorylation, were screened in recurrent GBM. Establishment of the proteomics and several candidate proteins identified could pose considerable access to understand complex biochemical processes and obtain a better picture of GBM biology.
2021-06-06 | PXD026503 | iProX