From mouse to humans: detecting preventing vaccination targets associated to breast cancer stem cells. Exon-level analysis
Ontology highlight
ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE21475 | GEO | 2013/11/30
SECONDARY ACCESSION(S): PRJNA129519
REPOSITORIES: GEO
Similar Datasets
Project description:TuBo cell line (E) was compared to passage 1 (P1), 2 (P2) and 3 (P3) mammospheres to detect specific transcription isoforms associated to cancer stem cell. TuBo cell line (E) was compared to passage 1 (P1), 2 (P2) and 3 (P3) mammospheres. Exon-level transcription profiling was done using Affimetrix GeneChip Exon 1.0 ST. Exon-level analysis is more complex than gene-level analysis. The number of probesets to be investigated is at least 10 times larger in number than gene-level probesets. Thus results, upon statistical analysis, are massively contaminated by type I statistical errors, i.e. false positive [Della Beffa et al. 2008]. Furthermore, exon-level probesets are based only on four probes, which makes exon-level signal summarization more noisy than gene-level, where signal summarization is based on the overall probes encompassed by all exons of a gene. To moderate these issues we have expanded the number of experimental replications: six for TuBo and passage 1 mammosphere, four for passage 3 mammosphere and three for passage 2 mammosphere. Furthermore, after data summarization with RMA and normalization with sketch quantile method, alternative splicing detection between epithelial and mammospheres passages, was assessed using MiDAS, a two way anova developed by Affymetrix for the detection of alternative splicing events. We considered suitable for further investigations the splicing events in common between the sets of exons detected as spliced in each of the following comparisons: E vs P1, E vs P2 and E vs P3.
2013-11-30 | E-GEOD-21475 | biostudies-arrayexpress
Project description:The efficacy of cancer treatments have improved constantly in the last decade. However, therapeutic resistance and the lack of curative treatments in metastatic disease, raises the question if conventional anticancer therapies target the right cells. Indeed, these treatments might miss cancer stem cells (CSCs), which might also represent a more chemoresistant and radioresistant subpopulation within cancer. In this view using vaccines in tertiary prevention of cancer, i.e. residual disease treatment, might be particularly effective if vaccine-elicited immune response is directed against CSC oncoantigens (OAs) — proteins required for the neoplastic process — the chance that the tumour will evade the vaccine should be reduced. An important task to devise effective CSC preventive vaccines is therefore the identification of CSC OAs. We used gene-level transcription profiling of TuBo epithelial cell and three mammosphere passages (P1, P2 and P3). This analysis allowed the identification of two new breast cancer CSC OAs: TMPRSS4 and xCT. Both genes are linked to invasion, migration and metastasis. These results were achieved integrating data derived by the analysis of transcription profile of CSCs derived by BALB-neuT mouse breast cancer model with meta-analyses of seven large independent breast tumour data sets. TuBo cell line (E) was compared to passage 1 (P1), 2 (P2) and 3 (P3) mammospheres (three independent experiments for each experimental condition). Transcription profiling was done using MouseWG-6 v2.0 Illumina beadchips. After normalization and removal of non significant probes (i.e. those not expressed and those not changing) differential expression between epithelial and mammospheres, was assessed using regularized t-test comparing each mammosphere passage with respect to TuBo cells using a FDR ≤ 0.05 together with an |log2(fold-change)|≥1. The union of the three sets of differentially expressed transcripts produced a total of 495 transcripts.
2013-11-30 | E-GEOD-21451 | biostudies-arrayexpress
Project description:The efficacy of cancer treatments have improved constantly in the last decade. However, therapeutic resistance and the lack of curative treatments in metastatic disease, raises the question if conventional anticancer therapies target the right cells. Indeed, these treatments might miss cancer stem cells (CSCs), which might also represent a more chemoresistant and radioresistant subpopulation within cancer. In this view using vaccines in tertiary prevention of cancer, i.e. residual disease treatment, might be particularly effective if vaccine-elicited immune response is directed against CSC oncoantigens (OAs) M-bM-^@M-^T proteins required for the neoplastic process M-bM-^@M-^T the chance that the tumour will evade the vaccine should be reduced. An important task to devise effective CSC preventive vaccines is therefore the identification of CSC OAs. In this experiment we used a cell line (TuBo) derived by the mouse breast cancer model BALB-neuT and its CSC subpupolation, enriched by mean of mammosphere formation. Integrating data derived by gene and exon-level transcription profiling of the above experiments with public available normal and tumor datasets we identified two new breast cancer CSC OAs: TMPRSS4 and xCT. Both genes are linked to invasion, migration and metastasis. Furthermore, we observed that alternative splicing events discriminating TuBo cells, grown in adherent medium, with respect of TuBo mammospheres, produced growing in no-adherent medium, are very limited. We detect only one clear splcing event characterizing the beta-isoform of Rabgap1l gene. This SuperSeries is composed of the SubSeries listed below. The adherent TuBo epithelial cells were generated from a mammary carcinoma arising in a BALB/c mouse female transgenic for the activated rat ErbB2 oncogene (BALB-neuT) and were cultured in DMEM supplemented with 20% FCS. Single TuBo cells were plated in ultra low attachment flasks in serum-free DMEM-F12 medium supplemented with bFGF, EGF and insulin. Nonadherent spherical clusters of cells, named mammospheres, were collected by gentle centrifugation after 7 days and dissociated enzymatically and mechanically, using trypsin and pipetting, respectively.
2013-11-30 | E-GEOD-21486 | biostudies-arrayexpress
Project description:The efficacy of cancer treatments have improved constantly in the last decade. However, therapeutic resistance and the lack of curative treatments in metastatic disease, raises the question if conventional anticancer therapies target the right cells. Indeed, these treatments might miss cancer stem cells (CSCs), which might also represent a more chemoresistant and radioresistant subpopulation within cancer. In this view using vaccines in tertiary prevention of cancer, i.e. residual disease treatment, might be particularly effective if vaccine-elicited immune response is directed against CSC oncoantigens (OAs) — proteins required for the neoplastic process — the chance that the tumour will evade the vaccine should be reduced. An important task to devise effective CSC preventive vaccines is therefore the identification of CSC OAs. We used gene-level transcription profiling of TuBo epithelial cell and three mammosphere passages (P1, P2 and P3). This analysis allowed the identification of two new breast cancer CSC OAs: TMPRSS4 and xCT. Both genes are linked to invasion, migration and metastasis. These results were achieved integrating data derived by the analysis of transcription profile of CSCs derived by BALB-neuT mouse breast cancer model with meta-analyses of seven large independent breast tumour data sets.
2013-11-30 | GSE21451 | GEO
Project description:The efficacy of cancer treatments have improved constantly in the last decade. However, therapeutic resistance and the lack of curative treatments in metastatic disease, raises the question if conventional anticancer therapies target the right cells. Indeed, these treatments might miss cancer stem cells (CSCs), which might also represent a more chemoresistant and radioresistant subpopulation within cancer. In this view using vaccines in tertiary prevention of cancer, i.e. residual disease treatment, might be particularly effective if vaccine-elicited immune response is directed against CSC oncoantigens (OAs) — proteins required for the neoplastic process — the chance that the tumour will evade the vaccine should be reduced. An important task to devise effective CSC preventive vaccines is therefore the identification of CSC OAs. In this experiment we used a cell line (TuBo) derived by the mouse breast cancer model BALB-neuT and its CSC subpupolation, enriched by mean of mammosphere formation. Integrating data derived by gene and exon-level transcription profiling of the above experiments with public available normal and tumor datasets we identified two new breast cancer CSC OAs: TMPRSS4 and xCT. Both genes are linked to invasion, migration and metastasis. Furthermore, we observed that alternative splicing events discriminating TuBo cells, grown in adherent medium, with respect of TuBo mammospheres, produced growing in no-adherent medium, are very limited. We detect only one clear splcing event characterizing the beta-isoform of Rabgap1l gene. This SuperSeries is composed of the SubSeries listed below.
2013-11-30 | GSE21486 | GEO
Project description:The efficacy of cancer treatments have improved constantly in the last decade. However, therapeutic resistance and the lack of curative treatments in metastatic disease, raises the question if conventional anticancer therapies target the right cells. Indeed, these treatments might miss cancer stem cells (CSCs), which might also represent a more chemoresistant and radioresistant subpopulation within cancer. In this view using vaccines in tertiary prevention of cancer, i.e. residual disease treatment, might be particularly effective if vaccine-elicited immune response is directed against CSC oncoantigens (OAs) — proteins required for the neoplastic process — the chance that the tumour will evade the vaccine should be reduced. An important task to devise effective CSC preventive vaccines is therefore the identification of CSC OAs. We used gene-level transcription profiling of TUBO mouse breast cancer epithelial cell and one mammosphere passage (P1). This analysis allowed the identification of some interesting CSC OAs which are undergoing further studies.
2014-12-31 | GSE60648 | GEO
Project description:Transcriptome profile was obtained from a set of human embryonic stem cell (hESCs) line (WA09: H9) with different passage numbers (P1: 40s, P2: 100s, P3: 200s, P4: 300s passage). Culture adaptation occurs in hESCs during repeated in vitro culture to acquire ‘survival advantage’ to be highly resistant to various stresses. In special, difference in gene expression profile of cell death or apoptotic gene signature was evident between P1/P2 and P3/P4 hESCs.
2018-09-04 | GSE119386 | GEO
Project description:The efficacy of cancer treatments has improved constantly in the last decade. However, therapeutic resistance and the lack of curative treatments in metastatic disease, raises the question if conventional anticancer therapies target the right cells. Indeed, these treatments might miss cancer stem cells (CSCs), which might also represent a more chemoresistant and radioresistant subpopulation within cancer. In this view using vaccines in tertiary prevention of cancer, i.e. residual disease treatment, might be particularly effective if vaccine-elicited immune response is directed against CSC oncoantigens (OAs) — proteins required for the neoplastic process — the chance that the tumour will evade the vaccine should be reduced. An important task to devise effective CSC preventive vaccines is therefore the identification of CSC OAs. We used gene-level transcription profiling of B16 mouse melanoma epithelial cell and one mammosphere passage (P1). This analysis allowed the identification of some interesting CSC OAs which are undergoing further studies.
2014-12-31 | GSE60556 | GEO
Project description:The efficacy of cancer treatments have improved constantly in the last decade. However, therapeutic resistance and the lack of curative treatments in metastatic disease, raises the question if conventional anticancer therapies target the right cells. Indeed, these treatments might miss cancer stem cells (CSCs), which might also represent a more chemoresistant and radioresistant subpopulation within cancer. In this view using vaccines in tertiary prevention of cancer, i.e. residual disease treatment, might be particularly effective if vaccine-elicited immune response is directed against CSC oncoantigens (OAs) — proteins required for the neoplastic process — the chance that the tumour will evade the vaccine should be reduced. An important task to devise effective CSC preventive vaccines is therefore the identification of CSC OAs. We used gene-level transcription profiling of CT26 mouse colon carcinoma epithelial cell and one spheroid passage (P1). This analysis allowed the identification of some interesting CSC OAs which are undergoing further studies.
2014-12-31 | GSE60647 | GEO
Project description:In the past few years, mammary cancer initiating cells (CICs) have been identified in mouse and human as a subpopulation of tumor cells that selectively posses tumor initiation and self-renewal capacity and the ability to give rise to bulk populations of non-tumorigenic cancer cells progeny through differentiation. They could also be responsible for tumor progression, metastasis, resistance to therapy and recurrence. Thus, the understanding of the pathways regulating CIC self-renewal, differentiation and tumorigenicity represents an important task in the development of effective anticancer therapies. To detect the set of genes associated to CIC in our mouse breast cancer model we analysed three prototypic situations: TUBO cells grown in DMEM under adherent conditions (called TDA in GSE26517 and epithelial bulk in GSE21451), TUBO cells grown in mammosphere medium under adherent conditions (called TMA in GSE26517), TUBO cells grown in mammosphere medium under low-attachment conditions (called mammospheres p1 in GSE21451), i.e. the conditions used to support the formation of mammospheres. This analysis led to the identification of growth factors and immune system-related genes, including toll-like receptor 2 (TLR2). The inhibition of TLR2 signaling pathway strongly impaired mammosphere generation, demonstrating the involvement of TLR2 in CSC self-renewal. We profiled on MouseWG?6 v2.0 Illumina beadchips two independent experiments: ADHERENT (GSE26517) made by the comparison between TDA and TMA and SOSPENSION (part of GSE21451) made by the comparison between epithelial bulk and mammospheres p1. Mammosphere medium contains epidermal growth factor (EGF), insulin and basic fibroblast growth factor (bFGF) that may influence transcript expression in a way not necessarily related to the assembly of mammospheres. Therefore, following normalization and removal of those transcripts not expressed and not changing, we used the Integrative Correlation coefficient (IC, Parmigiani et al. Clin Cancer Res 2004, 10:2922–2927) as filter to remove genes only associate to growth factors present in the mammosphere medium under adherent growth conditions, i.e IC > 0.1. Differential gene expression was then assessed by regularized t?test (Smyth GK. Stat Appl Genet Mol Biol 2004, 3:Article3) comparing mammospheres p1 with respect to epithelial bulk, using an uncorrected p-value ? 0.05, together with an absolute log2 fold change threshold ?1.
2013-11-30 | E-GEOD-26527 | biostudies-arrayexpress