Cf7cc097-bc4f-4000-aeff-f35090b902aa - samples
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ABSTRACT:
PROVIDER: EGAD00001004873 | EGA |
REPOSITORIES: EGA
Similar Datasets
Project description:Gene expression quantification of PanCancer IO genes from paired tumour biopsies from 24 patients with pan-cancer solid tumours, before and after treatment with MTL-CEBPA and pembrolizumab.
2024-10-23 | GSE233860 | GEO
Project description:Ascites or solid tumour from patients with ovarian cancer was collected and grown in culture as ex vivo models. Each sample has a mixture of tumour and stromal cells which were separated into individual cultures. Therefore each patient has tumour and stromal cultures originating from the same tissue collection. Variant calling (exome-seq) analysis was performed on these matched models to establish tumour specific mutations. Stromal cells were used to rule out germline mutations.
2020-03-13 | E-MTAB-7225 | biostudies-arrayexpress
Project description:Many cancer patients don’t benefit from currently-approved immune checkpoint inhibitors (ICI), suggesting that additional immunomodulation of the immunosuppressive tumour microenvironment (TME) is required. MTL-CEBPA specifically upregulates expression of master myeloid transcription factor, CEBPA, relieving myeloid-driven immunosuppression. Here, we report the safety, tolerability, pharmacokinetics, and efficacy of MTL-CEBPA in combination with pembrolizumab in patients with advanced solid tumours that typically show ICI resistance. Multimodal exploratory analyses of paired patient biopsies demonstrate biological changes associated with combination treatment of MTL-CEBPA and pembrolizumab, including increased infiltration of T cell and antigen-presenting cells supporting conversion from an immune desert towards a more immune-inflamed TME. Patients with disease stabilisation demonstrate reductions in immunosuppressive myeloid cells post-treatment. Collectively, these data support a role for MTL-CEBPA in reducing immunosuppression in the TME. This study was registered at ClinicalTrials.gov (NCT04105335). This manuscript also reports proteomic data from patients treated with MTL-CEBPA in combination with sorafenib from clinical trial, OUTREACH, accessible at ClinicalTrials.gov, number NCT02716012 and reported. Stored plasma from patients from this clinical trial were analysed using OLINK as described below.
2025-05-07 | PXD060726 | Pride
Project description:Background: Gene expression profiling has been used extensively within breast cancer research. Patient matched transcriptomic studies of tumour samples before and after treatment offer great potential and have been initiated, but tend not to include a control group. Here we examine gene expression changes between patient-matched core biopsies and surgical resection samples in the absence of treatment, to consider sampling methods and tumour heterogeneity. Patients and Methods: Illumina BeadArray technology was used to measure dynamic changes in gene expression from thirty-seven paired baseline and surgically excised breast tumour samples obtained from women receiving no treatment prior to surgery. Results: Patient-matched sample pairs had significantly higher correlations than samples between different individuals, demonstrating that tumour heterogeneity and intra-tumour differences are less prominent than inter-tumour/patient differences. Perhaps surprisingly, consistent changes in gene expression were identified during the diagnosis-surgery interval, despite a lack of treatment. 50 genes were significantly differentially expressed (48 up, 2 down; FDR 0.05) in a manner that appears independent of both subtype and the sampling-interval length. Gene set enrichment analysis using four independent treated datasets has implicated the tumour sampling method as the likely cause of these expression changes which include increases in early growth response genes such as EGR1, 2 and 3 along with DUSP1 and FOS. Our data does not support the idea that there is a significant wounding or immune response. Conclusion: This is the largest cohort of patient-matched transcriptome profiling of tumours from patients receiving no treatment between diagnosis and surgery to date. It has revealed that consistent changes in gene expression do exist between diagnostic core biopsy and the surgical excision sample. We have confirmed these findings in a number of published breast cancer datasets. Ultimately, researchers should be aware of the potential for the tumour sampling method to introduce a confounding factor in future neoadjuvant studies.
2016-08-08 | GSE76727 | GEO
Project description:Background: Gene expression profiling has been used extensively within breast cancer research. Patient matched transcriptomic studies of tumour samples before and after treatment offer great potential and have been initiated, but tend not to include a control group. Here we examine gene expression changes between patient-matched core biopsies and surgical resection samples in the absence of treatment, to consider sampling methods and tumour heterogeneity. Patients and Methods: Illumina BeadArray technology was used to measure dynamic changes in gene expression from thirty-seven paired baseline and surgically excised breast tumour samples obtained from women receiving no treatment prior to surgery. Results: Patient-matched sample pairs had significantly higher correlations than samples between different individuals, demonstrating that tumour heterogeneity and intra-tumour differences are less prominent than inter-tumour/patient differences. Perhaps surprisingly, consistent changes in gene expression were identified during the diagnosis-surgery interval, despite a lack of treatment. 50 genes were significantly differentially expressed (48 up, 2 down; FDR 0.05) in a manner that appears independent of both subtype and the sampling-interval length. Gene set enrichment analysis using four independent treated datasets has implicated the tumour sampling method as the likely cause of these expression changes which include increases in early growth response genes such as EGR1, 2 and 3 along with DUSP1 and FOS. Our data does not support the idea that there is a significant wounding or immune response. Conclusion: This is the largest cohort of patient-matched transcriptome profiling of tumours from patients receiving no treatment between diagnosis and surgery to date. It has revealed that consistent changes in gene expression do exist between diagnostic core biopsy and the surgical excision sample. We have confirmed these findings in a number of published breast cancer datasets. Ultimately, researchers should be aware of the potential for the tumour sampling method to introduce a confounding factor in future neoadjuvant studies.
2016-08-08 | GSE76726 | GEO
Project description:Background: Gene expression profiling has been used extensively within breast cancer research. Patient matched transcriptomic studies of tumour samples before and after treatment offer great potential and have been initiated, but tend not to include a control group. Here we examine gene expression changes between patient-matched core biopsies and surgical resection samples in the absence of treatment, to consider sampling methods and tumour heterogeneity. Patients and Methods: Illumina BeadArray technology was used to measure dynamic changes in gene expression from thirty-seven paired baseline and surgically excised breast tumour samples obtained from women receiving no treatment prior to surgery. Results: Patient-matched sample pairs had significantly higher correlations than samples between different individuals, demonstrating that tumour heterogeneity and intra-tumour differences are less prominent than inter-tumour/patient differences. Perhaps surprisingly, consistent changes in gene expression were identified during the diagnosis-surgery interval, despite a lack of treatment. 50 genes were significantly differentially expressed (48 up, 2 down; FDR 0.05) in a manner that appears independent of both subtype and the sampling-interval length. Gene set enrichment analysis using four independent treated datasets has implicated the tumour sampling method as the likely cause of these expression changes which include increases in early growth response genes such as EGR1, 2 and 3 along with DUSP1 and FOS. Our data does not support the idea that there is a significant wounding or immune response. Conclusion: This is the largest cohort of patient-matched transcriptome profiling of tumours from patients receiving no treatment between diagnosis and surgery to date. It has revealed that consistent changes in gene expression do exist between diagnostic core biopsy and the surgical excision sample. We have confirmed these findings in a number of published breast cancer datasets. Ultimately, researchers should be aware of the potential for the tumour sampling method to introduce a confounding factor in future neoadjuvant studies. 37 paired patient-matched whole-transcriptome profiled primary breast tumours from patients receiving no treatment between diagnosis and surgery. Superseries is a product of two integrated individual batches.
2016-08-08 | E-GEOD-76726 | biostudies-arrayexpress
Project description:Background: Gene expression profiling has been used extensively within breast cancer research. Patient matched transcriptomic studies of tumour samples before and after treatment offer great potential and have been initiated, but tend not to include a control group. Here we examine gene expression changes between patient-matched core biopsies and surgical resection samples in the absence of treatment, to consider sampling methods and tumour heterogeneity. Patients and Methods: Illumina BeadArray technology was used to measure dynamic changes in gene expression from thirty-seven paired baseline and surgically excised breast tumour samples obtained from women receiving no treatment prior to surgery. Results: Patient-matched sample pairs had significantly higher correlations than samples between different individuals, demonstrating that tumour heterogeneity and intra-tumour differences are less prominent than inter-tumour/patient differences. Perhaps surprisingly, consistent changes in gene expression were identified during the diagnosis-surgery interval, despite a lack of treatment. 50 genes were significantly differentially expressed (48 up, 2 down; FDR 0.05) in a manner that appears independent of both subtype and the sampling-interval length. Gene set enrichment analysis using four independent treated datasets has implicated the tumour sampling method as the likely cause of these expression changes which include increases in early growth response genes such as EGR1, 2 and 3 along with DUSP1 and FOS. Our data does not support the idea that there is a significant wounding or immune response. Conclusion: This is the largest cohort of patient-matched transcriptome profiling of tumours from patients receiving no treatment between diagnosis and surgery to date. It has revealed that consistent changes in gene expression do exist between diagnostic core biopsy and the surgical excision sample. We have confirmed these findings in a number of published breast cancer datasets. Ultimately, researchers should be aware of the potential for the tumour sampling method to introduce a confounding factor in future neoadjuvant studies. 37 paired patient-matched whole-transcriptome profiled primary breast tumours from patients receiving no treatment between diagnosis and surgery. Superseries is a product of two integrated individual batches.
2016-08-08 | E-GEOD-76727 | biostudies-arrayexpress
Project description:Apart from biochemical signals, tumour cells respond to biophysical and mechanical cues from their environment. The mechanical forces from the tumour microenvironment could be in the form of shear stress, tension, or solid stress compression. In this study, we explore the effects of solid stress compression on tumour cells. Solid stress compression, a prevalent biomechanical stimulus accumulated during tumour growth, has been shown to enhance invasive and metastatic phenotypes in cancer cells. However, the underlying molecular mechanism that elicits this aggressive metastatic phenotype, especially in breast cancer, is not well understood. Using an established 2D in vitro setup to apply incremental solid stress compression, we found that migratory and invasive capacities of aggressive breast cancer cells were enhanced in a biphasic manner. We also found that Interleukin-6 (IL-6) and SNAI1 transcripts and proteins were upregulated in response to solid stress. The resultant increased secretion of IL-6 could in turn lead to autocrine activation of downstream signalling pathways and impact on cancer cell migration and invasion.
2025-05-02 | GSE282791 | GEO
Project description:This is a genomic analysis of breast cancer metastasis using array based CGH and is part of a large study investigating the patterns and evolution of metastases from breast cancer using autopsy material accumulated over the last 50 years from a single institution. The samples used in the genomic profiling comprise the primary breast tumour and multiple matched metastases from each patient. The data demonstrate both the clonal nature of metastatic progression and the role of clonal evolution during progression.
2013-11-11 | GSE46826 | GEO