Expression profile of microenvironment of morphological structures in breast cancer
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PROVIDER: PRJNA763546 | ENA |
REPOSITORIES: ENA
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Project description:The aim of this work is to compare the expression profiles of the microenvironment of various morphological structures of luminal breast cancer obtained by laser microdissection. For this, sections of primary breast carcinoma were stained according to the RNA-preserving protocol, fragments of the stroma around alveolar, trabecular, solid structures and single tumor cells were isolated using a laser capture microdissection, and then RNA-sequencing was performed using Illumina NextSeq500. Our study presents the first analysis of DEGs and activated signaling pathways of the microenvironment of various morphological structures of breast cancer.
2021-09-22 | GSE184196 | GEO
Project description:Transcriptional profiling of morphologically-distinct structures of breast tumors: tubular, alveolar, solid, trabecular structures, and discrete groups of tumor cells in comparison with normal breast epithelium. The aim was to identify transcripts and cell signalling pathways which could be associated with the development of clinical relevant structures of tumor cells.
2016-04-29 | GSE80754 | GEO
Project description:Breast tumors: different structures of tumor cell
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Project description:Cytogenetic profiling of morphologically-distinct structures of breast tumors: tubular, alveolar, solid, trabecular structures, and discrete groups of tumor cells. The aim was to identify chromosomal aberrations which could be associated with the development of clinical relevant structures of tumor cells.
2016-04-29 | GSE80758 | GEO
Project description:RNA was isolated from FFPE tissue sections and expression profile of miRNAs determined by hybridization to Affymetrix GeneChip miRNA 4.0 Array Both normal and cancer samples were used. Normal cases included cosmetic reduction mammoplasties (the only true normal tissue) and tissues with some morphological abnormalities. Some benign, non-cancer, cases were also included. Breast cancer cases included invaive ductal and lobullar carcinomas as well as metaplastic breast cancer
2023-01-30 | GSE144534 | GEO
Project description:The breast tumor microenvironment plays an active role in tumorigenesis. Molecular alterations, including epigenetic modifications to DNA, and changes in RNA and protein expression have been identified in tumor-associated stroma; however, there is considerable debate as to whether the stroma is characterized by genomic instability or whether detection of chromosomal alterations in the breast stroma is a reflection of technological artifact rather than the true genomic content of the tumor microenvironment. Methods: Surgically-removed breast stroma specimens from 112 women undergoing reductive mammoplasty (n=15), prophylactic mastectomy (N=6) or mastectomy for a diagnosis of breast disease (n=92) were frozen in optimal cutting temperature medium. Allelic imbalance (AI) analysis was performed in 484 stromal specimens from 98 women using a panel of 52 microsatellite markers; SNP data was generated from a subset of 86 stromal specimens using 250K SNP arrays (Affymetrix). Copy number alterations were identified using Partek Genomics Suite. Results: AI was not detected in 92% (444/484) of stroma specimens. When compared to previously generated AI data from 77 formalin-fixed, paraffin-embedded stroma specimens (Ellsworth et al., Ann Surg Oncol 2004), 32 (42%) of which harbored at least one detectable AI event, the frequency of AI in the FFPE specimens (4.62%) was significantly higher (P<0.0001) than that found in frozen specimens (0.45%). Of the stroma specimens assayed using SNP arrays 95% (82/86) had no detectable alterations and the 11 copy number changes were small and not shared between specimens. Conclusions: The data presented here support a model in which the tumor microenvironment is genetically stable. The direct comparison of copy number alterations between FFPE and frozen research-grade specimens using identical methodologies suggests that past reports of significant AI in breast stroma, both adjacent to and distant from the tumor, reflects artifact in the archival specimens caused by formalin-fixation, paraffin-embedding and tissue storage. 250K STY data was generated for 86 breast stromal specimens. The tissue specimens were analyzed by paired analysis to the SNP data from matched genomic (blood) DNAs
2012-12-21 | E-GEOD-38071 | biostudies-arrayexpress
Project description:Considerable evidence suggests that breast cancer therapeutic resistance and relapse can be driven by polyploid giant cancer cells (PGCCs). The number of PGCCs increases with the stages of disease and therapeutic stress. Given the importance of PGCCs, it remains challenging to eradicate them. To discover effective anti-PGCC compounds, there is an unmet need to rapidly distinguish compounds that kill non-PGCCs, PGCCs, or both. Here, we establish a single-cell morphological analysis pipeline with a high throughput and great precision to characterize dynamics of individual cells. In this manner, we screen a library to identify promising compounds that inhibit all cancer cells or only PGCCs (e.g., regulators of HDAC, proteasome, and ferroptosis). Additionally, we perform scRNA-Seq to reveal altered cell cycle, metabolism, and ferroptosis sensitivity in breast PGCCs. The combination of single-cell morphological and molecular investigation reveals promising anti-PGCC strategies for breast cancer treatment and other malignancies.
2023-12-01 | GSE248717 | GEO
Project description:To better understand the role of tumor microenvironment in breast cancer progression, we combined laser capture microdissection and microarray analysis to provide a comprehensive catalog of gene expression changes in both tumor and tumor-associated stroma. Experiment Overall Design: We used LCM to isolate the epithelial and stroma compartments separately from each of 14 fresh frozen primary breast cancer biopsies. In the epithelial compartment, we captured normal (N) and malignant (DCIS or IDC or both where available) epithelium from each tissue slide. In the stroma compartment, we captured both normal stroma away from the malignant lesion (NSS) and the DCIS-associated stroma (ISS) and/or IDC-associated stroma (INVS) whenever possible.
2009-02-26 | E-GEOD-14548 | biostudies-arrayexpress
Project description:The tumor immune microenvironment (TIME) is a critical determinant of therapeutic response. However, the mechanisms regulating its modulation are not fully understood. HER2D16, an oncogenic splice variant of the human epidermal growth factor receptor (HER2), has been implicated in breast cancer and other tumor types as a driver of tumorigenesis and metastasis. Nevertheless, the underlying mechanisms of HER2Δ16-mediated oncogenicity remain poorly understood. Here, we show that HER2∆16 expression is not exclusive to the clinically HER2+ subtype and is associated with a poor clinical outcome in breast cancer. To understand how HER2 variants modulate the tumor microenvironment, we generated transgenic mouse models expressing either proto-oncogenic HER2 or HER2D16 in the mammary epithelium. We found that HER2∆16 tumors are immune cold, characterized by low immune infiltrate and an altered cytokine profile. Using an epithelial cell surface proteomic approach, we identified ENPP1 as a functional regulator of the immune cold microenvironment. We generated a knock-in model of HER2Δ16 under the endogenous promoter to understand the role of ENPP1 in aggressive HER2+ breast cancer. Knockdown of ENPP1 in HER2Δ16-derived tumor cells resulted in decreased tumor growth that was correlated with increased T-cell infiltration. These findings suggest that HER2Δ16-dependent ENPP1 activation is associated with aggressive HER2+ breast cancer through its immune modulatory function. Our study provides a better understanding of the mechanisms underlying HER2Δ16-mediated oncogenicity and highlights ENPP1 as a potential therapeutic target in aggressive HER2+ breast cancer.
2023-04-30 | GSE230179 | GEO
Project description:The One Step Nucleic Acid Amplification (OSNA) assay is used to identify occult metastases in the axillary Sentinel Lymph Nodes (SLNs) of early stage breast cancer patients by quantification of the expression of cytokeratin19 (CK19) gene. The discarded samples of OSNA assay were explored as a source of information of SLN microenvironment response in patients with early stage Luminal A breast cancer using an RNAseq panel. Funding: project “GenomePT—National Laboratory for Genome Sequencing and Analysis” (POCI-01-0145-FEDER-022184), and project “Central Region Training Project for Personalized/Precision Medicine, with a genomic basis”, financed by the program CENTRO2020 [CENTRO-08-5864-FSE-000039 (PEP IN1194) 07-2021].
2023-01-06 | GSE210006 | GEO