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MCF10 series 3D cultures: gene expression in association with epithelial p53 status and stromal milieu

ABSTRACT: MCF10 series 3D cultures: gene expression in association with epithelial p53 status and stromal milieu

PROVIDER: PRJNA682199 | ENA |

REPOSITORIES: ENA

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MCF10 series 3D cultures: gene expression in association with epithelial p53 status and stromal milieu

Project description:Basal-like breast cancers (BBC) exhibit subtype-specific phenotypic and transcriptional responses to stroma, but little research has addressed how stromal-epithelial interactions evolve during early BBC carcinogenesis. It is also unclear how common genetic defects, such as p53 mutations, modify these stromal-epithelial interactions. To address these knowledge gaps, we leveraged the MCF10 progression series of breast cell lines (MCF10A, MCF10AT1, and MCF10DCIS) to develop a longitudinal, tissue-contextualized model of p53-deficient, pre-malignant breast. Acinus asphericity, a morphogenetic correlate of cell invasive potential, was quantified with optical coherence tomography imaging, and gene expression microarrays were performed to identify transcriptional changes associated with p53 depletion and stromal context. Co-culture with stromal fibroblasts significantly increased the asphericity of acini derived from all three p53-deficient, but not p53-sufficient, cell lines, and was associated with the upregulation of 38 genes. When considered as a multigene score, these genes were upregulated in co-culture models of invasive BBC with increasing stromal content, as well as in basal-like relative to luminal breast cancers in two large human datasets. Taken together, stromal-epithelial interactions during early BBC carcinogenesis are dependent upon epithelial p53 status, and may play important roles in the acquisition of an invasive morphologic phenotype.

2021-01-16 | GSE162553 | GEO

Il-17 p53 Developmental Series

Project description:Il-17 p53 Developmental Series

| PRJNA953010 | ENA

Project description:RNA-seq MCF10 series

| PRJNA449418 | ENA

Single-cell RNA-Seq to study the effects of acute and chronic CENP-A overexpression depending on p53 status

Project description:We performed single-cell RNA-Seq to determine the effects of CENP-A overexpression and p53 status on cell fate over time. We established clonal MCF10-2A TetOn-CENPA-FLAG-HA cell lines where CENP-A can be reversibly induced by Doxycycline (Dox) treatment. We compared prolonged, continuous CENP-A overexpression (chronic induction) to acute CENP-A overexpression, as well as non-overexpressing conditions, in p53 wild-type and defective cells. We grew MCF10-2A TetOn-CENPA-FLAG-HA cells expressing either an empty control vector (p53-WT) or dominant-negative p53 (p53-DN) without Dox or with continuous exposure to Dox (10ng/ml, ++, chronic) for 69 days in parallel. Cells in the no Dox condition were split into two dishes at day 67 and Dox was added to one set on day 68 for 24h of CENP-A overexpression (10ng/ml, +, acute) while the other remained without Dox (-, control). We prepared samples in singlet according to the 10x Genomics Sample Preparation Demonstrated Protocol. In brief, we harvested cells by trypsinization, resuspended in typical media and mixed thoroughly by pipette, passed cells through a 40µm cell strainer, and counted cells by Beckman Automated Cell Counter. We resuspended cells in 1x PBS + 0.04% BSA, mixed, centrifuged gently, aspired supernatant and repeated wash two times. We passed cells through another cell strainer (40µm), counted again and diluted to a final concentration between 700 and 1200 cells/µl. We then proceeded directly to GEM generation and barcoding at the NGS platform, Institut Curie, using the Single-cell 3’ Reagent Kits v2 protocol with a targeted cell recovery of 2000 cells per sample, followed by post GEM-RT cleanup and cDNA amplification, then 3’ Gene Expression Library Construction, according to the manufacturer’s instructions. Sequencing was performed by the NGS platform with a NovaSeq 6000 sequencer.

2021-03-01 | E-MTAB-9861 | biostudies-arrayexpress

p53 status and AAI gene expression response

Project description:Human colon carcinoma cells (HCT116) differing in TP53 status were exposed to aristolochic acid I (AAI) (50 and 100 uM for up to 48 h), and their gene expression responses compared by cDNA microarray technology. Keywords: other

2008-07-28 | GSE10359 | GEO

SARS coronavirus series

Project description:SARS coronavirus series

| PRJNA85299 | ENA

p53 status and BaP or BPDE gene expression response

Project description:Human colon carcinoma cells (HCT116) differing in p53 status were exposed to benzo(a)pyrene (BaP) (2.5 and 5 uM for up to 48 h) or anti-benzo(a)pyrene-trans-7,8-dihydrodiol-9,10-epoxide (BPDE)(0.5 and 1 uM for up to 24 h), and their gene expression responses compared by cDNA microarray technology. Keywords: BaP or BPDE exposure

2007-11-13 | GSE9547 | GEO

A muco-inflammatory milieu characterizes early cf lung disease

Project description:A muco-inflammatory milieu characterizes early cf lung disease

| PRJEB22216 | ENA

Immune repertoire analysis using RNA for tumor milieu analysis

Project description:Immune repertoire analysis using RNA for tumor milieu analysis

| PRJNA672919 | ENA

An expression signature for p53 in breast cancer predicts mutation status, transcriptional effects, and patient survival

Project description:The biological tumor samples (ie, breast tumor specimens) consisted of freshly frozen breast tumors from a population-based cohort of 315 women representing 65% of all breast cancers resected in Uppsala County, Sweden, from January 1, 1987 to December 31, 1989. Estrogen receptor status was determined by biochemical assay as part of the routine clinical procedure. An experienced pathologist determined the Elston-Ellis grades of the tumors, classifying the tumors into low, medium and high-grade tumors. The clinico-pathological characteristics accompanying each tumor include p53 status, ER status, tumor grade, lymph node status and patient age. Keywords: Tumor sample comparisons

2005-10-21 | GSE3494 | GEO

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