Transcriptomics

Dataset Information

2

Outer ECM-attached vs. inner cells of MCF10A acini at day 6 of morphogenesis


ABSTRACT: Basal-like carcinoma is a subtype of breast cancer that is characterized by poor prognosis and high intratumor heterogeneity. Using a basal-like breast epithelial line, we have identified two anti-correlated gene-expression programs that arise among single extracellular matrix (ECM)-attached cells during organotypic 3D culture. The first program contains TGFBR3, a high-affinity receptor for transforming growth factor β (TGFβ) and other related ligands. The second program contains the JUND transcription factor together with the basal-like marker, KRT5. By disrupting the TGFBR3 and JUND programs individually, we reveal an important circuit for 3D morphogenesis that is wired together by four negative-feedback loops. Computational modeling of this circuit showed that it could exhibit damped, antiphase oscillations when excited with small impulses of TGFβ-like ligand. We directly visualize the circuit's spontaneous dynamics in organotypic cultures by using live-cell imaging with engineered pathway reporters. Importantly, we show that the essence of the JUND-TGFBR3 expression circuit holds true in early basal-like tumors that heterogeneously express KRT5. Correlated JUND-KRT5 expression depends critically on contact with stromal ECM and local expression of tenascin C. This work illustrates how complex tumor heterogeneities can be deconstructed into intrinsic single-cell expression circuits that are modulated by the microenvironment. Gene expression analysis of outer ECM-attached vs. inner cells of MCF10A-5E clones grown in organotypic 3D culture at day 6. Total RNA was isolated from ~50 outer ECM-attached cells and ~50 inner cells, each separately microdissected from 8 micron sections of MCF10A structures at day 6 of morphogenesis. Total RNA was amplified in quadruplicate, and hybridized to HumanRef-8 v2.0 Expression BeadChips (Illumina).

ORGANISM(S): Homo sapiens  

SUBMITTER: Kevin A Janes   Leen Jamal 

PROVIDER: E-GEOD-41527 | ArrayExpress | 2015-06-05

SECONDARY ACCESSION(S): GSE41527PRJNA177354

REPOSITORIES: GEO, ArrayExpress

altmetric image

Publications

A time- and matrix-dependent TGFBR3-JUND-KRT5 regulatory circuit in single breast epithelial cells and basal-like premalignancies.

Wang Chun-Chao CC   Bajikar Sameer S SS   Jamal Leen L   Atkins Kristen A KA   Janes Kevin A KA  

Nature cell biology 20140323 4


Basal-like breast carcinoma is characterized by poor prognosis and high intratumour heterogeneity. In an immortalized basal-like breast epithelial cell line, we identified two anticorrelated gene-expression programs that arise among single extracellular matrix (ECM)-attached cells during organotypic three-dimensional culture. The first contains multiple TGF-β-related genes including TGFBR3, whereas the second contains JUND and the basal-like marker KRT5. TGFBR3 and JUND interconnect through four  ...[more]

Similar Datasets

2009-07-02 | GSE15724 | GEO
2009-07-11 | E-GEOD-15724 | ArrayExpress
| PRJNA237556 | ENA
| GSE102737 | GEO
2014-04-25 | E-GEOD-57045 | ArrayExpress
2011-09-30 | E-GEOD-32495 | ArrayExpress
2018-09-18 | GSE120030 | GEO
2012-10-31 | E-GEOD-41274 | ArrayExpress
2010-06-09 | E-MEXP-2657 | ArrayExpress
| GSE87535 | GEO