Using Microarrays to Interrogate Microenvironmental Impact on Cellular Phenotypes in Cancer

Abstract

Understanding the impact of the microenvironment on the phenotype of cells is a difficult problem due to the complex mixture of both soluble growth factors and matrix-associated proteins in the microenvironment in vivo. Furthermore, readily available reagents for the modeling of microenvironments in vitro typically utilize complex mixtures of proteins that are incompletely defined and suffer from batch to batch variability. The microenvironment microarray (MEMA) platform allows for the assessment of thousands of simple combinations of microenvironment proteins for their impact on cellular phenotypes in a single assay. The MEMAs are prepared in well plates, which allows the addition of individual ligands to separate wells containing arrayed extracellular matrix (ECM) proteins. The combination of the soluble ligand with each printed ECM forms a unique combination. A typical MEMA assay contains greater than 2,500 unique combinatorial microenvironments that cells are exposed to in a single assay. As a test case, the breast cancer cell line MCF7 was plated on the MEMA platform. Analysis of this assay identified factors that both enhance and inhibit the growth and proliferation of these cells. The MEMA platform is highly flexible and can be extended for use with other biological questions beyond cancer research.

Crosstalk between invadopodia and the extracellular matrix

“…MEMAs were produced as described previously (Smith et al, 2019;Watson et al, 2018) with several minor modifications. The same set of 45 ECM or ECM combinations that we previously reported were plated into the bottom of 96 well plates (Ibidi).…”

A tumour-promoting senescent secretome triggered by platinum chemotherapy exploits a targetable TGFβR1/Akt-mTOR axis in lung cancer

“…To identify distinctive SASP factors potentially driving increased proliferation in recipient A549 cells, we used a microenvironment microarray (MEMA) platform. This recent technology allows the screening of the functional effects of multiple combinations of individual factors and cytokines in an unbiased high-throughput manner and the subsequent analysis of treated cell read-outs through advanced imaging 21, 22 . Remarkably, analysis of the proportion of high-EdU+ A549 cells upon 72 h treatment with an array of 64 human SASP-related ligands revealed that exposure to TGFβ-2 and TGFβ- 1 led to the highest A549 proliferation rate of all factors tested in the array (Fig.…”

A LINCS microenvironment perturbation resource for integrative assessment of ligand-mediated molecular and phenotypic responses

“…We selected six ligands based on the results of two high-throughput microenvironment microarray (MEMA) screens of 3024 combinations of 63 soluble ligands and 48 insoluble ECM proteins 46 ; one screen with and another without EGF, a typical component of MCF10A growth medium 39 . We focused on collagen-1 as the insoluble ECM component and selected EGF, HGF, and OSM as ligands that increased growth in the absence of EGF; and BMP2, IFNG, TGFB as ligands that decreased growth in the presence of EGF (Sup.…”