LINCS Workflow

Explore microenvironments that alter the lineages in human mammary epithelial cells (HMEC) cell lines

  • Are there microenvironments that alter the lineages in the human mammary epithelial cells (HMEC) cell lines?
  • What are some recommended tools and methods for discovering MEPs with extreme luminal or basal marker values?

The HMEC122L and HMEC240L cells often have subpopulations with distinct luminal and basal lineages[1]. These cells have been stained for KRT19 and KRT5, which are luminal and basal lineage markers, respectively. The ratio of KRT19 to KRT5 intensity values (lineage ratio) is calculated at the cell level and then summarized at the spot and MEP levels. In addition, the KRT19 intensities have a bimodal distribution and are gated into KRT19 low and high classes. The proportion of KRT19 high cells in a population can also be used to identify MEPs with altered lineage markers.

Beta-version HMEC lineage dashboards are available for the HMEC 240L cell line and the HMEC 122L cell line that show the responses subsetted and stratified by ligand and by ECM protein.

MEP-LINCS Proliferation Dashboard (HMEC 240L)

The HMEC122L syn7186831 and HMEC240L syn7186833 cell-level analysis reports have several figures that plot lineage markers against each other and against other signals such as cell count and proliferation.

MEP-LINCS Cell Line Analysis (HMEC 240L)

Also, the HMEC122L syn7122580 and HMEC240L syn7122584 staining set-level reports display the MEPs ordered by lineage ratio and can be zoomed in to identify the MEPs with extreme values.

MEP-LINCS Cell Line Analysis Lineage Marker (HMEC 240L)

Finally, the data explorer at syn4939350 can be used to generate boxplots and scatterplots of many features in the MCF10A and HMEC datasets.

  1. Pelissier, Fanny A., James C. Garbe, Badriprasad Ananthanarayanan, Masaru Miyano, ChunHan Lin, Tiina Jokela, Sanjay Kumar, Martha R. Stampfer, James B. Lorens, and Mark A. LaBarge. “Age-Related Dysfunction in Mechanotransduction Impairs Differentiation of Human Mammary Epithelial Progenitors.” Cell Reports 7, no. 6 (June 2014): 1926–39. doi:10.1016/j.celrep.2014.05.021.