Mass Cytometric and Transcriptomic Profiling of Epithelial-Mesenchymal Transitions in Human Mammary Cell Lines

Epithelial-mesenchymal transition (EMT) equips breast cancer cells for metastasis and treatment resistance. Inhibition and elimination of EMT-undergoing cells are therefore promising therapy approaches. However, detecting EMT-undergoing cells is challenging due to the intrinsic heterogeneity of cancer cells and the phenotypic diversity of EMT programs. Here, we profiled EMT transition phenotypes in four non-cancerous human mammary epithelial cell lines using a FACS surface marker screen, RNA sequencing, and mass cytometry. EMT was induced in the HMLE and MCF10A cell lines and in the HMLE-Twist-ER and HMLE-Snail-ER cell lines by chronic exposure to TGFβ1 or 4-hydroxytamoxifen, respectively. We observed a spectrum of EMT transition phenotypes in each cell line and the spectrum varied across the time course. Our data provide multiparametric insights at single-cell level into the phenotypic diversity of EMT at different time points and in four human cellular models. These insights are valuable to better understand the complexity of EMT, to compare EMT transitions between the cellular models used herein, and for the design of EMT time course experiments.

Small molecule control of neurotransmitter sulfonation

Controlling unmodified serotonin levels in brain synapses is a primary objective when treating major depressive disorder — a disease that afflicts ~20% of the world’s population. Roughly 60% of patients respond poorly to first-line treatments and thus new therapeutic strategies are sought. Toward this end, we have constructed isoform-specific inhibitors of the human cytosolic sulfotransferase 1A3 (SULT1A3) — the isoform responsible for sulfonating ~80% of the serotonin in extracellular brain fluid. The inhibitor design includes a core ring structure, which anchors the inhibitor into a SULT1A3-specific binding pocket located outside the active site, and a sidechain crafted to act as a latch to inhibit turnover by fastening down the SULT1A3 active-site cap. The inhibitors are allosteric, they bind with nanomolar affinity and are highly specific for the 1A3 isoform. The cap-stabilizing effects of the latch can be accurately calculated and are predicted to extend throughout the cap and into the surrounding protein. A free energy correlation demonstrates that the percent inhibition at saturating inhibitor varies linearly with cap stabilization — the correlation is linear because the rate-limiting step of the catalytic cycle, nucleotide release, scales linearly with the fraction of enzyme in the cap-open form. Inhibitor efficacy in cultured cells was studied using a human mammary epithelial cell line that expresses SULT1A3 at levels comparable to those found in neurons. The inhibitors perform similarly in ex vivo and in vitro studies; consequently, SULT1A3 turnover can now be potently suppressed in an isoform-specific manner in human cells.

The Effects of Triazine Herbicides on Critical Peroxide Metabolism Gene Expression in MCF-7 and MCF-10A Cells

Aim: To identify the oxidative stress impacts of chloro-s-triazine herbicides on human mammary epithelial cell lines. Study Design: MCF-7 mammary epithelial carcinoma and MCF-10A mammary epithelial cells were treated with levels of three triazine herbicides in concentrations flanking the US FDA safe levels. Place and Duration of Study: Department of Biology, Millikin University, in January 2015 through December 2015 and January 2019 through May 2020. Methodology: We examined the oxidative effects of two triazine herbicides, atrazine and simazine, on estrogen-dependent MCF-7 mammary epithelial carcinoma cells using three different bioluminescent assay techniques. We then utilized real time PCR to analyze gene expression through RT-PCR analysis, in both MCF-7 cells and a non-cancerous cell line, MCF-10A, for both of these triazine herbicides plus the related cyanazine. Results: At all concentrations of atrazine and simazine, no statistical differences were found in the levels of oxidized glutathione or total oxidized and reduced nicotinamide adenine dinucleotides phosphates. In stark contrast, levels of hydrogen peroxide were found to be statistically different from the control at all concentrations of atrazine and simazine tested. Using an Analysis of Variance (ANOVA) we determined that within the enzymatic portion of the hydrogen peroxide pathway there were statistically significant differences in the expression of Peroxiredoxin 1 (PRDX1), Sulfiredoxin (SRXN1), and Thioredoxin (TXN). Conclusion: Exposure to triazines alters the hydrogen peroxide pathway, which in turn can greatly affect the stability of the cell milieu.

YY1 is a cis-regulator in the organoid models of high mammographic density

Motivation Our previous study has shown that ERBB2 is overexpressed in the organoid model of MCF10A when the stiffness of the microenvironment is increased to that of high mammographic density (MD). We now aim to identify key transcription factors (TFs) and functional enhancers that regulate processes associated with increased stiffness of the microenvironment in the organoid models of premalignant human mammary cell lines. Results 3D colony organizations and the cis-regulatory networks of two human mammary epithelial cell lines (184A1 and MCF10A) are investigated as a function of the increased stiffness of the microenvironment within the range of MD. The 3D colonies are imaged using confocal microscopy, and the morphometries of colony organizations and heterogeneity are quantified as a function of the stiffness of the microenvironment using BioSig3D. In a surrogate assay, colony organizations are profiled by transcriptomics. Transcriptome data are enriched by correlative analysis with the computed morphometric indices. Next, a subset of enriched data are processed against publicly available ChIP-Seq data using Model-based Analysis of Regulation of Gene Expression to predict regulatory transcription factors. This integrative analysis of morphometric and transcriptomic data predicted YY1 as one of the cis-regulators in both cell lines as a result of the increased stiffness of the microenvironment. Subsequent experiments validated that YY1 is expressed at protein and mRNA levels for MCF10A and 184A1, respectively. Also, there is a causal relationship between activation of YY1 and ERBB2 when YY1 is overexpressed at the protein level in MCF10A. Supplementary information Supplementary data are available at Bioinformatics online.

Porcine Breast Extracellular Matrix Hydrogel for Spatial Tissue Culture

Porcine mammary fatty tissues represent an abundant source of natural biomaterial for generation of breast-specific extracellular matrix (ECM). Here we report the extraction of total ECM proteins from pig breast fatty tissues, the fabrication of hydrogel and porous scaffolds from the extracted ECM proteins, the structural properties of the scaffolds (tissue matrix scaffold, TMS), and the applications of the hydrogel in human mammary epithelial cell spatial cultures for cell surface receptor expression, metabolomics characterization, acini formation, proliferation, migration between different scaffolding compartments, and in vivo tumor formation. This model system provides an additional option for studying human breast diseases such as breast cancer.

Mechanisms of HERV-K (HML-2) Transcription during Human Mammary Epithelial Cell Transformation

ABSTRACTIncreasing evidence suggests that repetitive elements may play a role in host gene regulation, particularly through the donation of alternative promoters, enhancers, splice sites, and termination signals. Elevated transcript expression of the endogenous retrovirus group HERV-K (HML-2) is seen in many human cancers, although the identities of the individual proviral loci contributing to this expression as well as their mechanisms of activation have been unclear. Using high-throughput next-generation sequencing techniques optimized for the capture of HML-2 expression, we characterized the HML-2 transcriptome and means of activation in anin vitromodel of human mammary epithelial cell transformation. Our analysis showed significant expression originating from 15 HML-2 full-length proviruses, through four modes of transcription. The majority of expression was in the antisense orientation and from proviruses integrated within introns. We found two instances of long terminal repeat (LTR)-driven provirus transcription but no evidence to suggest that these active 5′ LTRs were influencing nearby host gene expression. Importantly, LTR-driven transcription was restricted to tumorigenic cells, suggesting that LTR promoter activity is dependent upon the transcriptional environment of a malignant cell.IMPORTANCEHere, we use anin vitromodel of human mammary epithelial cell transformation to assess how malignancy-associated shifts in the transcriptional milieu of a cell may impact HML-2 activity. We found 15 proviruses to be significantly expressed through four different mechanisms, with the majority of transcripts being antisense copies of proviruses located within introns. We saw active 5′ LTR use in tumorigenic cells only, suggesting that the cellular environment of a cancer cell is a critical component for induction of LTR promoter activity. These findings have implications for future studies investigating HML-2 as a target for immunotherapy or as a biomarker for disease.