Biology subjects

Traugh, N.

Publications and source records attributed to Traugh, N..

7 recordsLinked to original sources

bioRxiv2026

Environmental chemical mixtures reprogram mammary epithelial development to epigenetic states associated with breast cancer

Environmental exposures occur as complex mixtures, yet the mechanisms by which they alter human tissue development and confer cancer susceptibility remain poorly defined. Here, we establish a physiological 3D human breast organoid high-content screening (3D-HCS) platform that quantitatively links exposure-induced developmental disruption to cancer-relevant cell states. Screening of structurally diverse environmental chemicals as single agents but also as mixtures reveals heterogeneous but reproducible developmental responses, indicating that distinct environmental chemicals perturb different aspects of mammary morphogenesis. Focusing on bisphenols, we show that a physiological-dose mixture (BPA, BPS, and BPF; 3BPX) disrupts organoid development and induces transcriptional programs characterized by extracellular matrix remodeling, epithelial plasticity, and partial epithelial-mesenchymal transition (EMT), accompanied by widespread DNA methylation remodeling. The 3BPX exposure signature maps to ER luminal breast cancers and is preferentially enriched in invasive lobular carcinoma (ILC), a subtype characterized by epithelial plasticity and stromal interaction. Genome-wide DNA methylation profiling revealed that the 3BPX-associated methylation signature is detectable in primary tumors and adjacent normal tissue and is enriched in Normal-like tumors and ILC. Together, these findings demonstrate that environmentally relevant chemical exposures induce heterogeneous developmental perturbations that converge on conserved transcriptional and epigenetic programs associated with epithelial plasticity, tissue remodeling, and cancer susceptibility. These exposure-induced states persist as molecular "scars" that map to defined epithelial and stromal compartments in human breast cancers, supporting a model in which developmental exposures establish a field of increased oncogenic potential. Summary StatementUsing a human breast organoid high-content screening platform, we show that real-world chemical mixtures induce heterogeneous developmental disruption that converges on conserved EMT, wound-response, and epigenetic programs. These exposure-induced states persist as molecular "scars" and map to specific epithelial and stromal compartments in human breast cancers, particularly invasive lobular carcinoma, suggesting a developmental origin of cancer susceptibility.

cancer biology↗

bioRxiv2025

Immune-Epithelial Interactions via TGF-β Orchestrates Stem-Cell Niche Formation and Morphogenesis

Mesenchymal-epithelial interactions are well-established for organogenesis, but the role of immune cells in these processes remains less explored. Organoids offer powerful models for studying tissue development, especially where in vivo models are limited. In this study, we established an immune-epithelial co-culture model using an advanced 3D hydrogel-based breast organoid model that enables real-time investigation of human breast organogenesis. We employed live imaging and cell tracking techniques to visualize the induction process and the formation of an immune-mediated niche. Incorporation of immune cells into the organoid structure demonstrates their dual role as inducers of epithelial proliferation and as a persistent component of the stem cell niche. In addition, co-culturing epithelial cells with tissue-resident immune cells from healthy donors, particularly those enriched in double negative T cells, significantly accelerates organoid development and increases organoid formation through TGF-{beta} signaling. These findings highlight a previously unappreciated role for immune-epithelial crosstalk in early tissue development and provide insights into the dynamic nature of stem cell niches.

developmental biology↗

bioRxiv2024

DDR1 regulates RUNX1-CBFβ to control breast stem cell differentiation

The human breast is complex and comprised of multi-lineage and multi-structural elements. Recent work has shown that epithelial stem and progenitor cells use the collagen receptor Discoidin Domain Receptor 1 (DDR1) for differentiation into both basal and luminal cell lineages, which together are necessary for both ductal and alveolar morphogenesis. We developed a next-generation single cell derived organoid model that generates miniaturized breast tissue, to study how single stem cells can give rise to multiple cell types and compound tissue structures. We show that DDR1 activation triggers stem cell differentiation via RUNX1 in turn driving multilineage differentiation as well as complex ductal-lobular development. Mechanistically, DDR1 affects the interaction and expression of RUNX1 and its cofactor CBF{beta} thereby regulating its activity. Together, these findings contribute to the current understanding of how the extracellular matrix component within the stem cell niche drives organogenesis and tissue regeneration.

developmental biology↗

bioRxiv2023

Advancements in Human Breast Organoid Culture: Modeling Complex Tissue Structures and Developmental Insights

Organoids have emerged as a powerful tool for modeling tissue growth and diseases. In this study, we introduce a groundbreaking organotypic culture technique that replicates the morphology, scale, and heterogeneity of human breast tissue, and includes a mesenchymal-like stromal component. A standout feature of this approach is the use of long-term live imaging at high temporal resolution to directly observe stem cell dynamics during organogenesis, from single cells to mature organ tissue. The system is adaptable for high throughput applications and allows for genetic manipulation of the cells. Real-time imaging of ex-vivo tissue formation reveals a non-canonical process of ductal-lobular morphogenesis and branching, and de-novo generation of a supportive stroma. Incorporating patient-derived single cells from multiple donors offers an enhanced representation of the spectrum of individual responses and the impacts of distinct exposures. While developed for breast tissue, the principles of this technology can serve as a model for the development of similar systems in other tissues, where organoids do not merely reproduce the tissue, but where their regeneration can also be observed and studied. In addition, this model provides a quantitative experimental system to study mechanisms of embryogenesis, development, and tissue organization where biomechanics plays an important role.

developmental biology↗

bioRxiv2023

Selective inhibition of fibroblast-specific Domain Discoidin Receptor 1 (DDR1) reduces collagen deposition and modulates fibroblast-specific cytokine release within the breast microenvironment.

Fibroblasts are a major cell type within breast microenvironment which play key roles in tissue remodeling during the processes of normal development, injury, and malignancy. During wound healing and tumorigenesis, fibroblasts facilitate production and degradation of the extracellular matrix and produce inflammatory mediators which act as immune regulators. Domain Discoidin Receptor 1 (DDR1) is a cell surface tyrosine kinase receptor expressed by epithelial and stromal cells which is activated by collagen. In the breast, DDR1 expression and activity has been implicated in the development of fibrosis as well as chemotherapy resistance. We set out to examine whether selective inhibition of DDR1 would modulate fibroblast immunomodulatory function to generate an immune-permissive breast microenvironment and reduce stromal desmoplasia. In vivo, DDR1 inhibition resulted in mammary fibroblast tissue remodeling, reduced collagen deposition, and changes in immunomodulatory cytokine expression. Furthermore, DDR1 inhibition was associated with increased CD45.2+ immune cell infiltration and reduced Ly6G+/Ly6C- neutrophil infiltration. Mechanistically, we developed an ex-vivo 3D collagen hydrogel model of desmoplasia to study the effects of DDR1 inhibition on the expression of immune modulating factors and fibroblast functions and features. We found that DDR1 regulates the expression and secretion of key immunomodulatory cytokines (IL-6, IL-8, and MCP-1). Collectively these findings suggest that breast fibroblast-specific DDR1 mediates collagen deposition and immunomodulatory function within the mammary gland and warrants further investigation as a potential target for fibroblast-modulating therapy in benign and neoplastic breast disorders.

cell biology↗

bioRxiv2020

In Vivo CRISPR Screens Identify E3 Ligase Cop1 as a Modulator of Macrophage Infiltration and Cancer Immunotherapy Target

Despite remarkable clinical efficacies of immune checkpoint blockade (ICB) in cancer treatment, ICB benefits in triple-negative breast cancer (TNBC) remain limited. Through pooled in vivo CRISPR knockout (KO) screens in syngeneic TNBC mouse models, we found that inhibition of the E3 ubiquitin ligase Cop1 in cancer cells decreases the secretion of macrophage-associated chemokines, reduces tumor macrophage infiltration, and shows synergy in anti-tumor immunity with ICB. Transcriptomics, epigenomics, and proteomics analyses revealed Cop1 functions through proteasomal degradation of the C/ebp{delta} protein. Cop1 substrate Trib2 functions as a scaffold linking Cop1 and C/ebp{delta}, which leads to polyubiquitination of C/ebp{delta}. Cop1 inhibition stabilizes C/ebp{delta} to suppress the expression of macrophage chemoattractant genes. Our integrated approach implicates Cop1 as a target for improving cancer immunotherapy efficacy by regulating chemokine secretion and macrophage levels in the TNBC tumor microenvironment. HighlightsO_LILarge-scale in vivo CRISPR screens identify new immune targets regulating the tumor microenvironment C_LIO_LICop1 knockout in cancer cells enhances anti-tumor immunity C_LIO_LICop1 modulates chemokine secretion and macrophage infiltration into tumors C_LIO_LICop1 targets C/ebp{delta} degradation via Trib2 and influences ICB response C_LI

cancer biology↗

bioRxiv2019

Genome-wide CRISPR screens identify essential cell growth mediators in BRAF-inhibitor resistant melanoma

BRAF is a serine-threonine kinase that harbors activating mutations in [~]7% of human malignancies and [~]60% of melanomas. Despite initial clinical responses to BRAF inhibitors (BRAFi), patients frequently develop drug resistance. To identify candidate therapeutic targets for BRAFi-resistant melanoma, we conducted CRISPR screens in melanoma cells harboring an activating BRAF mutation that had also acquired resistance to BRAFi. The screens identified pathways and genes critical for BRAFi resistance in melanoma cells. To investigate the mechanisms and pathways enabling resistance to BRAFi in melanomas, we integrated expression data, ATAC-seq, and CRISPR screen results. We identified the JUN family of transcription factors and the ETS family transcription factor ETV5 as key regulators of CDK6 that enabled resistance to BRAFi in melanoma cells. Our findings reveal genes whose loss of function conferred resistance to a selective BRAF inhibitor, providing new insight into signaling pathways that contribute to acquired resistance in melanoma.

cancer biology↗