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Transcriptome and chromatin changes during CRC organoid outgrowth as proxy for metastatic outgrowth [bulkRNAseq_AKPS]

ABSTRACT: Transcriptome and chromatin changes during CRC organoid outgrowth as proxy for metastatic outgrowth [bulkRNAseq_AKPS]

PROVIDER: PRJNA853559 | ENA |

REPOSITORIES: ENA

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Project description:When tumor cells colonize distant organs during metastasis, they interact extensively with surrounding cells. These interactions often change the behavior of surrounding cell populations which collectively induce a pro-tumor microenvironment that permits tumor cell outgrowth into overt, clinically detectable metastatic disease. The lung is one of the most common sites of breast cancer (BC) metastasis, and alveolar epithelial cells are the most common cell type in the lung. A gap in our ability to treat patients with established lung metastases lies in our lack of knowledge regarding how the lung microenvironment is remodeled during metastatic outgrowth and how this contributes to disease progression. Immunocompetent preclinical mouse models of BC metastasis were used to study late-stage lung metastatic outgrowth, the stage at which most patients are diagnosed with metastatic disease. A custom imaging panel was developed to quantify lung wound repair and inflammation, and single-cell RNA-sequencing (scRNAseq) was performed on mouse lungs with high or low metastatic burden to identify cell-type specific genes altered during metastatic outgrowth. No-contact co-culture experiments were used to examine reciprocal paracrine interactions between lung type II alveolar epithelial (AT2) cells and BC cells. A chronic wound repair-related phenotype developed within the lung microenvironment during metastatic outgrowth, which was characterized by an increased number and activation of AT2 cells surrounding growing metastases. scRNAseq of lungs with a high versus low metastatic burden showed that metastatic outgrowth significantly changed AT2 gene expression, resulting in a modified secretome. No-contact co-culture experiments indicated that BC-derived secreted factors alter AT2 gene expression, while AT2-derived secreted factors promoted TNBC growth. We investigated the possible mechanism(s) responsible for these effects and found that AT2 secreted factor genes, regulated by the cAMP response element-binding protein (CREB), contribute to BC proliferation. Targeting CREB signaling with the phosphodiesterase 4 (PDE4) inhibitor roflumilast reduced AT2-BC reciprocal interactions in vitro and metastatic outgrowth in vivo. Our studies demonstrate the potential for targeting metastasis-associated wound repair and lung epithelial cell activation with PDE4 inhibitors. This strategy may be an effective way to treat and manage metastatic BC progression in established, clinically detectable disease.

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Transcriptome and chromatin changes during CRC organoid outgrowth as proxy for metastatic outgrowth [bulkRNAseq_AKPS]

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