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Enhancer reactivation mediates adaptive resistance to FGFR inhibitors in triple-negative breast cancer [RNA_seq]

ABSTRACT: A subset of triple negative breast cancers (TNBC) are characterized by genetic alterations in fibroblast growth factor receptors (FGFR) including amplifications, activating mutations or gene fusions. However, despite this genetic evidence of FGFR-dependency, FGFR inhibitors have shown only limited clinical efficacy in TNBC, suggesting the presence of intrinsic or adaptive resistance mechanisms. Using genome-wide CRISPR screens, we found that resistance to FGFR inhibition is mediated by activation of the mTORC1 and YAP pathways. Prolonged FGFR inhibition increased expression of several amino acid transporters resulting in increased cellular level of certain amino acids and activation of the mTORC1 amino acid sensing pathway. Epigenomic analyses revealed that FGFR inhibition reorganized YAP/TEAD associated enhancers leading to the upregulation of YAP target genes including the amino acid transporters upstream of mTORC1. Remarkably, mTORC1 and FGFR inhibitors synergistically blocked the growth of TNBC cells in vitro and in patient-derived xenografts. These findings define a novel epigenetic feedback mechanism involving intracellular amino acid levels leading to targeted therapy resistance in TNBC, and offers a combinatorial drug treatment strategy to improve clinical outcomes for this aggressive breast cancer subtype.

ORGANISM(S): Homo sapiens

PROVIDER: GSE168023 | GEO | 2021/09/09

REPOSITORIES: GEO

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Project description:Pancreas volume or mass varies more than 3-fold among adult humans. The heterogeneity is likely the result of genetics, diseases, and nutrition. Dietary protein intake and blood amino acid levels are known to affect pancreas mass, but the underlying mechanism is not well understood. The goal of this study is to determine how increased blood amino acid level (hyperaminoacidemia) induces pancreas expansion.Multiple complementary mouse and zebrafish models were used to study the impact of hyperaminoacidemia on pancreatic mass, acinar cell size and proliferation. Blood amino acid levels were manipulated by dietary protein content, or by pharmacologic or genetic interruption of glucagon signaling (IGS). The activation of mammalian target of rapamycin complex 1 (mTORC1) and Yes-associated protein 1 (YAP) were determined by pS6 and YAP staining. Sirolimus administration in mice and knockdown of solute carrier family 38 member 5b (slc38a5b) and yap/taz in zebrafish were used to determine the role of mTORC1, SLC38A5 and YAP/TAZ in acinar cell proliferation and pancreas expansion. We found that the IGS-induced pancreas expansion was the result of acinar cell proliferation and hypertrophy. Hyperaminoacidemia was the likely mediator as pancreas expansion was blunted by a low protein diet in mice and by knocking down the most highly expressed amino acid transporter gene, slc38a5b, in zebrafish lacking both glucagon receptor genes (gcgr-/-). In GCGR-Ab treated mice, inhibition of mTORC1 attenuated both hyperplasia and hypertrophy of acinar cells. There was a gene expression signature of YAP activation in acinar cells, consistent with increased YAP-expressing acinar cells in GCGR-Ab treated mice and increased fraction of acinar cells with nuclear YAP1 in gcgr-/- zebrafish. Knocking down yap1 or taz decreased mTORC1 activity and acinar cell hyperplasia and hypertrophy in gcgr-/- zebrafish. Hyperaminoacidemia leads to acinar cell proliferation and hypertrophy via activation of both mTORC1 and YAP pathways. The study discovered a previously unrecognized role of the YAP/Taz pathway in hyperaminoacidemia-induced acinar cell hypertrophy and hyperplasia.

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Enhancer reactivation mediates adaptive resistance to FGFR inhibitors in triple-negative breast cancer [RNA_seq]

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