ABSTRACT
Resistance to targeted therapies is an important clinical problem in HER2-positive (HER2+) breast cancer. “Drug-tolerant persisters” (DTPs), a sub-population of cancer cells that survive via reversible, non-genetic mechanisms, are implicated in resistance to tyrosine kinase inhibitors (TKIs) in other malignancies, but DTPs following HER2 TKI exposure have not been well characterized. We found that HER2 TKIs evoke DTPs with a luminal-like or a mesenchymal-like transcriptome. Lentiviral barcoding/single cell RNA-sequencing reveal that HER2+ breast cancer cells cycle stochastically through a “pre-DTP” state, characterized by a G0-like expression signature and enriched for diapause and/or senescence genes. Trajectory analysis/cell sorting show that pre-DTPs preferentially yield DTPs upon HER2 TKI exposure. Cells with similar transcriptomes are present in HER2+ breast tumors and are associated with poor TKI response. Finally, biochemical experiments indicate that luminal-like DTPs survive via estrogen receptor-dependent induction of SGK3,leading to rewiring of the PI3K/AKT/mTORC1 pathway to enable AKT-independent mTORC1 activation.
STATEMENT OF SIGNIFICANCE DTPs are implicated in resistance to TKIs, other targeted therapies, and chemotherapy, but their ontogeny and vulnerabilities remain unclear. We find that HER2 TKI-DTPs emerge from stochastically arising primed cells (“pre-DTPs”) that preferentially engage either of two distinct transcriptional programs upon TKI exposure. Our results provide new insights into DTP ontogeny and identify potential therapeutic vulnerabilities.
Competing Interest Statement
B.G.N. is a founder of, shareholder in, and receives consulting fees from Navire Pharma and Jengu Therapeutics, and is a founder of, and shareholder in, Northern Biologics, LP. He has a sponsored research agreement with Mirati Therapeutics, receives consulting fees and equity from Arvinas, Inc., holds equity in Recursion Pharma, and received consulting fees from MPM Capital and Gerson Lehrman Group. He also is an expert witness for Johnson and Johnson in the federal talc litigation. His spouse holds equity in Amgen, Inc. and held equity in Moderna and Regeneron at times during this study. J.M. is a founder and shareholder in Northern Biologics, LP, and Pionyr Immunotherapeutics, and is an advisor and shareholder of Century Therapeutics and Aelian Biotechnology. K.K.W. is a founder of and equity holder in G1 Therapeutics and has sponsored research agreements with Takeda, BMS, Mirati, Merus, Alkermes, Ansun Biopharma, Tvardi Therapeutics, Delfi Diagnostics, and Dracen Pharmaceuticals. He has consulting agreements with AstraZeneca, Novartis, Merck, Recursion, Navire, Prelude and Ono and has consulting & sponsored research agreements with Janssen, Pfizer, and Zentalis. S.A. has uncompensated consulting or advisory roles with Bristol Meyers Squibb, Genentech, and Merck as well as research funding to her institution from Amgen, Bristol Meyers Squibb, Celgene, Genentech, Merck, Daiichi, and Novartis. No disclosures were reported by the other authors.
Footnotes
↵* These authors contributed equally.
Competing interests: B.G.N. is a founder of, shareholder in, and receives consulting fees from Navire Pharma and Jengu Therapeutics, and is a founder of, and shareholder in, Northern Biologics, LP. He has a sponsored research agreement with Mirati Therapeutics, receives consulting fees and equity from Arvinas, Inc., holds equity in Recursion Pharma, and received consulting fees from MPM Capital and Gerson Lehrman Group. He also is an expert witness for Johnson and Johnson in the federal talc litigation. His spouse holds equity in Amgen, Inc. and held equity in Moderna and Regeneron at times during this study. J.M. is a founder and shareholder in Northern Biologics, LP, and Pionyr Immunotherapeutics, and is an advisor and shareholder of Century Therapeutics and Aelian Biotechnology. K.K.W. is a founder of and equity holder in G1 Therapeutics and has sponsored research agreements with Takeda, BMS, Mirati, Merus, Alkermes, Ansun Biopharma, Tvardi Therapeutics, Delfi Diagnostics, and Dracen Pharmaceuticals. He has consulting agreements with AstraZeneca, Novartis, Merck, Recursion, Navire, Prelude and Ono and has consulting & sponsored research agreements with Janssen, Pfizer, and Zentalis. S.A. has uncompensated consulting or advisory roles with Bristol Meyers Squibb, Genentech, and Merck as well as research funding to her institution from Amgen, Bristol Meyers Squibb, Celgene, Genentech, Merck, Daiichi, and Novartis. No disclosures were reported by the other authors.