Detection of heterogeneous resistance mechanisms to tyrosine kinase inhibitors from cell-free DNA

Heather A Parsons; Conor Messer; Katheryn Santos; Jakob Weiss; David Merrell; Brian P Danysh; Melissa E Hughes; Gregory J Kirkner; Ashka Patel; Julian Hess; Kerry Sendrick; Chip Stewart; Elizabeth Grant; Kristy Schlueter-Kuck; Albert Grinshpun; Nikhil Wagle; Jamunarani Veeraraghavan; Jose Pablo Leone; Rachel A Freedman; Otto Metzger; Rachel Schiff; Eric P Winer; Sara M Tolaney; Mothaffar Rimawi; Ian E Krop; Gad Getz; Nancy U Lin

doi:10.1016/j.xgen.2025.100987

Detection of heterogeneous resistance mechanisms to tyrosine kinase inhibitors from cell-free DNA

Cell Genom. 2025 Dec 10;5(12):100987. doi: 10.1016/j.xgen.2025.100987. Epub 2025 Sep 9.

Authors

Heather A Parsons¹, Conor Messer², Katheryn Santos³, Jakob Weiss², David Merrell², Brian P Danysh², Melissa E Hughes⁴, Gregory J Kirkner⁵, Ashka Patel⁵, Julian Hess², Kerry Sendrick⁵, Chip Stewart², Elizabeth Grant⁵, Kristy Schlueter-Kuck², Albert Grinshpun⁵, Nikhil Wagle⁶, Jamunarani Veeraraghavan⁷, Jose Pablo Leone⁸, Rachel A Freedman⁸, Otto Metzger⁸, Rachel Schiff⁷, Eric P Winer⁹, Sara M Tolaney⁸, Mothaffar Rimawi⁷, Ian E Krop⁹, Gad Getz¹⁰, Nancy U Lin⁸

Affiliations

¹ Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA. Electronic address: hparsons@fredhutch.org.
² Broad Institute of MIT and Harvard, Cambridge, MA, USA.
³ Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston, MA, USA.
⁴ Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Yale Cancer Center, New Haven, CT, USA.
⁵ Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
⁶ Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA.
⁷ Baylor College of Medicine, Houston, TX, USA.
⁸ Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston, MA, USA; Harvard Medical School, Boston, MA, USA.
⁹ Yale Cancer Center, New Haven, CT, USA.
¹⁰ Broad Institute of MIT and Harvard, Cambridge, MA, USA; Massachusetts General Hospital, Boston, MA, USA.

Abstract

Though there has been substantial progress in the development of anti-human epidermal growth factor receptor 2 (HER2) therapies to treat HER2-positive metastatic breast cancer (MBC) within the past two decades, most patients still experience disease progression and cancer-related death. HER2-directed tyrosine kinase inhibitors can be highly effective therapies for patients with HER2-positive MBC; however, an understanding of resistance mechanisms is needed to better inform treatment approaches. We performed whole-exome sequencing on 111 patients with 73 tumor biopsies and 120 cell-free DNA samples to assess mechanisms of resistance. In 11 of 26 patients with acquired resistance, we identified alterations in previously characterized genes, such as PIK3CA and ERBB2, that could explain treatment resistance. Mutations in growing subclones identified potential mechanisms of resistance in 5 of 26 patients and included alterations in ESR1, FGFR2, and FGFR4. Additional studies are needed to assess the functional role and clinical utility of these alterations in driving resistance.

Keywords: HER2; cell-free DNA; metastatic breast cancer; resistance; tyrosine kinase inhibitors.

MeSH terms

Breast Neoplasms* / drug therapy
Breast Neoplasms* / genetics
Breast Neoplasms* / pathology
Cell-Free Nucleic Acids* / genetics
Class I Phosphatidylinositol 3-Kinases / genetics
Drug Resistance, Neoplasm* / genetics
Erb-b2 Receptor Tyrosine Kinases / antagonists & inhibitors
Erb-b2 Receptor Tyrosine Kinases / genetics
Erb-b2 Receptor Tyrosine Kinases / metabolism
Estrogen Receptor alpha / genetics
Exome Sequencing
Female
Humans
Middle Aged
Mutation
Protein Kinase Inhibitors* / pharmacology
Protein Kinase Inhibitors* / therapeutic use
Receptor, Fibroblast Growth Factor, Type 2 / genetics
Tyrosine Kinase Inhibitors

Substances

Protein Kinase Inhibitors
Cell-Free Nucleic Acids
Erb-b2 Receptor Tyrosine Kinases
Class I Phosphatidylinositol 3-Kinases
Receptor, Fibroblast Growth Factor, Type 2
Estrogen Receptor alpha
Tyrosine Kinase Inhibitors
PIK3CA protein, human
ERBB2 protein, human
FGFR2 protein, human
ESR1 protein, human