Calmodulin-like Protein 3 Is an Estrogen Receptor Alpha Coregulator for Gene Expression and Drug Response in a SNP, Estrogen, and SERM-dependent Fashion

Breast Cancer Res. 2017 Aug 18;19(1):95. doi: 10.1186/s13058-017-0890-x.


Background: We previously performed a case-control genome-wide association study in women treated with selective estrogen receptor modulators (SERMs) for breast cancer prevention and identified single nucleotide polymorphisms (SNPs) in ZNF423 as potential biomarkers for response to SERM therapy. The ZNF423rs9940645 SNP, which is approximately 200 bp away from the estrogen response elements, resulted in the SNP, estrogen, and SERM-dependent regulation of ZNF423 expression and, "downstream", that of BRCA1.

Methods: Electrophoretic mobility shift assay-mass spectrometry was performed to identify proteins binding to the ZNF423 SNP and coordinating with estrogen receptor alpha (ERα). Clustered, regularly interspaced short palindromic repeats (CRISPR)/Cas9 genome editing was applied to generate ZR75-1 breast cancer cells with different ZNF423 SNP genotypes. Both cultured cells and mouse xenograft models with different ZNF423 SNP genotypes were used to study the cellular responses to SERMs and poly(ADP-ribose) polymerase (PARP) inhibitors.

Results: We identified calmodulin-like protein 3 (CALML3) as a key sensor of this SNP and a coregulator of ERα, which contributes to differential gene transcription regulation in an estrogen and SERM-dependent fashion. Furthermore, using CRISPR/Cas9-engineered ZR75-1 breast cancer cells with different ZNF423 SNP genotypes, striking differences in cellular responses to SERMs and PARP inhibitors, alone or in combination, were observed not only in cells but also in a mouse xenograft model.

Conclusions: Our results have demonstrated the mechanism by which the ZNF423 rs9940645 SNP might regulate gene expression and drug response as well as its potential role in achieving more highly individualized breast cancer therapy.

Keywords: ERα coregulator; Estrogen; Selective estrogen receptor modulator treatment; Single nucleotide polymorphism.

MeSH terms

  • Animals
  • BRCA1 Protein / genetics
  • Breast Neoplasms / drug therapy*
  • Breast Neoplasms / genetics
  • Breast Neoplasms / pathology
  • CRISPR-Cas Systems
  • Calmodulin / genetics*
  • DNA-Binding Proteins / genetics*
  • Estrogen Receptor alpha / antagonists & inhibitors
  • Estrogen Receptor alpha / genetics*
  • Female
  • Gene Expression Regulation, Neoplastic / drug effects
  • Genome-Wide Association Study
  • Humans
  • Mice
  • Poly(ADP-ribose) Polymerase Inhibitors / administration & dosage
  • Polymorphism, Single Nucleotide
  • Proteins
  • Selective Estrogen Receptor Modulators / adverse effects
  • Selective Estrogen Receptor Modulators / therapeutic use*
  • Xenograft Model Antitumor Assays


  • BRCA1 Protein
  • BRCA1 protein, human
  • CALML3 protein, human
  • Calmodulin
  • DNA-Binding Proteins
  • Estrogen Receptor alpha
  • Poly(ADP-ribose) Polymerase Inhibitors
  • Proteins
  • Selective Estrogen Receptor Modulators
  • estrogen receptor alpha, human
  • ornithine decarboxylase antizyme