A Designed Small Molecule Inhibitor of a Non-Coding RNA Sensitizes HER2 Negative Cancers to Herceptin

J Am Chem Soc. 2019 Feb 20;141(7):2960-2974. doi: 10.1021/jacs.8b10558. Epub 2019 Feb 6.

Abstract

A small molecule (1) with overlapping affinity for two microRNA (miRNA) precursors was used to inform design of a dimeric compound (2) selective for one of the miRNAs. In particular, 2 selectively targets the microRNA(miR)-515 hairpin precursor to inhibit production of miR-515 that represses sphingosine kinase 1 (SK1), a key enzyme in the biosynthesis of sphingosine 1-phosphate (S1P). Application of 2 to breast cancer cells enhanced SK1 and S1P levels, triggering a migratory phenotype. Knockout of SK1, forced overexpression of miR-515, and application of a small molecule SK1 inhibitor all ablated 2's effect on phenotype, consistent with its designed mode of action. Target profiling studies via Chem-CLIP showed that 2 bound selectively to the miR-515 hairpin precursor in cells. Global neoprotein synthesis upon addition of 2 to MCF-7 breast cancer cells demonstrated 2's selectivity and upregulation of cancer-associated proteins regulated by S1P. The most upregulated protein was human epidermal growth factor receptor 2 (ERBB2/HER2), which is regulated by the SK1/S1P pathway and is normally not expressed in MCF-7 cells. Like triple negative breast cancer (TNBC) cells, the lack of HER2 renders them insusceptible to Herceptin and its antibody-drug conjugate Kadcyla. In addition to proteomics, an RNA-seq study supports that 2 has limited off target effects and other studies support that 2 is more selective than an oligonucleotide. We therefore hypothesized that 2 could sensitize MCF-7 cells to anti-HER2 therapies. Indeed, application of 2 sensitized cells to Herceptin. These results were confirmed in two other cell lines that express miR-515 and are HER2-, the hepatocellular carcinoma cell line HepG2 and the TNBC line MDA-MB-231. Importantly, normal breast epithelial cells (MCF-10A) that do not express miR-515 are not affected by 2. These observations suggest a precision medicine approach to sensitize HER2- cancers to approved anticancer medicines. This study has implications for broadening the therapeutic utility of known targeted cancer therapeutics by using a secondary targeted approach to render otherwise insensitive cells, sensitive to a targeted therapeutic.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Ado-Trastuzumab Emtansine / pharmacology
  • Antineoplastic Agents / pharmacology*
  • Base Sequence
  • Benzimidazoles / metabolism
  • Benzimidazoles / pharmacology*
  • Cell Line, Tumor
  • Drug Design
  • Humans
  • Lysophospholipids / metabolism
  • MicroRNAs / antagonists & inhibitors*
  • MicroRNAs / metabolism
  • Phosphotransferases (Alcohol Group Acceptor) / metabolism
  • Proteome / metabolism
  • RNA Precursors / metabolism
  • Receptor, ErbB-2 / metabolism
  • Sphingosine / analogs & derivatives
  • Sphingosine / metabolism
  • Trastuzumab / pharmacology*
  • Triazoles / metabolism
  • Triazoles / pharmacology*

Substances

  • Antineoplastic Agents
  • Benzimidazoles
  • Lysophospholipids
  • MIRN515 microRNA, human
  • MicroRNAs
  • Proteome
  • RNA Precursors
  • Triazoles
  • sphingosine 1-phosphate
  • Phosphotransferases (Alcohol Group Acceptor)
  • sphingosine kinase
  • ERBB2 protein, human
  • Receptor, ErbB-2
  • Sphingosine
  • Trastuzumab
  • Ado-Trastuzumab Emtansine