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

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.