Shah et al. · Cell Reports · 2025

LncRNA SLNCR phenocopies the E2F1 DNA binding site to promote melanoma progression

Shah Kushani, Anastasakou Eleni, Sejour Leinal, Wang Yufei, Wert-Lamas Leon, Rauchet Christopher, Studer Sabine, Goller Simon, Distel Robert J., Marasco Wayne, Perera Lalith, Vlachos Ioannis S., Novina Carl D.

Read the paper The product used

The study

What was asked, and what was found

Shah et al., Cell Reports, 2025 asked whether the melanoma oncogene E2F1 needs its partner long non-coding RNA SLNCR in order to drive disease, and whether that partnership can be broken without changing how much of either is present. A proteome-wide yeast three-hybrid screen, RNA electrophoretic mobility shift assays and chemical probing inside cells mapped five stretches of SLNCR that read as RNA versions of the DNA element E2F1 normally binds. Sites 2 and 3 sit next to each other, are almost perfectly complementary, and fold into a hairpin that bound E2F1 at concentrations as low as 12.5 nM. In patient data from The Cancer Genome Atlas, only tumours high in both SLNCR and E2F1 tracked with shorter survival, a median of 431 days against 777 days for the matched control group, p = 0.015.

The interaction was then interrupted with AUMblock sdASO made by AUM BioTech. A 60 nucleotide oligonucleotide reproducing binding sites 2 and 3, called RNA mimic 2+3 in the paper, was put on SLNCR-overexpressing A375 melanoma cells and on the patient-derived short-term cultures WM1575 and WM1976 at 1 μM for 48 hours, against an AUMblock scramble control listed in the same methods table. Invasion and proliferation each fell by a minimum of 2-fold against the matched controls. The oligonucleotide blocked the SLNCR to E2F1 complex while leaving both the E2F1 protein and the SLNCR transcript at their normal levels, which is what separates this result from a knockdown.

The same treatment was carried into an animal experiment. A375-Luc2 cells overexpressing SLNCR were held for 48 hours with 1 μM of either the AUMblock scramble or the blocking oligonucleotide, washed twice in phosphate buffered saline, and injected into the tail vein of NSG mice. Lung bioluminescence, the readout for melanoma cells leaving the bloodstream and settling in the lung, was significantly lower in the animals that received the blocked cells. Alongside this, molecular dynamics simulations and competition assays showed that RNA and DNA compete for the same surface of E2F1, with 250 nM of RNA displacing bound DNA while 40 μM of DNA was needed to displace 50 nM of RNA.

Key findings

An AUMblock sdASO reproducing the E2F1 binding sites inside SLNCR cut melanoma invasion and proliferation by at least half against a matched AUMblock scramble control.(Results, SLNCR-E2F1 complex formation promotes melanoma invasion and proliferation; Figures 3A and 3B)
The AUMblock sdASO worked by occupying E2F1 rather than by removing anything: neither the E2F1 protein nor the SLNCR transcript changed in amount.(Results, SLNCR-E2F1 complex formation promotes melanoma invasion and proliferation; Figures S3A to S3C)
Melanoma cells carrying the AUMblock sdASO gave significantly less lung signal after tail vein injection into NSG mice than cells carrying the scramble control.(Results, SLNCR-E2F1 complex formation promotes melanoma invasion and proliferation; Figures 3C, 3D and S3D)
SLNCR carries five sequence stretches that read as RNA versions of the DNA element E2F1 normally binds, and the pair at sites 2 and 3 binds E2F1 most tightly.(Results, E2F1 binds to the RNA analog of the cognate E2F1 BS on DNA; Figures 2A and 2B)
Sites 2 and 3 are almost perfectly complementary to each other, so the 60 nucleotide fragment that carries both folds back on itself into a double stranded structure, and it is the double stranded oligonucleotides that bound E2F1 most tightly.(Results, E2F1 binds to the RNA analog of the cognate E2F1 BS on DNA; Figure S2G)
RNA and DNA compete for the same surface of E2F1, and the RNA displaced bound DNA at far lower concentrations than the reverse.(Results, E2F1 binds RNA via its DNA binding domain; Figure 4B)

Product: AUMblock sdASO
Targets: SLNCR · human · long non-coding RNAE2F1 · human · protein, transcription factor bound by the decoy oligonucleotide
Models: A375 human melanoma cells, including the A375-Luc2 luciferase line · cell lineWM1575 and WM1976 melanoma short-term cultures · patient-derived short-term culturesNSG mouse, tail vein injection, lung extravasation model · in vivo
Delivery: 1 μM oligonucleotide applied to the cells for 48 hours; the paper writes transfected but names no transfection reagent for the oligonucleotides
Readouts: Matrigel invasion assay, proliferation by manual cell counting with trypan blue, RNA electrophoretic mobility shift assay, electrophoretic mobility shift assay, RT-qPCR, immunoblot, RNA immunoprecipitation with qPCR, bioluminescence imaging in vivo, bulk RNA sequencing, dimethyl sulfate probing with mutational profiling, molecular dynamics simulation
Measured: fall in melanoma cell invasion and proliferation on blocking the SLNCR to E2F1 interaction: a minimum of 2-fold each (1 μM RNA mimic 2+3 against matched controls, in SLNCR-overexpressing A375 cells and in the WM1575 and WM1976 short-term cultures)rise in A375 invasion and proliferation when SLNCR is overexpressed: invasion by 1.6-fold and proliferation by ~1.5-fold (SLNCR overexpression against empty vector control)overall survival of patients whose tumours carry both high SLNCR and high E2F1: 431 days, p = 0.015, against 777 days for the matched control group (TCGA skin cutaneous melanoma primary tumour samples, n = 76)lowest RNA concentration giving an E2F1 mobility shift with binding site 3: 12.5 nM (0.5 μM purified full-length E2F1)length of the oligonucleotide reproducing a pair of binding sites, and the concentration at which it shifted E2F1: 60-mer, shift detected at 12.5 nM (0.5 μM purified full-length E2F1, oligonucleotides carrying BS1+2, BS2+3 or BS4+5)E2F1 bound by a saturating concentration of the binding site 2 plus 3 oligonucleotide: 100 nM of BS2 +3 bound to 0.085 μM of E2F1 (titration of recombinant E2F1 against labelled BS2+3)oligonucleotide concentration and exposure used before the mouse injection: 1 μM ... for 48 h (SLNCR-overexpressing A375-Luc2 cells, washed twice in PBS before injection)
Figures: Figure 3 The oligonucleotide that blocks the SLNCR to E2F1 interaction reduces invasion and proliferation in three melanoma cultures and reduces lung extravasation in mice.Figure 3A Matrigel invasion after treatment with the scramble or the blocking oligonucleotide in three melanoma cultures.Figure 3B Proliferation after treatment with the scramble or the blocking oligonucleotide in the same three cultures.Figure 3C Whole animal bioluminescence images of the two treatment groups.Figure 3D Growth curve of the lung signal over the 7 day experiment for both groups.Figure 1C Survival of melanoma patients split by SLNCR and E2F1 level.
Citation: Shah et al. LncRNA SLNCR phenocopies the E2F1 DNA binding site to promote melanoma progression. Cell Reports 2025;44:115608. doi:10.1016/j.celrep.2025.115608

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