RNA-Binding Proteomics Reveals MATR3 Interacting with lncRNA SNHG1 To Enhance Neuroblastoma Progression

The interaction of
long noncoding RNAs (lncRNAs) with one or more
RNA-binding proteins (RBPs) is important to a plethora of cellular
and physiological processes. The lncRNA SNHG1 was reported to be aberrantly
expressed and associated with poor patient prognosis in several cancers
including neuroblastoma. However, the interacting RBPs and biological
functions associated with SNHG1 in neuroblastoma remain unknown. In
this study, we identified 283, 31, and 164 SNHG1-interacting proteins
in SK-N-BE(2)­C, SK-N-DZ, and SK-N-AS neuroblastoma cells, respectively,
using a RNA-protein pull-down assay coupled with liquid chromatography–tandem
mass spectrometry (LC–MS/MS). Twenty-four SNHG1-interacting
RBPs were identified in common from these three neuroblastoma cell
lines. RBPs MATR3, YBX1, and HNRNPL have the binding sites for SNHG1
predicted by DeepBind motif analysis. Furthermore, the direct binding
of MATR3 with SNHG1 was validated by Western blot and confirmed by
RNA immunoprecipitation assay (RIP). Coexpression analysis revealed
that the expression of SNHG1 is positively correlated with MATR3 (P = 3.402 × 10–13). The high expression
of MATR3 is associated with poor event-free survival (P = 0.00711) and overall survival (P = 0.00064).
Biological functions such as ribonucleoprotein complex biogenesis,
RNA processing, and RNA splicing are significantly enriched and in
common between SNHG1 and MATR3. In conclusion, we identified MATR3
as binding to SNHG1 and the interaction might be involved in splicing
events that enhance neuroblastoma progression.