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Modulation of PDCD1 exon 3 splicing.

Junjie Sun1, Jialin Bai1, Tao Jiang1

  • 1Institute of Neuroscience, Soochow University, Suzhou, Jiangsu, China.

RNA Biology
|August 24, 2019
PubMed
Summary

Researchers identified how the PDCD1 gene is spliced to create PD-1Δ3, an isoform that may counteract PD-1 immune checkpoint therapy. They found MATR3 protein activates this splicing, and developed ASOs to promote exon skipping for potential cancer treatments.

Keywords:
DDX5MATR3PD-1PDCD1antisense oligonucleotidecancer

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Area of Science:

  • Molecular Biology
  • Immunology
  • Cancer Research

Background:

  • The PDCD1 gene encodes PD-1, a crucial immune checkpoint protein and target for cancer immunotherapy.
  • Alternative splicing of PDCD1 generates the PD-1Δ3 isoform, which may antagonize PD-1 function, but its splicing mechanism is unknown.

Purpose of the Study:

  • To elucidate the molecular mechanisms regulating PDCD1 alternative splicing, specifically exon 3 skipping.
  • To identify factors involved in PDCD1 exon 3 splicing and explore therapeutic strategies targeting this process.

Main Methods:

  • Minigene system analysis in multiple cell lines to study PDCD1 splicing patterns.
  • Deletion and mutagenesis analysis to map splicing enhancers (ESE3a, ESE3b) within exon 3.
  • RNA-affinity chromatography, mass spectrometry, and protein depletion/overexpression studies to identify splicing factors, including MATR3 and DDX5.

Main Results:

  • Exon 3 skipping was confirmed as the predominant alternative splicing event for PDCD1.
  • MATR3 was identified as a splicing activator that binds to the ESE3b enhancer to promote exon 3 skipping.
  • An RNA secondary structure and the RNA helicase DDX5 were found to counteract MATR3's stimulatory activity.
  • Antisense oligonucleotides (ASOs) were developed that efficiently promote PDCD1 exon 3 skipping in both minigene and endogenous contexts.

Conclusions:

  • MATR3 acts as a key splicing activator for PDCD1 exon 3 skipping, modulated by RNA structure and DDX5.
  • The identified ASOs demonstrate potential as therapeutic agents for cancer treatment by modulating PDCD1 splicing.