Deleterious mis-splicing of STK11 caused by a novel single-nucleotide substitution in the 3' polypyrimidine tract of intron five

Cancer Risk of Peutz-Jeghers Syndrome and Treatment Experience: A Chinese Medical Center

Peutz-Jeghers syndrome (PJS), also known as hereditary mucocutaneous pigmented gastrointestinal polyposis, is a clinically rare autosomal dominant genetic disease, which falls into the category of hereditary colorectal cancer. There are ∼7,000 new cases of PJS in China every year, and 170,000 PJS patients may survive for a long time in society. PJS polyps are characterized by an early age of onset, difficult diagnosis and treatment, and easy recurrence. With repeated growth, polyps can lead to serious complications such as intestinal obstruction, intussusception, gastrointestinal bleeding, and cancerization, which cause serious clinical problems. Due to repeated hospitalization and endoscopic follow-up, PJS patients and their families suffer from great physical and mental pain and economic burden. With the in-depth understanding of PJS and the development and popularization of endoscopic techniques in the past decade, an integrated treatment modality based on endoscopy plus surgery has gradually become the preferred treatment in most hospitals, which greatly improves the quality of life of PJS patients. However, there is still a lack of effective drug prevention and cure means. In this paper, the current clinical treatment means for PJS polyps were summarized by literature review combined with the treatment experience of our medical center, with a focus on their clinical diagnosis, treatment, and cancer risk.

Can tandem alternative splicing and evasion of premature termination codon surveillance contribute to attenuated Peutz-Jeghers syndrome?

Alternative use of short distance tandem sites such as NAGN_n AG are a common mechanism of alternative splicing; however, single nucleotide variants are rarely reported as likely to generate or to disrupt tandem splice sites. We identify a pathogenic intron 5 STK11 variant (NM_000455.4:c.[735-6A>G];[=]) segregating with the mucocutaneous features but not the hamartomatous polyps of Peutz-Jeghers syndrome in two individuals. By RNAseq analysis of peripheral blood mRNA, this variant was shown to generate a novel and preferentially used tandem proximal splice acceptor (AAGTGAAG). The variant transcript (NM_000455.4:c.734_734 + 1insTGAAG), which encodes a frameshift (p.[Tyr246Glufs*43]) constituted 36%-43% of STK11 transcripts suggesting partial escape from nonsense mediated mRNA decay and translation of a truncated protein. A review of the ClinVar database identified other similar variants. We suggest that nucleotide changes creating or disrupting tandem alternative splice sites are a pertinent disease mechanism and require contextualization for clinical reporting. Additionally, we hypothesize that some pathogenic STK11 variants cause an attenuated phenotype.

Deleterious mis-splicing of STK11 caused by a novel single-nucleotide substitution in the 3' polypyrimidine tract of intron five

Background

Pathogenic variants in STK11, also designated as LKB1, cause Peutz–Jeghers syndrome, which is a rare autosomal dominant disorder characterized by mucocutaneous pigmentation changes, polyposis, and a high risk of cancer.

Methods

A male meeting the clinical diagnostic criteria for Peutz–Jeghers syndrome underwent next‐generation sequencing. To validate the predicted splicing impact of a detected STK11 variant, we performed RNA‐Seq on mRNA extracted from patient‐derived Epstein‐Barr virus‐transformed lymphocytes treated with cycloheximide to inhibit nonsense‐mediated decay ex vivo.

Results

Blood testing identified a novel single‐nucleotide substitution, NM_000455.4:c.735‐10C>A, at the end of the 3′ polypyrimidine tract of intron five in STK11. RNA‐Seq confirmed a predicted eight base pair insertion in the mRNA transcript. Following inhibition of nonsense‐mediated decay, the out‐of‐frame insertion was detected in 50% of all RNA‐Seq reads. This confirmed a strong, deleterious splicing impact of the variant.

Conclusion

We characterized a novel likely pathogenic germline variant in intron five of STK11 associated with Peutz–Jeghers syndrome. The study highlights RNA‐Seq as a useful supplement in hereditary cancer predisposition testing.