Genetic variation at a splicing branch point in intron 7 of STK11: a rare variant decreasing its expression in a Chinese family with Peutz-Jeghers syndrome

Abstract

Background: Peutz-Jeghers syndrome (PJS), a rare dominantly inherited disease, is primarily characterized by hamartomatous polyps and melanotic macules as well as by an increased risk of cancer. The current study aimed to identify the pathogenic gene and pathogenic mechanism of a proband with PJS, thereby offering precise prevention and treatment strategies for PJS.

Methods: A detailed clinical examination was performed of the proband diagnosed with PJS and her family members. In addition, peripheral venous blood was collected from the family members to extract genomic DNA. The pathogenic genes of the proband were identified using whole-exome sequencing, and the candidate pathogenic variants were verified via Sanger sequencing. Meanwhile, co-segregation tests were performed among six family members. Finally, reverse transcription-polymerase chain reaction (RT-PCR) was performed to assess transcript variants in the peripheral blood cells of patients and non-related healthy controls.

Results: Genetic testing revealed a rare splicing variant c.921-1G > C in STK11 in the proband and in her sister and nephew, and the variant co-segregated among the affected family members and nonrelated healthy controls. The proband phenotypically presented with a rare gastric-type adenocarcinoma of the cervix. RT-PCR revealed that the STK11 c.921-1G > C variant could produce two transcripts. Of note, 40 base pairs were deleted in the aberrant transcript between exons 3 and 4, resulting in a frameshift variant and premature termination of the amino acid in exon 6 and ultimately leading to the loss of its functional domain in the STK11 protein. Finally, RT-PCR showed that compared with healthy controls, STK11 mRNA expression level was < 50% in patients.

Conclusion: The present study results indicated that the rare splicing variant c.921-1G > C in intron 7 of STK11 may be a pathogenic variant in patients with PJS. However, this variant (in intron 7) may not produce abnormal transcripts (deletion of 40 base pairs between exons 3 and 4), and PJS may be attributed to the decrease in STK11 expression. Therefore, this study emphasized the importance of genetic counseling, pre-symptomatic monitoring, and early complication management in PJS.

Keywords: STK11; Gastric-type adenocarcinoma of the cervix; Genetic testing; Peutz–Jeghers syndrome; Variant.

Fig. 1

Clinicopathological features of patients with Peutz–Jeghers syndrome (PJS). A: Family pedigree. Squares represent males and circles represent females. An arrow denotes the proband, a solid black box indicates PJS, and a black slash represents death. B–E: pelvic magnetic resonance imaging showing B) sagittal T2WI and C) coronal T2WI. The scan revealed a metabolically active soft tissue mass in the upper right of the vaginal stump (size, approximately 31 × 40 mm); recurrence and invasion of the right ureter were considered. D) Sagittal T2WI and E) coronal T2WI identified a vegetable-patterned mass in the bladder top wall on the right. F–G: Pathological biopsy of the cervix suggested GAS (II-2, 400×). H: STK11 wild type (c.921-1G). I: STK11 heterozygote (c.921–1 C)

Fig. 2

Alternative splicing of STK11 c.921-1G > C. A: RT-PCR was performed to detect the splicing patterns of STK11, with exons 2–9 as the amplified region; M: markers; 1 and 4: healthy control 1; 2 and 5: proband II-2; 3 and 6: healthy control 2, 4, 5, and 6 electrophoresis channels were for the internal control (GAPDH) expression. The expression level of STK11 mRNA in the proband was < 50% of that in healthy controls. B–C: Sanger sequencing of alternatively spliced products; C) wild type and D) deletion of 40 base pairs between exons 3 and 4. (B) Schematic representation of splicing models