In vitro data suggest a role for PMS2 Kozak sequence mutations in Lynch syndrome risk

Evanjalina J Matoy; Jocelyn N Plowman; Cynthia J Watson; Michael A Belshan; Elizabeth E Blue; Chad D Huff; Holly A F Stessman

doi:10.1016/j.xhgg.2024.100298

In vitro data suggest a role for PMS2 Kozak sequence mutations in Lynch syndrome risk

HGG Adv. 2024 Apr 22;5(3):100298. doi: 10.1016/j.xhgg.2024.100298. Online ahead of print.

Authors

Evanjalina J Matoy¹, Jocelyn N Plowman¹, Cynthia J Watson², Michael A Belshan³, Elizabeth E Blue⁴, Chad D Huff⁵, Holly A F Stessman⁶

Affiliations

¹ Department of Pharmacology and Neuroscience, Creighton University, Omaha, NE 68178, USA.
² Creighton University Core Facilities, Creighton University, Omaha, NE 68178, USA.
³ Department of Medical Microbiology and Immunology, Creighton University, Omaha, NE 68178, USA.
⁴ Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA 98195, USA; Institute for Public Health Genetics, University of Washington, Seattle, WA 98195, USA; Brotman Baty Institute, Seattle, WA 98195, USA.
⁵ Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
⁶ Department of Pharmacology and Neuroscience, Creighton University, Omaha, NE 68178, USA; Creighton University Core Facilities, Creighton University, Omaha, NE 68178, USA. Electronic address: hollystessman@creighton.edu.

Abstract

Lynch syndrome (LS) is the most common hereditary cancer syndrome. Heterozygous loss-of-function variants in PMS2 are linked to LS. While these variants are not directly cancer causing, reduced PMS2 function results in the accumulation of somatic variants and increased cancer risk over time due to DNA mismatch repair dysfunction. It is reasonable that other types of genetic variation that impact the expression of PMS2 may also contribute to cancer risk. The Kozak sequence is a highly conserved translation initiation motif among higher eukaryotes and is defined as the nine base pairs upstream of the translation start codon through the first four bases of the translated sequence (5'-[GTT]GCATCCATGG-3'; human PMS2: NM_000535.7). While Kozak sequence variants in PMS2 have been reported in ClinVar in patients with suspected hereditary cancer, all variants upstream of the translation start site are currently classified as variants of undetermined significance (VUSs). We hypothesized that variants significantly disrupting the Kozak sequence of PMS2 would decrease PMS2 protein expression, contributing to increased cancer risk over time. Using a dual-luciferase reporter plasmid and site-directed mutagenesis, we generated the wild-type human PMS2 and the ClinVar VUSs within the PMS2 Kozak sequence. Besides the c.1A>C variant, which is already known to be pathogenic, we implicate six additional variants as American College of Medical Genetics and Genomics (ACMG)/Association for Molecular Pathology (AMP) pathogenic supporting (PP) variants and classify ten as benign supporting (BP). In summary, we present a method developed for the classification of human PMS2 Kozak sequence variants that can contribute to the re-classification of VUSs identified in patients.

Keywords: Kozak sequence; Lynch syndrome; PMS2; cancer risk; hereditary cancer; non-coding variation.