A novel disease mechanism leading to the expression of a disallowed gene in the pancreatic beta-cell identified by non-coding, regulatory mutations controlling HK1

Abstract

Gene expression is tightly regulated with many genes exhibiting cell-specific silencing when their protein product would disrupt normal cellular function. This silencing is largely controlled by non-coding elements and their disruption might cause human disease. We performed gene-agnostic screening of the non-coding regions to discover new molecular causes of congenital hyperinsulinism. This identified 14 non-coding de novo mutations affecting a 42bp conserved region encompassed by a regulatory element in intron 2 of Hexokinase 1 (HK1), a pancreatic beta-cell disallowed gene. We demonstrated that these mutations resulted in expression of HK1 in the pancreatic beta-cells causing inappropriate insulin secretion and congenital hyperinsulinism. These mutations identify a regulatory region critical for cell-specific silencing. Importantly, this has revealed a new disease mechanism for non-coding mutations that cause inappropriate expression of a disallowed gene.

Congenital Hyperinsulinism: Current Laboratory-Based Approaches to the Genetic Diagnosis of a Heterogeneous Disease

“…The approach to the interpretation of exome and genome sequencing data will differ between centres with some analysing variants called within a pre-defined set of known disease-causing genes whilst other laboratories will perform a gene-agnostic analysis. The latter approach has the advantage of being able to identify new genes for HI, with recent successes including the discovery of the syndromic HI genes CACNA1D , PMM2 , FOXA2 , TRMT10A , EIF2S3 , YARS , and KMT2D by exome sequencing and more recently the finding of regulatory variants deep within intron 2 of the beta-cell disallowed gene, HK1 , by genome sequencing in individuals with isolated hyperinsulinism ( 15 , 37 , 45 , 47 , 51 , 59 , 62 , 63 ). The ability of a laboratory to utilise next-generation sequencing data for genetic discovery will largely depend on their ability to perform robust genetic and functional studies to assess novel variation.…”

“…Unlike targeted next-generation sequencing, which screens a predetermined list of genes, exome sequencing provides an extremely effective method to comprehensively analyse the coding regions and intron/exon boundaries of all known HI genes and to assess copy number status. The major limitation of the approach is that it will not detect non-coding mutations such as the deep intronic mutations reported in ABCC8 , HADH and HK1 or promoter variants in genes such as HNF4A , PMM2 , and SLC16A1 ( 15 , 21 , 22 , 59 , 82 ).…”

Bi‐allelic pathogenic variants in PABPC1L cause oocyte maturation arrest and female infertility

“…In addition, there is a good understanding of the functional impact of protein-coding variants in female infertility (Jiao et al, 2021), but less understanding of variants in non-coding regions, which accounts for 98% of the human genome. In the last decade, many studies have identified that variants in non-coding regions cause different diseases (Turro et al, 2020;Wright et al, 2021;Wakeling et al, 2022), which suggests that the analysis of non-coding regions in female infertility patients with unknown causes is also a powerful strategy to find novel pathogenic variants.…”