Disruption of a DNA G-quadruplex causes a gain-of-function SCL45A1 variant relevant to developmental disorders

Abstract

SLC45A1 encodes a glucose transporter protein highly expressed in the brain. Mutations in SLC45A1 may lead to neurological diseases and developmental disorders, but its exact role is poorly understood. DNA G-quadruplexes (DNA G4s) are stable structures formed by four guanine bases and play a role in gene regulation and genomic stability. Changes in DNA G4s may affect brain development and function. The mechanism linking alterations in DNA G-quadruplex structures to SLC45A1 pathogenicity remains unknown. In this study, we identify a functional DNA G-quadruplex and its key binding site on SLC45A1 (NM_001080397.3: exon 2: c.449 G>A: p.R150K). This variant results in the upregulation of mRNA and protein expression, which may lead to intellectual developmental disorder with neuropsychiatric features. Mechanistically, the mutation is found to disrupt DNA G-quadruplex structures on SLC45A1, leading to transcriptional enhancement and a gain-of-function mutation, which further causes increased expression and function of the SLC45A1 protein. The identification of the functional DNA G-quadruplex and its effects on DNA G4s may provide new insights into the genetic basis of SLC45A1 pathogenicity and highlight the importance of DNA G4s of SLC45A1 in regulating gene expression and brain development.

1. Introduction

SLC45A1 is located on chromosome 1q42.3 and encodes a membrane protein that is predominantly expressed in melanocytes. SLC45A1 encodes a glucose transporter protein highly expressed in the brain, which plays an important role in the uptake and utilization of glucose by the brain [1]. Mutations in SLC45A1 may therefore lead to neurological diseases and developmental disorders [2,3]. Intellectual developmental disorder with neuropsychiatric features (IDDNPF) is a term used to describe a group of conditions that involve intellectual disability and neuropsychiatric symptoms, such as behavioral problems, mood disorders, and psychosis [4‒6]. An intellectual developmental disorder with neuropsychiatric features is a moderate intellectual disability disorder caused by autosomal recessive inheritance. Patients with this disorder typically exhibit mild seizures and neuropsychiatric abnormalities, including anxiety, obsessive-compulsive behavior, and autistic features. Mild facial dysmorphic features may also be present [5,7]. These symptoms can be challenging to manage and have a significant impact on the individual’s quality of life, as well as the lives of their family members and caregivers. IDDNPF can be caused by a variety of factors, including genetic mutations, environmental factors, and brain abnormalities. Although the exact causes of IDDNPF are still being studied, there is growing evidence to suggest that genetic factors play a significant role in the development of this condition [5,6]. One candidate gene that may be involved in the development of IDDNPF is SLC45A1 [5,6]. The precise mechanisms underlying the role of SLC45A1 in these processes remain poorly understood. Therefore, further investigation of SLC45A1 is necessary to better understand the exact mechanism by which mutations in the SLC45A1 gene may contribute to the development of IDDNPF.

DNA G-quadruplexes (DNA G4s) are regions of DNA that are formed when four guanine bases come together to form a stable structure [8‒10]. These structures are found in the telomeres of chromosomes, as well as in other regions of the genome, and they play important roles in regulating gene expression and maintaining genomic stability [11‒13]. It is thought that changes in the stability or formation of these structures may disrupt the regulation of gene expression, leading to changes in brain development and function [14‒16]. Further research into the genetics and epigenetics of IDDNPF may help to identify new targets for treatment and intervention, and ultimately improve outcomes for individuals with this condition. However, the exact mechanism by which alterations in DNA G4 structures affect target gene expression, which contributes to the development of IDDNPF, has not been reported. This study identified the potential DNA G4s of SLC45A1. By evaluating the G-quadruplex formation score and conducting gene conservation analysis, we identified the crucial site responsible for this process, c.449G>A. Bioinformatics analysis predicted the pathogenicity of this variant, and its enhanced effect on the expression of SLC45A1 was examined in HEK293T cells.