Influence of genetic copy number variants of the human GLUT3 glucose transporter gene SLC2A3 on protein expression, glycolysis and rheumatoid arthritis risk: A genetic replication study

Elliott Greenspan,Timothy W. Behrens,Michael J. Townsend,Hongxiu Wen,Arthur Wuster,Kim R. Simpfendorfer,Julie Hunkapiller,Andrew Shih,Edward A. Einsidler,Doron M. Behar,Harini P. Kothari,Peter K. Gregersen,Rui Hu,Robert R. Graham,Wentian Li

doi:10.1016/j.ymgmr.2019.100470

Abstract

ObjectivesThe gene encoding glucose transporter 3 (GLUT3, SLC2A3) is present in the human population at variable copy number. An overt disease phenotype of SLC2A3 copy number variants has not been reported; however, deletion of SLC2A3 has been previously reported to protect carriers from rheumatoid arthritis, implicating GLUT3 as a therapeutic target in rheumatoid arthritis. Here we aim to perform functional analysis of GLUT3 copy number variants in immune cells, and test the reported protective association of the GLUT3 copy number variants for rheumatoid arthritis in a genetic replication study. MethodsCells from genotyped healthy controls were analyzed for SLC2A3/GLUT3 expression and glycolysis capacity. We genotyped the SLC2A3 copy number variant in four independent cohorts of rheumatoid arthritis and controls and one cohort of multiple sclerosis and controls. ResultsHeterozygous deletion of SLC2A3 correlates directly with expression levels of GLUT3 and influences glycolysis rates in the human immune system. The frequency of the SLC2A3 copy number variant is not different between rheumatoid arthritis, multiple sclerosis and control groups. ConclusionsDespite a robust SLC2A3 gene copy number dependent phenotype, our study of large groups of rheumatoid arthritis cases and controls provides no evidence for rheumatoid arthritis disease protection in deletion carriers. These data emphasize the importance of well powered replication studies to confirm or refute genetic associations, particularly for relatively rare variants.

Highlights

Distinct metabolic profiles characterize the main players in rheumatoid arthritis (RA) pathogenesis
By plotting B allele frequency (BAF) and logR ratios (LRR) we verified that visual inspection could corroborate Quantitative PCR (qPCR) Copy number variants (CNVs) calls (Fig. 1A–C)
Prompted by a previous study of protection from RA, we explored the biological effects of SLC2A3 deletion on immune cell function

Summary

Introduction

Distinct metabolic profiles characterize the main players in rheumatoid arthritis (RA) pathogenesis. CD4+ effector T cells preferentially utilize glycolysis upon activation and upregulate their expression of glucose transporters GLUT1 and GLUT3, while induced regulatory T cells favor oxidative lipid metabolism [1,2]. The gene encoding GLUT3, SLC2A3, is copy number variable in humans [3] and heterozygous deletion is reported to protect carriers from developing. A deletion or duplication of 129 kb at chromosome 12p13.31 results in variants of one or three (or more) total SLC2A3 gene copies respectively. Heterozygous deletion at SLC2A3 is consistently found in 0.5–1% of individuals, while one or more duplications are found in approximately 4% of normal subjects across multiple populations [3,4]. The protective association of SLC2A3 for RA implicates GLUT3 as a potential therapeutic target in treatment or prevention of RA

Objectives

Results

Conclusion