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de Klerk JA, Beulens JWJ, Mei H, Bijkerk R, van Zonneveld AJ, Koivula RW, Elders PJM, 't Hart LM, Slieker RC. Altered blood gene expression in the obesity-related type 2 diabetes cluster may be causally involved in lipid metabolism: a Mendelian randomisation study. Diabetologia 2023; 66:1057-1070. [PMID: 36826505 PMCID: PMC10163084 DOI: 10.1007/s00125-023-05886-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 01/17/2023] [Indexed: 02/25/2023]
Abstract
AIMS/HYPOTHESIS The aim of this study was to identify differentially expressed long non-coding RNAs (lncRNAs) and mRNAs in whole blood of people with type 2 diabetes across five different clusters: severe insulin-deficient diabetes (SIDD), severe insulin-resistant diabetes (SIRD), mild obesity-related diabetes (MOD), mild diabetes (MD) and mild diabetes with high HDL-cholesterol (MDH). This was to increase our understanding of different molecular mechanisms underlying the five putative clusters of type 2 diabetes. METHODS Participants in the Hoorn Diabetes Care System (DCS) cohort were clustered based on age, BMI, HbA1c, C-peptide and HDL-cholesterol. Whole blood RNA-seq was used to identify differentially expressed lncRNAs and mRNAs in a cluster compared with all others. Differentially expressed genes were validated in the Innovative Medicines Initiative DIabetes REsearCh on patient straTification (IMI DIRECT) study. Expression quantitative trait loci (eQTLs) for differentially expressed RNAs were obtained from a publicly available dataset. To estimate the causal effects of RNAs on traits, a two-sample Mendelian randomisation analysis was performed using public genome-wide association study (GWAS) data. RESULTS Eleven lncRNAs and 175 mRNAs were differentially expressed in the MOD cluster, the lncRNA AL354696.2 was upregulated in the SIDD cluster and GPR15 mRNA was downregulated in the MDH cluster. mRNAs and lncRNAs that were differentially expressed in the MOD cluster were correlated among each other. Six lncRNAs and 120 mRNAs validated in the IMI DIRECT study. Using two-sample Mendelian randomisation, we found 52 mRNAs to have a causal effect on anthropometric traits (n=23) and lipid metabolism traits (n=10). GPR146 showed a causal effect on plasma HDL-cholesterol levels (p = 2×10-15), without evidence for reverse causality. CONCLUSIONS/INTERPRETATION Multiple lncRNAs and mRNAs were found to be differentially expressed among clusters and particularly in the MOD cluster. mRNAs in the MOD cluster showed a possible causal effect on anthropometric traits, lipid metabolism traits and blood cell fractions. Together, our results show that individuals in the MOD cluster show aberrant RNA expression of genes that have a suggested causal role on multiple diabetes-relevant traits.
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Affiliation(s)
- Juliette A de Klerk
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, the Netherlands
- Department of Internal Medicine (Nephrology), Leiden University Medical Center, Leiden, the Netherlands
| | - Joline W J Beulens
- Amsterdam Public Health Institute, Amsterdam UMC, Amsterdam, the Netherlands
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, the Netherlands
- Department of Epidemiology and Data Science, Amsterdam UMC, location VUmc, Amsterdam, the Netherlands
| | - Hailiang Mei
- Sequencing Analysis Support Core, Leiden University Medical Center, Leiden, the Netherlands
| | - Roel Bijkerk
- Department of Internal Medicine (Nephrology), Leiden University Medical Center, Leiden, the Netherlands
| | - Anton Jan van Zonneveld
- Department of Internal Medicine (Nephrology), Leiden University Medical Center, Leiden, the Netherlands
| | - Robert W Koivula
- Department of Clinical Sciences, Lund University, Genetic and Molecular Epidemiology, CRC, Skåne University Hospital Malmö, Malmö, Sweden
| | - Petra J M Elders
- Amsterdam Public Health Institute, Amsterdam UMC, Amsterdam, the Netherlands
- Department of General Practice and Elderly Care Medicine, Amsterdam Public Health Research Institute, Amsterdam UMC, location VUmc, Amsterdam, the Netherlands
| | - Leen M 't Hart
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, the Netherlands
- Amsterdam Public Health Institute, Amsterdam UMC, Amsterdam, the Netherlands
- Department of Epidemiology and Data Science, Amsterdam UMC, location VUmc, Amsterdam, the Netherlands
- Department of Biomedical Data Sciences, Section Molecular Epidemiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Roderick C Slieker
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, the Netherlands.
- Amsterdam Public Health Institute, Amsterdam UMC, Amsterdam, the Netherlands.
- Department of Epidemiology and Data Science, Amsterdam UMC, location VUmc, Amsterdam, the Netherlands.
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