GENETIC POLYMORPHISMS OF SERINE RACEMASE AND PROTEIN TYROSINE PHOSPHATASE RECEPTOR TYPE D ASSOCIATED WITH TYPE 2 DIABETES IN MALAY SUBJECTS

Riyadh Saif-Aliimage 

Department of Biochemistry and Molecular Biology, Faculty of Medicine, Sana’a University, Sana’a, Yemen.

ABSTRACT 

Background and objectives: Serine racemase (SRR) and protein tyrosine phosphatase receptor type D (PTPRD) were suggested as Type 2 diabetes mellitus (T2DM) candidate genes by a genome-wide association study (GWAS) in the Chinese population. Association of SRR and PTPRD with T2DM have been reported among East Asian Populations. The association of SRR and PTPRD genetic polymorphisms with T2DM still needs to be studied in Southeast Asian Populations. 

Materials and Methods: This study aimed to evaluate the association of SRR and PTPRD genetic polymorphisms with T2DM in Malay subjects. The single nucleotide polymorphisms (SNPs) of SRR (rs4523957, rs391300, and rs8081273) and PTPRD (rs17584499 and rs649891) were genotyped in 440 T2DM and 398 normal Malay subjects. 

Results: The recessive genetic model showed that SRR genotype GG of rs4523957 and genotype TT of rs391300 are risk factors for T2DM (OR=1.42; 1.45, p=0.022; 0.020, respectively), whereas the dominant and additive genetic models showed that PTPRD SNPs rs17584499 were protective for T2DM (OR=0.76; 0.77, p=0.033; 0.031, respectively).

Conclusion: This study replicated the association of SRR rs4523957, rs391300, and PTPRD rs17584499 genetic polymorphisms with T2DM in Malay, while more investigation in different populations is required to confirm this finding.

Keywords: Genetic polymorphism, risk factors, single-nucleotide polymorphism, type 2 diabetes mellitus.

 

INTRODUCTION

 

Diabetes is a metabolic disorder affecting 537 million people (10.5%) worldwide in 2021, and it is predicted that 783 million people will develop diabetes by 20451. Type 2 diabetes mellitus (T2DM) is presented with decreased insulin secretion and is associated with insulin resistance and obesity2. Both environmental risk factors and genetic susceptibility may contribute to T2DM development3. Genome-wide association (GWAS) study identified 1,791 susceptibility loci for T2DM4. The serine racemase gene (SRR) is located on chromosome 17 and has been suggested to be associated with T2DM5 and gestational diabetes in Chinese6. The association of the SRR genetic variations with T2DM was not replicated in another study7. Serine racemase enzyme is encoded by the SRR gene that synthesizes D-serine from L-serine, which is a co-agonist of glutamate signaling and thus may regulate insulin secretion in pancreatic beta cells and glucagon secretion in pancreatic alpha cells and hence may play a role in the etiology of T2DM8. Recently, Raza et al.,9 reported that SRR gene expression is downregulated in pancreatic islands, which might be associated with metabolic disorders and T2DM. In addition, knockdown SRR has been reported to be involved in T2DM development by decreasing insulin secretion10,11. A recent study showed that insulin secretion is impaired by chronic supplementation with d-serine impairs12. PTPRD genetic variants have been suggested to be associated with T2DM in Chinese using two GWAS studies5,8. Another GWAS study in Mexican‑Americans with 837 T2DM patients and 436 normoglycemic subjects, followed by a meta‑analysis, confirmed the association of PTPRD variants with T2DM13. The PTPRD is a tyrosine phosphatase that may affect insulin signaling in muscle and adipose tissue8. Another study suggested that PTPRD genetic polymorphisms are associated with insulin resistance and the development of diabetes in Han Chinese5. Furthermore, silencing the PTPRD gene by hypermethylation significantly decreased the PTPRD expression resulting in a decrease in insulin signaling14.

The association of SRR and PTPRD genetic polymorphisms with T2DM was conducted in the Chinese population, while the Southeast Asian population remains necessary to be investigated. In addition, the association studies of SRR with T2DM are controversial. Therefore, we aimed to study the association of SRR and PTPRD polymorphisms with T2DM in Malay subjects.  

 

MATERIALS AND METHODS

 

University Malaya Medical Ethics Committee approved this study (Reference No. 387.15). The purpose and nature of the study were explained to each participant, and written consent forms were provided to all participants.

Data sources

Malay normal subjects who engaged in a health check-up at UMMC were invited to join this study (control group). The previously diagnosed Malay patients with T2DM who attended the UMMC, Kuala Lumpur, for treatment, were recruited (case group). The age of all participants was 30-70 years old. Fasting venous blood (5 ml) was withdrawn from each subject into a K2EDTA tube (for glycated hemoglobin measurement and genetic analysis) and a plain blood tube (for biochemical analysis). The participant’s waist circumference (WC) was measured midway between the superior iliac spine and the lower rib margin. The height and weight were measured for each included subject, and BMI was calculated. Automatic Digital Blood Pressure Omron IntelliSense (Omron Healthcare Co. Ltd. Kyoto Japan) was used to measure the participant’s blood pressure (BP).

Genetic Analyses

Wizard Genomic DNA Purification Kit (Promega Corporation, Madison, WI, USA) was used to extract peripheral blood leukocyte DNA according to the manufacturer’s instructions. The predesign TaqMan genotype assay (Applied Biosystems Inc, Foster City, USA) was used for genotyping the SNPs of SRR (rs4523957, rs391300, and rs8081273) and PTPRD (rs649891 and rs17584499) according to the manufacturer’s instruction using the StepOnePlus Real-Time PCR system (Applied Biosystems Inc, Foster City, USA). No template control (NTC) was included in each real-time PCR run as quality control and to exclude DNA contamination.

Biochemical Analyses 

Dimension® RxL Max® (Fully automated analyzer) Integrated Chemistry System (Siemens Healthcare Diagnostics Inc. Deerfield, IL USA) was used to measure diabetic parameters, glucose and HbA1c and lipid profile, triglyceride (TG), total cholesterol, and high-density lipoprotein cholesterol (HDL-c). 

Statistical Analysis

The statistical analyses were executed by IBM SPSS 22 program (SPSS, Inc, Chicago, USA). Logistic regression controlling for age, gender, and body mass index was used to analyze the association of each SNP recessive, dominant, and additive genetic model with T2DM. The SNPs deviations from the Hardy-Weinberg equilibrium were evaluated online 

(http://shesisplus.bio-x.cn/SHEsis.html). 

 

RESULTS 

 

Eight hundred thirty-eight Malay subjects signed the consent forms and donated blood, 440 T2DM, and 398 normal subjects. The anthropometric measurement and biochemical analytes of the subjects were depicted in Table 1. As a consequence of T2DM, the diabetic patients had larger waist circumferences, higher BMI, high FBG, HbA1c, and TG compared to normal subjects. The total cholesterol and HDL-c levels were lower in T2DM patients compared to normal individuals, whereas there were no differences between normal and T2DM subjects in systolic and diastolic blood pressure. In addition, the diabetic patients were significantly older than normal subjects. Table 2 shows the Hardy-Weinberg equilibrium (HWE), call rates, and SNP positions of the included SNPs in this study. The included SNPs in this study did not deviate from HWE in normal subjects, and all SNPs were further analyzed. The results found that homozygous genotype GG of rs4523957 and genotype TT of rs391300 were frequent in diabetic patients (34.6%; 31.3) compared to normal subjects (27.7%; 25.2), respectively.

In contrast, the homozygous genotype CC of rs17584499 is more frequent among normal individuals (50.9%) than diabetic patients (57.4%) (Table 3). There were no differences in genotype frequencies of SRR SNP (rs8081273) and PTPRD SNP (rs649891 between normal subjects and diabetic patients. The recessive, dominant, and additive genetic models were applied to analyze the association of SRR SNPs, rs4523957, rs391300, and rs8081273 and PTPRD SNPs, rs17584499, rs649891 with T2DM (Table 4). 

The recessive genetic model showed that SRR rs4523957 genotype GG and rs391300 genotype TT were risk factors for T2DM (OR=1.42; 1.45, p=0.022; 0.020, respectively), while rs8081273 and rs649891 were not associated with T2DM (p=0.236; 0.54, respectively). In addition, the dominant genetic model showed that PTPRD SNPs rs17584499 were associated with T2DM (OR=0.76, p=0.033), whereas rs4523957, rs391300, and rs8081273, and rs649891 were not associated with T2DM (p=0.67; 0.91; 0.53; 0.80, respectively). The additive genetic model showed that SNPs rs17584499 associated with T2DM (OR=0.77, p=0.031), whereas rs4523957, rs391300, and rs80812 73, and rs649891, were not associated with T2DM (p=0.10; 0.31; 0.30; 0.64, respectively).

 

DISCUSSION 

 

The associations of SRR SNPs rs4523957, rs391300, and rs8081273, as well as PTPRD SNPs rs649891 and rs17584499 with T2DM, were investigated in Malay subjects. This study showed that SRR rs4523957 and rs391300 were associated with T2DM among Malay subjects, which agreed with previous studies on Chinese8. However, this finding disagreed with previous studies on Chinese Han individuals7 and the Japanese population15. The controversial data might be attributed to gene-environmental and gene-gene interactions that may contribute to the differences in the reported gene-disease association between ethnic or racial groups16. Another opinion imputed this to linkage disequilibrium patterns and ethnic differences, combined with the involvement of lifestyle changes and non-genetic factors that can modulate the risk of T2DM17. The presented study showed that the SRR rs8081273 was not associated with T2DM. To the best of our knowledge, no published data on the association of this SNP with T2DM in other populations.The present study found that the PTPRD rs17584499 was associated with T2DM, which agreed with previous studies5,8,18,19 but disagreed with two other studies on the Chinese20 and the Japanese populations15. The difference between our study and the Chinese study20 might be due to the low number of subjects in their study (136 T2DM and 136 control subjects). While in the Japanese study15, they included control participants with fasting plasma glucose <7 mmol/L instead of <6.1 mmol/L, which means they included prediabetic subjects (fasting plasma glucose ≥6.1 to <7 mmol/L), which may have contributed to a higher minor allele frequency in controls in the Japanese study. In our study, rs649891 showed no association with T2DM, which agreed with the previous report on Japanese15.

PTPRD encodes a protein belonging to the receptor type IIA (R2A) subfamily of protein tyrosine phosphatase D (PTPD) and is expressed in the pancreas and skeletal muscle21 and reported to be implicated in diabetes22. The genetic variations of PTPRD may modulate insulin resistance to develop T2DM5,19. The SRR gene encodes SRR enzymes, is widely expressed in the tissue, including the pancreas23, and synthesizes D-serine from L-serine24. D-serine is a co-agonist of glutamate receptors25, and thus glutamate signaling may positively modulate insulin and glucagon secretion in beta cells26. Dysregulation of D-serine could alter glutamate signaling and affect insulin or glucagon secretion in T2DM8. A recent study found that SRR significantly downregulated in diabetes compared to controls9. 

Limitations of the study

The sampling method of this study is non-probability and is hospital-based, and thus the results of this study cannot generalize to the whole population.

 

CONCLUSION 

 

This study replicated the association of SRR SNPs rs4523957, rs391300, and PTPRD rs17584499 with T2DM in Malay. However, more investigations in different populations are required to confirm this association. PTPRD protein is involved in insulin sensitivity, and its genetic variants may participate in the dysregulation of insulin action in muscle and adipose tissues, while SRR genetic variants may disturb insulin secretion through glutamate signaling transduction.

 

CONFLICT OF INTEREST

 

No potential conflict of interest relevant to this article was reported.

 

AUTHOR CONTRIBUTIONS

 

Design the work, practical analysis, statistical analysis, and write the manuscript: R.S.A. 

 

ACKNOWLEDGEMENTS

 

The author thanks all the participants in this research and all medical staff at UMMC for their diligence in this study.

 

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