Body mass index modulates the association between CDKAL1 rs10946398 variant and type 2 diabetes among Taiwanese women

Association of CDKAL1 gene polymorphism (rs10946398) with gestational diabetes mellitus in Pakistani population

BACKGROUND

CDK5 regulatory subunit associated protein 1 like 1 (CDKAL1) encodes a tRNA modifying enzyme involved in the proper protein translation and regulation of insulin production encoded by the CDKL gene. Sequence variations in the CDKAL1 gene lead to the misreading of the Lys codon in proinsulin, resulting in decreased glucose-stimulated proinsulin production. Various polymorphic sequence variants of the CDKAL1 gene such as rs7754840, rs7756992, rs9465871, and rs10946398 are reported to be associated with type 2 diabetes mellitus and gestational diabetes mellitus (GDM) incidence. One of these single nucleotide polymorphisms i.e., rs10946398 has been reported to impact the risk of GDM and its outcomes in pregnant women of different ethnicities i.e., Egypt, Chinese, Korean, Indian, Arab, and Malaysian. Numerous findings have shown that rs10946398 overturns the regulation of CDKAL1 expression, resulting in decreased insulin production and elevated risk of GDM. However, there is no data regarding rs10946398 genotype association with GDM incidence in our population.

METHODOLOGY

In this study, 47 GDM patients and 40 age-matched controls were genotyped for rs10946398 CDKAL1 variant using Tetra primer Amplification Refractory Mutation System Polymerase Chain Reaction (Tetra ARMS-PCR).

RESULTS

Analysis of the results showed the significant association of the C allele of CDKAL1 SNP rs10946398 (χ² = 0.02 p = 0.001) with the risk of GDM development. Conclusively, the results support the role of SNP i.e., rs10946398 of CDKAL1 gene in GDM development in Pakistani female patients. However, future large-scale studies are needed to functionally authenticate the role of variant genotypes in the disease pathogenesis and progression.

Sex Differences in the Effects of CDKAL1 Variants on Glycemic Control in Diabetic Patients: Findings from the Korean Genome and Epidemiology Study

BACKGROUND

Using long-term data from the Korean Genome and Epidemiology Study, we defined poor glycemic control and investigated possible risk factors, including variants related to type 2 diabetes mellitus (T2DM). In addition, we evaluated interaction effects among risk factors for poor glycemic control.

METHODS

Among 436 subjects with newly diagnosed diabetes, poor glycemic control was defined based on glycosylated hemoglobin trajectory patterns by group-based trajectory modeling. For the variants related to T2DM, genetic risk scores (GRSs) were calculated and divided into quartiles. Risk factors for poor glycemic control were assessed using a logistic regression model.

RESULTS

Of the subjects, 43% were in the poor-glycemic-control group. Body mass index (BMI) and triglyceride (TG) were associated with poor glycemic control. The risk for poor glycemic control increased by 11.0% per 1 kg/m2 increase in BMI and by 3.0% per 10 mg/dL increase in TG. The risk for GRS with poor glycemic control was sex-dependent (Pinteraction=0.07), and a relationship by GRS quartiles was found in females but not in males. Moreover, the interaction effect was found to be significant on both additive and multiplicative scales. The interaction effect was evident in the variants of cyclin-dependent kinase 5 regulatory subunit-associated protein 1-like (CDKAL1).

CONCLUSION

Females with risk alleles of variants in CDKAL1 associated with T2DM had a higher risk for poor glycemic control than males.

Relationship between Depression with Physical Activity and Obesity in Older Diabetes Patients: Inflammation as a Mediator

Obesity and physical activity (PA) may affect inflammation and are also related to depression. This study aimed to explore the association between depression, obesity, and PA in older diabetes patients mediated by inflammation. We conducted a cross-sectional study with 197 elderly diabetes patients (≥65 y/o). Participants were interviewed to gather demographic and lifestyle data. Assessment of depression was based on the Diagnostic and Statistical Manual of Mental Disorders, Fourth Edition (DSM-IV) criteria. High-sensitivity C-reactive protein was used as a marker of inflammation. Participants with a body mass index (kg/m2) ≥ 27 were considered to be obese. Our data indicated that among all participants with (n = 57) and without (n = 140) depression, older diabetes patients with depression had a lower intake of energy and protein and a lower prevalence of smoking and alcohol consumption than those without depression (p < 0.05). We also found that inflammation may be a partial mediator in the relationship between obesity and depression, and a significant mediator between PA and depression. Additionally, a regression model of obesity and PA showed that PA was a significant predictor of inflammation. However, the association between obesity and inflammation was not significant. When obesity, PA, and inflammation were included in a regression model together, inflammation significantly predicted depression (OR = 4.18, p = 0.004). The association between obesity and depression was also significant (OR = 2.45, p = 0.038). However, the association between PA and depression was not significant, and the mediating effect of inflammation was significant according to the Sobel test (z = −2.01, p = 0.045). In conclusion, the beneficial effects of PA may lower levels of inflammation produced by obesity, thus reducing inflammatory effects that may be related to depression. Overall, inflammation may mediate the relationship between depression and PA in older diabetes patients.

Risk of uterine leiomyoma based on BET1L rs2280543 single nucleotide polymorphism and vegetarian diet

Background

Bet1 Golgi vesicular membrane trafficking protein-like (BET1L) rs2280543 single nucleotide polymorphism (SNP) and diet have been independently associated with uterine leiomyoma (UL). However, whether the SNP and diet could jointly influence the risk of UL is yet to be assessed. Therefore, we investigated the independent and interactive effects of vegetarian diet and BET1L rs2280543 on uterine fibroids in Taiwanese women.

Methods

We linked participants’ electronic data in the Taiwan Biobank (TWB) database to their medical records in the National Health Insurance Research Database (NHIRD). The TWB had genotypic, lifestyle, and biochemical data between 2008 and 2015 and the NHIRD had data on disease diagnoses between 1998 and 2015. In this study, we included 1997 premenopausal women with complete data.

Results

Compared  to participants with the BET1L rs2280543 CC genotype (wildtype), those with CT/CC genotype had an odds ratio (OR) of 0.69 and a 95% confidence interval (CI) of 0.51–0.93. Vegetarian diet and UL were not significantly associated: OR = 1.09 and 95% CI = 0.77–1.55. However, the test for interaction between rs2280543 and vegetarian diet was significant (p = 0.046). Compared to individuals with the CC genotype, the risk of UL was lower among vegetarians with the CT/TT genotype: OR (95% CI) = 0.15 (0.05–0.47).

Conclusion

The BET1L rs2280543 CT/TT genotype was associated with a lower risk of UL especially among vegetarians.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12905-022-01721-1.

Type 2 Diabetes, PNPLA3 rs738409 Polymorphism, and the Risk of Liver Cirrhosis: Analysis of Taiwan Biobank

Type 2 diabetes (T2D) and liver cirrhosis remain significant public health threats in Taiwan. These conditions are reported to be associated with the rs738409 polymorphism of the patatin-like phospholipase domain-containing protein three gene (PNPLA3) in European populations. We assessed the effect of T2D and PNPLA3 rs738409 polymorphism on liver cirrhosis among Taiwan Biobank (TWB) participants. In total, 17,985 participants in TWB had their health records linked to the National Health Insurance Research Database (NHIRD). Participants included those who visited the assessment centers between 2008 and 2015, with an age range between 30 and 70 years of age. We performed logistic regression analysis to investigate the odds ratios (OR) for liver cirrhosis among participants based on the T2D status and rs738409 genotypes. Genotyping was performed using the Axiom Genome-Wide TWB Array Plate. In our analysis, 150 of the 17,619 eligible participants were identified as cirrhosis cases. Based on the univariate analysis, liver cirrhosis was positively associated with T2D (OR, 1.83; 95% CI 1.23–2.70) whereas, the variant rs738409 was not (regardless of the genetic model). The variant and T2D, however, showed significant interactions in the additive, genotype, and dominant models (p values of 0.0302, 0.0395, and 0.0455, respectively). We observed a statistically significant association between T2D and liver cirrhosis and variant rs738409 with an OR of 1.71 (95% CI, 1.03–2.84) for individuals carrying a G allele compared to those with a C allele and 2.92 (95% CI 1.07–7.99) for GG compared to CC individuals. According to our study, Taiwanese adults with T2D and the rs738409 GG genotype are more likely to develop liver cirrhosis.

Detecting Genetic Ancestry and Adaptation in the Taiwanese Han People

The Taiwanese people are composed of diverse indigenous populations and the Taiwanese Han. About 95% of the Taiwanese identify themselves as Taiwanese Han, but this may not be a homogeneous population because they migrated to the island from various regions of continental East Asia over a period of 400 years. Little is known about the underlying patterns of genetic ancestry, population admixture, and evolutionary adaptation in the Taiwanese Han people. Here, we analyzed the whole-genome single-nucleotide polymorphism genotyping data from 14,401 individuals of Taiwanese Han collected by the Taiwan Biobank and the whole-genome sequencing data for a subset of 772 people. We detected four major genetic ancestries with distinct geographic distributions (i.e., Northern, Southeastern, Japonic, and Island Southeast Asian ancestries) and signatures of population mixture contributing to the genomes of Taiwanese Han. We further scanned for signatures of positive natural selection that caused unusually long-range haplotypes and elevations of hitchhiked variants. As a result, we identified 16 candidate loci in which selection signals can be unambiguously localized at five single genes: CTNNA2, LRP1B, CSNK1G3, ASTN2, and NEO1. Statistical associations were examined in 16 metabolic-related traits to further elucidate the functional effects of each candidate gene. All five genes appear to have pleiotropic connections to various types of disease susceptibility and significant associations with at least one metabolic-related trait. Together, our results provide critical insights for understanding the evolutionary history and adaption of the Taiwanese Han population.

Association of CDKAL1 RS10946398 Gene Polymorphism with Susceptibility to Diabetes Mellitus Type 2: A Meta-Analysis

BACKGROUND

Diabetes is one of the common chronic diseases in which susceptibility is determined by a combination of genetic and environmental factors, and more than 90% of diabetic patients are diabetes mellitus type 2 (T2DM). The existing studies on the association between CDKAL1 rs10946398 gene polymorphism and susceptibility to type 2 diabetes are inconsistent across populations.

AIM

We aim to explore the association between CDKAL1 rs10946398 gene polymorphism and susceptibility to type 2 diabetes in different populations.

METHODS

We examined all studies before June 12, 2021, that associated CDKAL1 rs10946398 with T2DM. Heterogeneity was assessed by meta-analysis of allelic inheritance models (A vs. C), dominant inheritance models (AA vs. AC+CC), and recessive inheritance model (AA+AC vs. CC); I ² was used to assess the heterogeneity (if I ² < 50%, the fixed-effects model was used; if I ² ≥ 50%, the random-effects model was used for data consolidation); correlation was judged by a forest map; potential publication bias was tested by the Egger test (p > 0.05 indicates that there is no publication bias).

RESULTS

Fourteen data totaling 30288 subjects, including 19272 controls and 11016 patients with T2DM, met our inclusion criteria. In the Asian population, the differences were statistically significant (p < 0.01) for dominant genetic model (OR = 0.75, 95%CI = 0.64-0.88, p = 0.0003). But the allelic effect model (OR = 0.87, 95%CI = 0.75-1.02, p = 0.08) and the recessive genetic model (OR = 0.85, 95%CI = 0.66-1.10, p = 0.23) were not statistically significant (p > 0.01). In the non-Asian population, the differences were statistically significant (p < 0.01) for the allelic effect model (OR = 0.83, 95%CI = 0.77-0.88, p < 0.00001), the dominant model (OR = 0.79, 95%CI = 0.72-0.87, p < 0.00001), and the recessive model (OR = 0.78, 95%CI = 0.70-0.87, p < 0.0001).

CONCLUSION

In this study, CDKAL1 RS10946398 was positively associated with T2DM, but the association was different in Asian populations.

Association of the CDKAL1 polymorphism rs10946398 with type 2 diabetes mellitus in adults: A meta-analysis

Previous studies had reported that the CDKAL1 (cyclin-dependent kinase 5 (CDK5) regulatory subunit-associated protein 1-like 1) rs10946398 C/A polymorphism associated with type 2 diabetes mellitus (T2DM) in various ethnic groups, however, inconsistent results have been obtained in studies of different populations.We performed a meta-analysis of 13 studies for rs10946398 of CDKAL1 on genetic susceptibility for T2DM.The results showed that CDKAL1 rs10946398 C/A polymorphism associated with T2DM under allelic (odds risk (OR): 1.17, 95% CI: 1.07-1.28, P = .0007), homozygous (OR: 1.39, 95% CI: 1.15-1.69, P = .0008), and dominant models (OR: 1.26, 95% CI: 1.09-1.46, P = .001).We found that rs10946398 C/A polymorphism was associated with T2DM, and this association was significantly in population of western country (Europe and United States) and Asian populations.

Interactive Effect of IGF2BP2 rs4402960 Variant, Smoking and Type 2 Diabetes

PURPOSE

Genetic and environmental factors are related to type 2 diabetes (T2D). Genetic modifiers of T2D have not been widely determined among smoking individuals. In this population-based study, we investigated the interactive association between rs4402960 polymorphism of the insulin-like growth factor 2 mRNA-binding protein 2 (IGF2BP2) gene and smoking with T2D among Taiwanese adults.

MATERIALS AND METHODS

We obtained genetic data collected between 2008 and 2018 for 22,039 participants (aged 30-70 years) from the Taiwan Biobank (TWB) database. These data were analyzed using the t-test, Chi-square (χ ²) test, and multiple logistic regression.

RESULTS

The mean ages for participants with and without diabetes were 58.11±8.75 and 48.58±11, respectively. Compared with the rs4402960 GG genotype, the odds ratio (OR) for T2D was 1.261 among GT and 1.545 among TT genotype individuals (p<0.05). Current smokers compared to nonsmokers were associated with a higher risk of T2D (OR=1.266, p=0.0404). There was a significant interaction between the IGF2BP2 rs4402960 variant and smoking on T2D (p = 0.0497). After stratification by rs4402960 genotypes and smoking status, the OR was substantial only in current smokers with GG genotype (OR, 1.663, p = 0.0008).

CONCLUSION

This population-based study indicated that the risk for T2D was stronger among current smoking rs4402960 GG individuals recruited between 2008 and 2019 in Taiwan.

A Novel Polymorphism (rs35612982) in CDKAL1 Is a Risk Factor of Type 2 Diabetes: A Case-Control Study

BACKGROUND

The interaction of environmental factors and genetic factors may contribute to the risk of type 2 diabetes (T2D). We aimed to investigate whether age, gender, body mass index (BMI) and lifestyle factors have an effect on the association between the CDKAL1 polymorphisms and T2D.

METHODS

Eight single nucleotide polymorphisms in CDKAL1 were genotyped by Agena MassARRAY in 508 T2D patients and 503 controls. The association between the CDKAL1 polymorphisms and T2D was evaluated using logistic regression model by calculating OR and 95% CIs.

RESULTS

We found a significant association between CDKAL1 polymorphisms (rs4712523, OR 1.42, p = 9.44 × 10-5; rs4712524, OR 1.38, p = 3.28 × 10-4; rs10946398, OR 1.43, p = 6.21 × 10-5; rs7754840, OR 1.43, p = 6.33 × 10-5; rs35612982, OR 1.34, p = 0.0010; and rs10440833, OR 1.32, p = 0.0018) and T2D risk among the Han population from Northwest China. We also found that genetic variants of CDKAL1 could modify the risk of T2D that might be influenced by age, BMI and the status of smoking and drinking. Besides, rs35612982-CT (p = 0.038) and rs10440833-AT (p = 0.044) genotypes were higher insulin level.

CONCLUSION

CDKAL1 rs35612982 (C/T) polymorphism, as a new polymorphism, was associated with the increased risk of T2D in the Han Chinese population. Moreover, the contribution of CDKAL1 polymorphisms to T2D risk seems to be associated with age, gender, BMI, smoking and drinking.

Genetic Basis of Obesity and Type 2 Diabetes in Africans: Impact on Precision Medicine

PURPOSE OF REVIEW

Recent advances in genomics provide opportunities for novel understanding of the biology of human traits with the goal of improving human health. Here, we review recent obesity and type 2 diabetes (T2D)-related genomic studies in African populations and discuss the implications of limited genomics studies on health disparity and precision medicine.

RECENT FINDINGS

Genome-wide association studies in Africans have yielded genetic discovery that would otherwise not be possible; these include identification of novel loci associated with obesity (SEMA-4D, PRKCA, WARS2), metabolic syndrome (CA-10, CTNNA3), and T2D (AGMO, ZRANB3). ZRANB3 was recently demonstrated to influence beta cell mass and insulin response. Despite these promising results, genomic studies in African populations are still limited and thus genomics tools and approaches such as polygenic risk scores and precision medicine are likely to have limited utility in Africans with the unacceptable possibility of exacerbating prevailing health disparities. African populations provide unique opportunities for increasing our understanding of the genetic basis of cardiometabolic disorders. We highlight the need for more coordinated and sustained efforts to increase the representation of Africans in genomic studies both as participants and scientists.

Matching tRNA modifications in humans to their known and predicted enzymes

tRNA are post-transcriptionally modified by chemical modifications that affect all aspects of tRNA biology. An increasing number of mutations underlying human genetic diseases map to genes encoding for tRNA modification enzymes. However, our knowledge on human tRNA-modification genes remains fragmentary and the most comprehensive RNA modification database currently contains information on approximately 20% of human cytosolic tRNAs, primarily based on biochemical studies. Recent high-throughput methods such as DM-tRNA-seq now allow annotation of a majority of tRNAs for six specific base modifications. Furthermore, we identified large gaps in knowledge when we predicted all cytosolic and mitochondrial human tRNA modification genes. Only 48% of the candidate cytosolic tRNA modification enzymes have been experimentally validated in mammals (either directly or in a heterologous system). Approximately 23% of the modification genes (cytosolic and mitochondrial combined) remain unknown. We discuss these 'unidentified enzymes' cases in detail and propose candidates whenever possible. Finally, tissue-specific expression analysis shows that modification genes are highly expressed in proliferative tissues like testis and transformed cells, but scarcely in differentiated tissues, with the exception of the cerebellum. Our work provides a comprehensive up to date compilation of human tRNA modifications and their enzymes that can be used as a resource for further studies.

Type 2 Diabetes-Associated Genetic Polymorphisms as Potential Disease Predictors

Diabetes is a major cause of mortality worldwide. There are several types of diabetes, with type 2 diabetes mellitus (T2DM) being the most common. Many factors, including environmental and genetic factors, are involved in the etiology of the disease. Numerous studies have reported the role of genetic polymorphisms in the initiation and development of T2DM. While genome-wide association studies have identified around more than 200 susceptibility loci, it remains unclear whether these loci are correlated with the pathophysiology of the disease. The present review aimed to elucidate the potential genetic mechanisms underlying T2DM. We found that some genetic polymorphisms were related to T2DM, either in the form of single-nucleotide polymorphisms or direct amino acid changes in proteins. These polymorphisms are potential predictors for the management of T2DM.