Replication of genome-wide association signals in Asian Indians with early-onset type 2 diabetes

Gene-environment interaction identification via penalized robust divergence

In high-throughput cancer studies, gene-environment interactions associated with outcomes have important implications. Some commonly adopted identification methods do not respect the "main effect, interaction" hierarchical structure. In addition, they can be challenged by data contamination and/or long-tailed distributions, which are not uncommon. In this article, robust methods based on γ$\gamma$ -divergence and density power divergence are proposed to accommodate contaminated data/long-tailed distributions. A hierarchical sparse group penalty is adopted for regularized estimation and selection and can identify important gene-environment interactions and respect the "main effect, interaction" hierarchical structure. The proposed methods are implemented using an effective group coordinate descent algorithm. Simulation shows that when contamination occurs, the proposed methods can significantly outperform the existing alternatives with more accurate identification. The proposed approach is applied to the analysis of The Cancer Genome Atlas (TCGA) triple-negative breast cancer data and Gene Environment Association Studies (GENEVA) Type 2 Diabetes data.

Impact of Genetic Risk Score and Dietary Protein Intake on Vitamin D Status in Young Adults from Brazil

Given the relationship between vitamin D deficiency (VDD) and adverse outcomes of metabolic diseases, we investigated the interplay of dietary and genetic components on vitamin D levels and metabolic traits in young adults from Brazil. Genetic analysis, dietary intake, and anthropometric and biochemical measurements were performed in 187 healthy young adults (19−24 years). Genetic risk scores (GRS) from six genetic variants associated with vitamin D (vitamin D-GRS) and 10 genetic variants associated with metabolic disease (metabolic-GRS) were constructed. High vitamin D-GRS showed a significant association with low 25(OH)D concentrations (p = 0.001) and high metabolic-GRS showed a significant association with high fasting insulin concentrations (p = 0.045). A significant interaction was found between vitamin D-GRS and total protein intake (g/day) (adjusted for non-animal protein) on 25(OH)D (pinteraction = 0.006), where individuals consuming a high protein diet (≥73 g/d) and carrying >4 risk alleles for VDD had significantly lower 25(OH)D (p = 0.002) compared to individuals carrying ≤4 risk alleles. Even though our study did not support a link between metabolic-GRS and vitamin D status, our study has demonstrated a novel interaction, where participants with high vitamin D-GRS and consuming ≥73 g of protein/day had significantly lower 25(OH)D levels. Further research is necessary to evaluate the role of animal protein consumption on VDD in Brazilians.

Interaction between Vitamin D-Related Genetic Risk Score and Carbohydrate Intake on Body Fat Composition: A Study in Southeast Asian Minangkabau Women

Metabolic diseases have been shown to be associated with low vitamin D status; however, the findings have been inconsistent. Hence, the objective of our study was to investigate the relationship between vitamin D status and metabolic disease-related traits in healthy Southeast Asian women and examine whether this relationship was modified by dietary factors using a nutrigenetic study. The study included 110 Minangkabau women (age: 25–60 years) from Padang, Indonesia. Genetic risk scores (GRS) were constructed based on five vitamin D-related single nucleotide polymorphisms (SNPs) (vitamin D-GRS) and ten metabolic disease-associated SNPs (metabolic-GRS). The metabolic-GRS was significantly associated with lower 25-hydroxyvitamin D (25(OH)D) concentrations (p = 0.009) and higher body mass index (BMI) (p = 0.016). Even though the vitamin D-GRS had no effect on metabolic traits (p > 0.12), an interaction was observed between the vitamin D-GRS and carbohydrate intake (g) on body fat percentage (BFP) (p_interaction = 0.049), where those individuals who consumed a high carbohydrate diet (mean ± SD: 319 g/d ± 46) and carried >2 vitamin D-lowering risk alleles had significantly higher BFP (p = 0.016). In summary, we have replicated the association of metabolic-GRS with higher BMI and lower 25(OH)D concentrations and identified a novel interaction between vitamin D-GRS and carbohydrate intake on body fat composition.

Impact of type 2 diabetes variants identified through genome-wide association studies in early-onset type 2 diabetes from South Indian population

The prevalence of early-onset type 2 diabetes (EOT2D) is increasing in Asian countries. Genome-wide association studies performed in European and various other populations have identified associations of numerous variants with type 2 diabetes in adults. However, the genetic component of EOT2D which is still unexplored could have similarities with late-onset type 2 diabetes. Here in the present study we aim to identify the association of variants with EOT2D in South Indian population. Twenty-five variants from 18 gene loci were genotyped in 1,188 EOT2D and 1,183 normal glucose tolerant subjects using the MassARRAY technology. We confirm the association of the HHEX variant rs1111875 with EOT2D in this South Indian population and also the association of CDKN2A/2B (rs7020996) and TCF7L2 (rs4506565) with EOT2D. Logistic regression analyses of the TCF7L2 variant rs4506565(A/T), showed that the heterozygous and homozygous carriers for allele ‘T’ have odds ratios of 1.47 (95% confidence interval [CI], 1.17 to 1.83; p = 0.001) and 1.65 (95% CI, 1.18 to 2.28; p = 0.006) respectively, relative to AA homozygote. For the HHEX variant rs1111875 (T/C), heterozygous and homozygous carriers for allele ‘C’ have odds ratios of 1.13 (95% CI, 0.91 to 1.42; p = 0.27) and 1.58 (95% CI, 1.17 to 2.12; p = 0.003) respectively, relative to the TT homozygote. For CDKN2A/2B variant rs7020996, the heterozygous and homozygous carriers of allele ‘C’ were protective with odds ratios of 0.65 (95% CI, 0.51 to 0.83; p = 0.0004) and 0.62 (95% CI, 0.27 to 1.39; p = 0.24) respectively, relative to TT homozygote. This is the first study to report on the association of HHEX variant rs1111875 with EOT2D in this population.

Different prevalence of T2DM risk alleles in Roma population in comparison with the majority Czech population

BACKGROUND

The Czech governmental study suggests up to a 25% higher prevalence of type 2 diabetes mellitus (T2DM) in the Roma population than within the majority population. It is not known whether and to what extent these differences have a genetic background.

METHODS

To analyze whether the frequencies of the alleles/genotypes of the FTO, TCF7L2, CDKN2A/2B, MAEA, TLE4, IGF2BP2, ARAP1, and KCNJ11 genes differ between the two major ethnic groups in the Czech Republic, we examined them in DNA samples from 302 Roma individuals and 298 Czech individuals.

RESULTS

Compared to the majority population, Roma are more likely to carry risk alleles in the FTO (26% vs. 16% GG homozygotes, p < .01), IGF2BP2 (22% vs. 10% TT homozygotes, p < .0001), ARAP1 (98% vs. 95% of A allele carriers, p < .005), and CDKN2A/2B (81% vs. 66% of TT homozygotes, p < .001) genes; however, less frequently they are carriers of the TCF7L2 risk allele (34% vs. 48% of the T allele p < .0005). Finally, we found significant accumulation of T2DM-associated alleles between the Roma population in comparison with the majority population (25.4% vs. 15.2% of the carriers of at least 12 risk alleles; p < .0001).

CONCLUSION

The increased prevalence of T2DM in the Roma population may have a background in different frequencies of the risk alleles of genes associated with T2DM development.

Cell-free long non-coding RNAs (LY86-AS1 & HCG27_201and GAS5) as biomarkers for pre-diabetes and type 2 DM in Egypt

Background

Increasing interest has been focused on lncRNAs as potential markers in the pathogenesis and progression of numerous diseases.

Aim

We aimed to investigate the expression pattern and role of cell-free lncRNAs (GAS5, HCG27_201 and LY86-AS1) in pre-diabetic, diabetic and T2DM groups.

Subjects & methods

Quantification of the expression level of cell-free lncRNAs (GAS5, HCG27_201 and LY86-AS1) was performed by real-time PCR in 210 individuals classified in diabetic (T2DM), pre-diabetic and control groups.

Results

Significant differences were observed in the relative expression level of lncRNAs (GAS5, LY86-AS1 and HCG27_201) among the three studied groups. The LncRNA expression levels decreased gradually from the control to the pre-diabetic group and reached the lowest values in the T2DM group. The A receiver operating characteristic curve (ROC) was applied to identify a cut-off value for each of the three genes among our groups. The three lncRNAs showed promising results in discriminating between the diabetic patients and controls, with HCG27_201 gene expression having the best performance. Furthermore, lncRNA expression was able to predict the future development of DM in the pre-diabetics because ROC analysis among diabetics and pre-diabetics revealed considerable results. GAS5 gene expression showed the best performance. Additionally, HCG27_201 expression was the most valuable biomarker for differentiating between pre-diabetics and controls and presented a sensitivity of 91% and specificity of 64%.

Conclusions

We concluded that cell free lncRNAs (GAS5, LY86-AS1 and HCG27_201) could be considered promising diagnostic and predictive biomarkers for DM and that HCG27_201 could act as a potential diagnostic biomarker for pre-diabetes.

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lncRNAs are involved in T2DM pathological process.

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lncRNA showed ability to predict development of DM.

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GAS5, LY86-AS1 and HCG27_201 could be considered as diagnostic biomarkers for DM.

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The three studied lncRNA could also be considered as predictive biomarkers for DM.

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HCG27_201 could act as a potential diagnostic biomarker for pre-diabetes.

Targeted deletion of Tcf7l2 in adipocytes promotes adipocyte hypertrophy and impaired glucose metabolism

OBJECTIVE

Activation of the Wnt-signaling pathway is known to inhibit differentiation in adipocytes. However, there is a gap in our understanding of the transcriptional network regulated by components of the Wnt-signaling pathway during adipogenesis and in adipocytes during postnatal life. The key intracellular effectors of the Wnt-signaling pathway occur through TCF transcription factors such as TCF7L2 (transcription factor-7-like 2). Several genetic variants in proximity to TCF7L2 have been linked to type 2 diabetes through genome-wide association studies in various human populations. Our work aims to functionally characterize the adipocyte specific gene program regulated by TCF7L2 and understand how this program regulates metabolism.

METHODS

We generated Tcf7l2^F/F mice and assessed TCF7L2 function in isolated adipocytes and adipose specific knockout mice. ChIP-sequencing and RNA-sequencing was performed on the isolated adipocytes with control and TCF7L2 knockout cells. Adipose specific TCF7L2 knockout mice were challenged with high fat diet and assessed for body weight, glucose tolerance, and lipolysis.

RESULTS

Here we report that TCF7L2 regulates adipocyte size, endocrine function, and glucose metabolism. Tcf7l2 is highly expressed in white adipose tissue, and its expression is suppressed in genetic and diet-induced models of obesity. Genome-wide distribution of TCF7L2 binding and gene expression analysis in adipocytes suggests that TCF7L2 directly regulates genes implicated in cellular metabolism and cell cycle control. When challenged with a high-fat diet, conditional deletion of TCF7L2 in adipocytes led to impaired glucose tolerance, impaired insulin sensitivity, promoted weight gain, and increased adipose tissue mass. This was accompanied by reduced expression of triglyceride hydrolase, reduced fasting-induced free fatty acid release, and adipocyte hypertrophy in subcutaneous adipose tissue.

CONCLUSIONS

Together our studies support that TCF7L2 is a central transcriptional regulator of the adipocyte metabolic program by directly regulating the expression of genes involved in lipid and glucose metabolism.

Hsa_circRNA_0054633 is highly expressed in gestational diabetes mellitus and closely related to glycosylation index

Background

Circular RNA (circRNA) is involved in the pathological processes of various diseases. CircRNA is more stable than linear RNAs and is expressed in high levels in tissues, making it a better biomarker candidate than linear RNAs. In this study, we aimed to identify potential circRNA biomarkers of gestational diabetes mellitus (GDM).

Methods

A retrospective case–control study was conducted using data and samples from women treated at a hospital in China between July 10, 2017, and February 15, 2018. We collected serum samples from 40 healthy pregnant women (controls) and 40 women with GDM (cases) during the second trimester as well as 65 controls and 65 cases during the third trimester of pregnancy. Placenta tissues and neonatal cord blood were each from another 20 cases and 20 controls. We selected six circRNAs (hsa_circRNA_0054633, hsa_circRNA_103410, hsa_circRNA_063981, hsa_circRNA_102682, hsa_circRNA_0018508, and hsa_circRNA_406918) as candidate biomarkers and used quantitative reverse transcriptase polymerase chain reaction (qRT-PCR) to measure their concentrations in the serum and placental tissues. The Pearson correlation test was used to assess the correlation between various circRNAs and between circRNA and clinical variables. The area under the receiver operating characteristic (ROC) curve was used to assess the diagnostic value of circRNAs for GDM at each stage.

Results

Hsa_circRNA_0054633 was highly expressed in the blood during the second and third trimesters; its expression was also high in the placenta but low in the cord blood (P < 0.05). Hsa_cirRNA_0054633 was highly correlated with GHBA1 and GHBA1c levels in maternal blood samples at various stages of the GDM group (including placental tissue and umbilical cord blood) (P < 0.05). Hsa_circRNA_063981, hsa_circRNA_102682, and hsa_circRNA_103410 were also differentially expressed between the case and control groups at different stages (P < 0.05). There was a strong correlation between hsa_circRNA_0054633 and hsa_circRNA_103410 levels in third-trimester maternal blood (P = 0.000, r = 0.554) and in neonatal umbilical cord blood (P = 0.000, r = 0.866). Hsa_circRNA_0054633 showed a significant diagnostic value in the second and third trimesters of pregnancy, placenta, and cord blood (AUC = 0.793, 0.664, 0.747, and 0.783, respectively, P < 0.001).

Conclusion

This study suggests that hsa_cirRNA_0054633 is abnormally expressed in GDM patients and may play a potential role in the development of GDM. The possibility of using circRNAs for the diagnosis of GDM requires additional investigation in future studies.

Electronic supplementary material

The online version of this article (10.1186/s13148-019-0610-8) contains supplementary material, which is available to authorized users.

Lifestyle-tailored interventions for South Asians with type 2 diabetes living in high-income countries: a systematic review

AIM

To summarize evidence on the effectiveness of educational interventions for type 2 diabetes control in South Asians living in high-income countries.

METHODS

We systematically searched PubMed, EMBASE, Cinahl and the Cochrane Library, using Medical Subject Heading and free-text terms. The considered outcomes were: mortality, morbidity, glycaemic control, blood pressure, practice (diet, physical activity and self-care), attitudes/awareness and knowledge. Papers published up to July 2015 were considered. Two reviewers independently screened the title and abstract and then read the full text of selected papers.

RESULTS

Nine studies were included, four non-randomized studies of interventions and five randomized controlled trials. All studies except one were conducted in the UK. Target population ranged from 39 to 1486 individuals; the follow-up ranged from 1 to 24 months. The interventions were mostly based on a tailored educational package, individually or group administered, conducted by lay link workers, health professionals or both. No study measured mortality or morbidity. An effect on glycaemic control was observed only in before/after studies, while a randomized study showed a non-significant improvement (percentage of glycated haemoglobin -0.15, P = 0.11). Two randomized studies found a reduction in blood pressure. Changes in practice and attitudes showed heterogeneous results, mostly favouring intervention.

CONCLUSIONS

There was weak evidence that interventions using link workers and tailored education can modify attitudes, self-care skills and blood pressure in South Asian migrants to industrialized countries. Only one larger trial, with adequate follow-up, showed a small non-significant improvement of glycaemic control.

Hsa_circ_0054633 in peripheral blood can be used as a diagnostic biomarker of pre-diabetes and type 2 diabetes mellitus

AIMS

The purpose of the current study was to investigate the characteristic expression of circular RNAs (circRNAs) in the peripheral blood of type 2 diabetes mellitus (T2DM) patients and their potential as diagnostic biomarkers for pre-diabetes and T2DM.

METHODS

CircRNAs in the peripheral blood from six healthy individuals and six T2DM patients were collected for microarray analysis, and an independent cohort study consisting of 20 normal cases, 20 pre-diabetes patients and 20 T2DM patients was conducted to verify the five chosen circRNAs. We then tested hsa_circ_0054633 in a third cohort (control group, n = 60; pre-diabetes group, n = 63; and T2DM group, n = 64) by quantitative real-time polymerase chain reaction (Q-PCR).

RESULTS

In total, 489 circRNAs were discovered to be differentially expressed between the two groups, and of these, 78 were upregulated and 411 were downregulated in the T2DM group. Five circRNAs were then selected as candidate biomarkers and further verified in a second cohort. Hsa_circ_0054633 was found to have the largest area under the curve (AUC). The diagnostic capacity of hsa_circ_0054633 was tested in a third cohort. After introducing the risk factors of T2DM, the hsa_circ_0054633 AUCs for the diagnosis of pre-diabetes and T2DM slightly increased from 0.751 (95% confidence interval [0.666-0.835], P < 0.001) to 0.841 ([0.773-0.910], P < 0.001) and from 0.793 ([0.716-0.871], P < 0.001) to 0.834 ([0.762-0.905], P < 0.001), respectively.

CONCLUSIONS

Hsa_circ_0054633 presented a certain diagnostic capability for pre-diabetes and T2DM.