Common genetic variants and pathways in diabetes and associated complications and vulnerability of populations with different ethnic origins

Investigating the association between FOK1 polymorphism in the vitamin D receptor (VDR) gene and type 2 diabetes prevalence: A comprehensive analysis

There is mounting evidence that suggests vitamin D insufficiency may have a role in the emergence of type 2 diabetes. Additionally, as VDR mediates the actions of vitamin D, variants in its sequence could have implications in this disease. One of these polymorphisms, Fok1 (rs2228570), has been demonstrated to generate changes in the receptor's structure, causing a shorter protein. The purpose of this research is to establish a potential association between the Fok1 polymorphism and DM2. To achieve such goal, a comprehensive study of this SNP was conducted using functional in-silico analysis and a systematic review with meta-analysis. Additionally, an examination of VDR gene expression in patients with diabetes compared to controls was performed in order to investigate possible differences in expression levels. Our expression analysis showed that VDR has no differential expression between these two groups. To study its functional consequences and stability, different tools were combined, without consistent results. Finally, our systematic review and meta-analysis showed that theFok1 variant was not significantly associated with the DM2 prevalence. This extensive analysis did not provide support for an association between the presence of Fok1 polymorphism and DM2. This result aligns with some previous studies but contrasts others that have reported both protective and risk factors.

Distinct Roles of Common Genetic Variants and Their Contributions to Diabetes: MODY and Uncontrolled T2DM

Type 2 diabetes mellitus (T2DM) encompasses a range of clinical manifestations, with uncontrolled diabetes leading to progressive or irreversible damage to various organs. Numerous genes associated with monogenic diabetes, exhibiting classical patterns of inheritance (autosomal dominant or recessive), have been identified. Additionally, genes involved in complex diabetes, which interact with environmental factors to trigger the disease, have also been discovered. These genetic findings have raised hopes that genetic testing could enhance diagnostics, disease surveillance, treatment selection, and family counseling. However, the accurate interpretation of genetic data remains a significant challenge, as variants may not always be definitively classified as either benign or pathogenic. Research to date, however, indicates that periodic reevaluation of genetic variants in diabetes has led to more consistent findings, with biases being steadily eliminated. This has improved the interpretation of variants across diverse ethnicities. Clinical studies suggest that genetic risk information may motivate patients to adopt behaviors that promote the prevention or management of T2DM. Given that the clinical features of certain monogenic diabetes types overlap with T2DM, and considering the significant role of genetic variants in diabetes, healthcare providers caring for prediabetic patients should consider genetic testing as part of the diagnostic process. This review summarizes current knowledge of the most common genetic variants associated with T2DM, explores novel therapeutic targets, and discusses recent advancements in the pharmaceutical management of uncontrolled T2DM.

Impact of IL-6 rs1800795 and rs1800796 polymorphisms on clinical outcomes of COVID-19: a study on severity of disease in Turkish population

Coronavirus disease (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is exacerbated by cytokine storms, leading to severe inflammation. Interleukin-6 (IL-6) plays a critical role in this process, and variations in its promoter may influence disease severity. This study aims to investigate the relationship between IL6 promoter polymorphisms rs1800795 (G > C) and rs1800796 (G > C) and the severity of COVID-19 in the Turkish population. A total of 332 participants were included: 84 control, 80 with mild COVID-19, and 168 with severe COVID-19. IL6 polymorphisms were genotyped using the restriction fragment length polymorphism (RFLP) method. The genotypes rs1800795 GC (OR = 3.00, 95% CI: 1.669-5.398, p < 0.000), CC (OR = 7.44, 95% CI: 2.899-19.131, p < 0.000), and rs1800796 GC (OR = 2.76, 95% CI: 1.603-4.761, p < 0.000), as well as the alleles rs1800795 C (OR = 3.01, p < 0.000) and rs1800796 C (OR = 1.97, p = 0.002), may be associated with the severity of COVID-19. According to the Jonckheere-Terpstra (J-T) test, the most significant trends that vary linearly with disease severity were observed for D-dimer [J-T = 15.896, Effect size = 0.68 (0.61 to 0.76), p < 0.000] and CRP [J-T = 15.389, Effect size = 0.66 (0.59 to 0.73), p < 0.000]. The distribution of clinical parameters across genotype combinations (rs1800796/rs1800795*) showed that GC/GC* and GC/CC* were linked to a higher risk of severe inflammation, clotting, and organ damage. Additionally, it has been determined that the G-C and C-C haplotypes may be associated with increased severity of COVID-19. The rs1800795 and rs1800796 polymorphisms are linked to COVID-19 severity and could help guide future treatment strategies.

Diabetic kidney disease and polymorphisms of the ELMO1 and AGTR1 genes: Systematic review

BACKGROUND

Diabetic kidney disease (DKD) is one of the main complications of diabetes, the main cause of chronic kidney disease (CKD) and end-stage renal disease (ESRD) worldwide. The etiopathogenesis of DKD is complex and multifactorial; recently, genetic susceptibility has gained relevance since certain ethnicities, such as Native Americans and Mexican Americans, have a higher risk of developing this disease. Numerous studies have described that single nucleotide polymorphisms (SNPs), including those for ELMO1 and AGTR1 genes, could be associated with DKD.

OBJECTIVE

To carry out a systematic review of the scientific literature on the association of SNPs of the ELMO1 and AGTR1 gene with DKD in adult patients with type 2 diabetes mellitus (T2D).

METHODS

Systematic review in PubMed, Google Scholar, Worldwide Science, and Science Direct databases. The selection of publications was carried out following the guidelines proposed by PRISMA (Preferred Reporting Items for Systematic Reviews and Meta Analyses). Original articles that reported results in the adult population with T2D were included. Information about the allelic and genotypic frequencies of the SNPs and their association with DKD was obtained.

RESULTS

The polymorphisms most frequently associated with a DKD higher risk were rs741301, rs1345365, and rs10951509 for the ELMO1 gene, whereas the rs5186 and rs388915 for the AGTR1 gene.

CONCLUSION

The risk of developing DKD depends on several factors, including the genetic susceptibility conferred by the ELMO1 and AGTR1 gene polymorphisms, without ignoring the patient's lifestyle and environmental factors. The studies about these polymorphisms' association with DKD will allow a better understanding of non-modifiable risk factors for developing this disease and recognize the differences between different studied ethnicities, which would allow faster detection of patients with T2D susceptible to developing DKD, become early markers of kidney damage, as well as implementing preventive strategies on the most susceptible ethnicities.

Integrating Polygenic Risk Scores (PRS) for Personalized Diabetes Care: Advancing Clinical Practice with Tailored Pharmacological Approaches

The rising global prevalence of diabetes poses a serious threat to public health, national economies, and the healthcare system. Despite a high degree of disease heterogeneity and advancing techniques, there is still an unclear diagnosis of patients with diabetes compounded by the array of long-term microvascular and macrovascular complications associated with the disease. In addition to environmental variables, diabetes susceptibility is significantly influenced by genetic components. The risk stratification of genetically predisposed individuals may play an important role in disease diagnosis and management. Precision medicine methods are crucial to reducing this global burden by delivering a more personalised and patient-centric approach. Compared to the European population, genetic susceptibility variants of type 2 diabetes mellitus (T2DM) are still not fully understood in other major populations, including South Asians, Latinos, and people of African descent. Polygenic risk scores (PRS) can be used to identify individuals who are more susceptible to complex diseases such as diabetes. PRS is selective and effective in developing novel diagnostic interventions. This comprehensive predictive approach facilitates the understanding of distinct response profiles, resulting in the development of more effective management strategies. The targeted implementation of PRS is especially advantageous for people who fall into a higher-risk category for diabetes. Through early risk assessment and the creation of individualised diabetes treatment plans, the integration of PRS in clinical practice shows potential for reducing the prevalence of diabetes and its complications. Diabetes self-management depends significantly on patient empowerment, with behavioural monitoring emerging as a vital facilitator. The main aim of this review article is to formulate a more structured intervention strategy by advocating for increased awareness of the clinical utility of PRS and counseling among healthcare practitioners, patients, and individuals at risk of diabetes.

Maternal periconception hyperglycemia, preconception diabetes, and risk of major congenital malformations in offspring

STUDY QUESTION

What are the roles of maternal preconception diabetes and related periconceptional hyperglycemia on the risk of major congenital malformations (MCMs) in offspring?

SUMMARY ANSWER

Maternal periconceptional glycated hemoglobin (HbA1c) levels over 5.6% were associated with an increased risk of congenital heart defects (CHD) in the offspring, and maternal preconception diabetes was associated with an increased risk of CHD, including when HbA1c levels were within euglycemic ranges.

WHAT IS KNOWN ALREADY

Maternal preconception diabetes has been linked with MCMs in the offspring. However, evidence concerning associations with specific periconception serum measures of hyperglycemia, and susceptibility of different organ systems, is inconsistent. Moreover, limited evidence exists concerning the effectiveness of antidiabetic medications in mitigating diabetes-related teratogenic risks.

STUDY DESIGN, SIZE, DURATION

A large Israeli birth cohort of 46 534 children born in 2001-2020.

PARTICIPANTS/MATERIALS, SETTING, METHODS

Maternal HbA1c test results were obtained from 90 days before conception to mid-pregnancy. Maternal diabetes, other cardiometabolic conditions, and MCMs in newborns were ascertained based on clinical diagnoses, medication dispensing records, and laboratory test results using previously validated algorithms. Associations were modeled using generalized additive logistic regression models with thin plate penalized splines.

MAIN RESULTS AND THE ROLE OF CHANCE

Maternal periconceptional HbA1c value was associated with CHD in newborns, with the risk starting to increase at HbA1c values exceeding 5.6%. The association between HbA1c and CHD was stronger among mothers with type 2 diabetes mellitus (T2DM) compared to the other diabetes groups. Maternal pre-existing T2DM was associated with CHD even after accounting for HbA1C levels and other cardiometabolic comorbidities (odds ratio (OR)=1.89, 95% CI 1.18, 3.03); and the OR was materially unchanged when only mothers with pre-existing T2DM who had high adherence to antidiabetic medications and normal HbA1c levels were considered.

LIMITATIONS, REASONS FOR CAUTION

The rarity of some specific malformation groups limited the ability to conduct more granular analyses. The use of HbA1c as a time-aggregated measure of glycemic control may miss transient glycemic dysregulation that could be clinically meaningful for teratogenic risks.

WIDER IMPLICATIONS OF THE FINDINGS

The observed association between pre-existing diabetes and the risk of malformations within HbA1c levels suggests underlying causal pathways that are partly independent of maternal glucose control. Therefore, treatments for hyperglycemia might not completely mitigate the teratogenic risk associated with maternal preconception diabetes.

STUDY FUNDING/COMPETING INTEREST(S)

The work was supported by NIH grants K99ES035433, R01HD097778, and P30ES000002. None of the authors reports competing interests.

TRIAL REGISTRATION NUMBER

N/A.

Unveiling the link between arsenic toxicity and diabetes: an in silico exploration into the role of transcription factors

Arsenic-induced diabetes, despite being a relatively newer finding, is now a growing area of interest, owing to its multifaceted nature of development and the diversity of metabolic conditions that result from it, on top of the already complicated manifestation of arsenic toxicity. Identification and characterization of the common and differentially affected cellular metabolic pathways and their regulatory components among various arsenic and diabetes-associated complications may aid in understanding the core molecular mechanism of arsenic-induced diabetes. This study, therefore, explores the effects of arsenic on human cell lines through 14 transcriptomic datasets containing 160 individual samples using in silico tools to take a systematic, deeper look into the pathways and genes that are being altered. Among these, we especially focused on the role of transcription factors due to their diverse and multifaceted roles in biological processes, aiming to comprehensively investigate the underlying mechanism of arsenic-induced diabetes as well as associated health risks. We present a potential mechanism heavily implying the involvement of the TGF-β/SMAD3 signaling pathway leading to cell cycle alterations and the NF-κB/TNF-α, MAPK, and Ca2+ signaling pathways underlying the pathogenesis of arsenic-induced diabetes. This study also presents novel findings by suggesting potential associations of four transcription factors (NCOA3, PHF20, TFDP1, and TFDP2) with both arsenic toxicity and diabetes; five transcription factors (E2F5, ETS2, EGR1, JDP2, and TFE3) with arsenic toxicity; and one transcription factor (GATA2) with diabetes. The novel association of the transcription factors and proposed mechanism in this study may serve as a take-off point for more experimental evidence needed to understand the in vivo cellular-level diabetogenic effects of arsenic.

Supplementary Information

The online version contains supplementary material available at 10.1007/s43188-024-00255-y.

Ethnic and region-specific genetic risk variants of stroke and its comorbid conditions can define the variations in the burden of stroke and its phenotypic traits

Burden of stroke differs by region, which could be attributed to differences in comorbid conditions and ethnicity. Genomewide variation acts as a proxy marker for ethnicity, and comorbid conditions. We present an integrated approach to understand this variation by considering prevalence and mortality rates of stroke and its comorbid risk for 204 countries from 2009 to 2019, and Genome-wide association studies (GWAS) risk variant for all these conditions. Global and regional trend analysis of rates using linear regression, correlation, and proportion analysis, signifies ethnogeographic differences. Interestingly, the comorbid conditions that act as risk drivers for stroke differed by regions, with more of metabolic risk in America and Europe, in contrast to high systolic blood pressure in Asian and African regions. GWAS risk loci of stroke and its comorbid conditions indicate distinct population stratification for each of these conditions, signifying for population-specific risk. Unique and shared genetic risk variants for stroke, and its comorbid and followed up with ethnic-specific variation can help in determining regional risk drivers for stroke. Unique ethnic-specific risk variants and their distinct patterns of linkage disequilibrium further uncover the drivers for phenotypic variation. Therefore, identifying population- and comorbidity-specific risk variants might help in defining the threshold for risk, and aid in developing population-specific prevention strategies for stroke.

Ethnicity-related differences in mitochondrial regulation by insulin stimulation in diabetes

Mitochondrial dysfunction has long been implicated in the development of insulin resistance, which is a hallmark of type 2 diabetes. However, recent studies reveal ethnicity-related differences in mitochondrial processes, underscoring the need for nuance in studying mitochondrial dysfunction and insulin sensitivity. Furthermore, the higher prevalence of type 2 diabetes among African Americans and individuals of African descent has brought attention to the role of ethnicity in disease susceptibility. In this review, which covers existing literature, genetic studies, and clinical data, we aim to elucidate the complex relationship between mitochondrial alterations and insulin stimulation by considering how mitochondrial dynamics, contact sites, pathways, and metabolomics may be differentially regulated across ethnicities, through mechanisms such as single nucleotide polymorphisms (SNPs). In addition to achieving a better understanding of insulin stimulation, future studies identifying novel regulators of mitochondrial structure and function could provide valuable insights into ethnicity-dependent insulin signaling and personalized care.

Effects of tumor necrosis factor-α rs1800629 and interleukin-10 rs1800872 genetic variants on type 2 diabetes mellitus susceptibility and metabolic parameters among Jordanians

OBJECTIVES

Diabetes mellitus (DM) is a complex chronic illness with diverse pathogenesis and associations with health complications. Genetic factors significantly contribute to DM development, and tumor necrosis factor alpha (TNF-α) and interleukin-10 (IL-10) genes play major roles. This study aims to explore the influence of TNF-α rs1800629 and IL-10 rs1800872 genetic variants on T2DM development in Jordanian patients at Jordan University Hospital.

METHODS

One-hundred and 60 diabetic and 159 non-diabetic subjects were genotyped for TNF-α rs1800629. Additionally, 181 diabetic and 191 non-diabetic subjects were genotyped for IL-10 rs1800872 using PCR-RFLP genotyping method. The demographic, lipid, and glycemic parameters of the patients were obtained from the computer records in the hospital.

RESULTS

TNF-α rs1800629 and IL-10 rs1800872 genetic variants exhibited significant different frequencies in non-T2DM subjects and T2DM patients. The difference in TNF-α rs1800629 genotype frequency between non-T2DM and T2DM participants was significant under the dominant model, while the IL-10 rs1800872 genotype frequency was significant under the recessive model. A significant association (p<0.05) was observed between TNF-α rs1800629 and total cholesterol levels, and between IL-10 rs1800872 polymorphism and glycosylated hemoglobin (HbA1c) and creatinine levels among T2DM patients.

CONCLUSIONS

TNF-α rs1800629 and IL-10 rs1800872 are identified as genetic risk factors for T2DM. These variants also correlate with variations in cholesterol, HbA1c, and creatinine levels among T2DM patients. Larger clinical studies are warranted to validate these findings.

Impact of the trans-ancestry polygenic risk score on type 2 diabetes risk, onset age and progression among population in Taiwan

Type 2 diabetes (T2D) prevalence in adults at a younger age has increased but the disease status may go unnoticed. This study aimed to determine whether the onset age and subsequent diabetic complications can be attributed to the polygenic architecture of T2D in the Taiwan Han population. A total of 9,627 cases with T2D and 85,606 controls from the Taiwan Biobank were enrolled. Three diabetic polygenic risk scores (PRSs), PRS_EAS and PRS_EUR, and a trans-ancestry PRS (PRS_META), calculated using summary statistic from East Asian and European populations. The onset age was identified by linking to the National Taiwan Insurance Research Database, and the incidence of different diabetic complications during follow-up was recorded. PRS_META (7.4%) explained a higher variation for T2D status. And the higher percentile of PRS is also correlated with higher percentage of T2D family history and prediabetes status. More, the PRS was negatively associated with onset age (β = -0.91 yr), and this was more evident among males (β = -1.11 vs. -0.76 for males and females, respectively). The hazard ratio of diabetic retinopathy (DR) and diabetic foot were significantly associated with PRS_EAS and PRS_META, respectively. However, the PRS was not associated with other diabetic complications, including diabetic nephropathy, cardiovascular disease, and hypertension. Our findings indicated that diabetic PRS which combined susceptibility variants from cross-population could be used as a tool for early screening of T2D, especially for high-risk populations, such as individuals with high genetic risk, and may be associated with the risk of complications in subjects with T2D. NEW & NOTEWORTHY Our findings indicated that diabetic polygenic risk score (PRS) which combined susceptibility variants from Asian and European population affect the onset age of type 2 diabetes (T2D) and could be used as a tool for early screening of T2D, especially for individuals with high genetic risk, and may be associated with the risk of diabetic complications among people in Taiwan.

Association between Interleukin-6 Gene Polymorphism (rs1800795 and rs1800796) and Type 2 Diabetes Mellitus in a Ghanaian Population: A Case-Control Study in the Ho Municipality

Background

There is no conclusive evidence on the association between interleukin- (IL-) 6 gene polymorphism and type 2 diabetes mellitus (type 2 DM). Thus, this study is aimed at evaluating the role of rs1800795 and rs1800796 polymorphisms in the pathogenesis of type 2 DM among Ghanaians in the Ho Municipality.

Materials and Methods

We recruited into this hospital-based case-control study 174 patients with type 2 DM (75 DM alone and 99 with DM+HTN) and 149 healthy individuals between 2018 and 2020. Demographic, lifestyle, clinical, anthropometric, and haemodynamic variables were obtained. Fasting blood samples were collected for haematological, biochemical, and molecular analyses. Genomic DNA was extracted, amplified using Tetra-primer amplification refractory mutation system-polymerase chain reaction (T-ARMS-PCR) technique, and genotyped for IL-6 gene polymorphism. Logistic regression analyses were performed to assess the association between IL-6 gene polymorphism and type 2 DM.

Results

The minor allele frequency (MAF) of the rs1800795 and rs1800796 polymorphisms was higher in DM alone (57.5%, 62.0%) and DM with HTN groups (58.3%, 65.3%) than controls (33.1%, 20.0%). Carriers of the rs1800795GC genotype (aOR = 2.35, 95% CI: 1.13-4.90, p = 0.022) and mutant C allele (aOR = 2.41, 95% CI: 1.16-5.00, p = 0.019) as well as those who carried the rs1800796GC (aOR = 8.67, 95% CI: 4.00-18.90, p < 0.001) and mutant C allele (aOR = 8.84, 95% CI: 4.06-19.26, p = 0.001) had increased odds of type 2 DM. For both polymorphisms, carriers of the GC genotype had comparable levels of insulin, HOMA-IR, and fasting blood glucose (FBG) with those who carried the GG genotype. IL-6 levels were higher among carriers of the rs1800796GC variant compared to carriers of the rs1800796GG variant (p = 0.023). The rs1800796 polymorphism, dietary sugar intake, and exercise status, respectively, explained approximately 3% (p = 0.046), 3.2% (p = 0.038, coefficient = 1.456), and 6.2% (p = 0.004, coefficient = -2.754) of the variability in IL-6 levels, suggesting weak effect sizes.

Conclusion

The GC genotype and mutant C allele are risk genetic variants associated with type 2 DM in the Ghanaian population. The rs1800796 GC variant, dietary sugar intake, and exercise status appear to contribute significantly to the variations in circulating IL-6 levels but with weak effect sizes.

Genotype-based precision nutrition strategies for the prediction and clinical management of type 2 diabetes mellitus

Globally, type 2 diabetes mellitus (T2DM) is one of the most common metabolic disorders. T2DM physiopathology is influenced by complex interrelationships between genetic, metabolic and lifestyle factors (including diet), which differ between populations and geographic regions. In fact, excessive consumptions of high fat/high sugar foods generally increase the risk of developing T2DM, whereas habitual intakes of plant-based healthy diets usually exert a protective effect. Moreover, genomic studies have allowed the characterization of sequence DNA variants across the human genome, some of which may affect gene expression and protein functions relevant for glucose homeostasis. This comprehensive literature review covers the impact of gene-diet interactions on T2DM susceptibility and disease progression, some of which have demonstrated a value as biomarkers of personal responses to certain nutritional interventions. Also, novel genotype-based dietary strategies have been developed for improving T2DM control in comparison to general lifestyle recommendations. Furthermore, progresses in other omics areas (epigenomics, metagenomics, proteomics, and metabolomics) are improving current understanding of genetic insights in T2DM clinical outcomes. Although more investigation is still needed, the analysis of the genetic make-up may help to decipher new paradigms in the pathophysiology of T2DM as well as offer further opportunities to personalize the screening, prevention, diagnosis, management, and prognosis of T2DM through precision nutrition.

Impact of IL-6 rs1800795 and IL-17A rs2275913 gene polymorphisms on the COVID-19 prognosis and susceptibility in a sample of Iranian patients

BACKGROUND

From asymptomatic to acute and life-threatening pulmonary infection, the clinical manifestations of COVID-19 are highly variable. Interleukin (IL)-6 and IL-17A are key drivers of hyper inflammation status in COVID-19, and their elevated levels are hallmarks of the infection progression. To explore whether prognosis and susceptibility to COVID-19 are linked to IL-6 rs1800795 and IL-17A rs2275913, these single-nucleotide polymorphisms (SNPs) were assessed in a sample of Iranian COVID-19 patients.

METHODS

This study enrolled two hundred and eighty COVID-19 patients (140 non-severe and 140 severe). Genotyping for IL-6 rs1800795 and IL-17A rs2275913 was performed using tetra primer-amplification refractory mutation system-polymerase chain reaction (tetra-ARMS-PCR). IL-6 and IL-17A circulating levels were measured using enzyme-linked immunosorbent assay (ELISA). Also, mortality predictors of COVID-19 were investigated.

RESULTS

The rs1800795 GG genotype (78/140 (55.7 %)) and G allele (205/280 (73.2 %)) were significantly associated with a positive risk of COVID-19 severe infection (OR = 2.19, 95 %CI: 1.35-3.54, P =.006 and OR = 1.79, 95 %CI: 1.25-2.56, P <.001, respectively). Also, rs1800795 GG genotype was significantly linked to disease mortality (OR = 1.95, 95 %CI: 1.06-3.61, P =.04). The rs2275913 GA genotype was protective against severe COVID-19 (OR = 0.5, 95 %CI: 0.31--0.80, P =.012). However, the present study did not reveal any significant link between rs2275913 genotypes with disease mortality. INR ≥ 1.2 (OR = 2.19, 95 %CI: 1.61-3.78, P =.007), D-dimer ≥ 565.5 ng/mL (OR = 3.12, 95 %CI: 1.27-5.68, P =.019), respiratory rate ≥ 29 (OR = 1.19, 95 %CI: 1.12-1.28, P =.001), IL-6 serum concentration ≥ 28.5 pg/mL (OR = 1.97, 95 %CI: 1.942-2.06, P =.013), and IL-6 rs1800795 GG genotype (OR = 1.95, 95 %CI: 1.06-3.61, P =.04) were predictive of COVID-19 mortality.

CONCLUSION

The rs1800795 GG genotype and G allele were associated with disease severity, and INR, D-dimer, respiratory rate, IL-6 serum concentration, and IL-6 rs1800795 GG genotype were predictive of COVID-19 mortality.

High-accuracy prediction of colorectal cancer chemotherapy efficacy using machine learning applied to gene expression data

Introduction: FOLFOX and FOLFIRI chemotherapy are considered standard first-line treatment options for colorectal cancer (CRC). However, the criteria for selecting the appropriate treatments have not been thoroughly analyzed. Methods: A newly developed machine learning model was applied on several gene expression data from the public repository GEO database to identify molecular signatures predictive of efficacy of 5-FU based combination chemotherapy (FOLFOX and FOLFIRI) in patients with CRC. The model was trained using 5-fold cross validation and multiple feature selection methods including LASSO and VarSelRF methods. Random Forest and support vector machine classifiers were applied to evaluate the performance of the models. Results and Discussion: For the CRC GEO dataset samples from patients who received either FOLFOX or FOLFIRI, validation and test sets were >90% correctly classified (accuracy), with specificity and sensitivity ranging between 85%-95%. In the datasets used from the GEO database, 28.6% of patients who failed the treatment therapy they received are predicted to benefit from the alternative treatment. Analysis of the gene signature suggests the mechanistic difference between colorectal cancers that respond and those that do not respond to FOLFOX and FOLFIRI. Application of this machine learning approach could lead to improvements in treatment outcomes for patients with CRC and other cancers after additional appropriate clinical validation.

Identification of Genetic Variants for Diabetic Retinopathy Risk Applying Exome Sequencing in Extreme Phenotypes

Background

Diabetic retinopathy (DR) risk has been shown to vary depending on ethnic backgrounds, and thus, it is worthy that underrepresented populations are analyzed for the potential identification of DR-associated genetic variants. We conducted a case-control study for the identification of DR-risk variants in Mexican population.

Methods

We ascertained 60 type 2 diabetes mellitus (T2DM) patients. Cases (n = 30) were patients with advanced proliferative DR (PDR) with less than 15 years after a T2DM diagnosis while controls (n = 30) were patients with no DR 15 years after the diagnosis of T2DM. Exome sequencing was performed in all patients, and the frequency of rare variants was compared. In addition, the frequency of variants occurring in a set of 169 DR-associated genes were compared.

Results

Statistically significant differences were identified for rare missense and splice variants and for rare splice variants occurring more than once in either group. A strong statistical difference was observed when the number of rare missense variants with an aggregated prediction of pathogenicity and occurring more than once in either group was compared (p = 0.0035). Moreover, 8 variants identified more than once in either group, occurring in previously identified DR-associated genes were recognized. The p.Pro234Ser KIR2DS4 variant showed a strong protective effect (OR = 0.04 [0.001-0.36]; p = 0.04).

Conclusions

Our study showed an enrichment of rare splice acceptor/donor variants in patients with PDR and identified a potential protective variant in KIR2DS4. Although statistical significance was not reached, our results support the replication of 8 previously identified DR-associated genes.

The genetic polymorphisms and activity of glyoxalase 1 as a risk factor for acute coronary syndrome in South Indians with type 2 diabetes mellitus

OBJECTIVE

The individuals' genetic traits predispose them to a higher or lower risk of Type 2 diabetes mellitus (T2DM) and its complications, for example, acute coronary syndrome (ACS). As carbonyl stress is responsible for the pathogenesis and complications of T2DM, and glyoxalase 1 (GLO1) is the most crucial determinant of carbonyl stress, the study aimed to explore the association between GLO1 gene polymorphism, GLO1 activity in red blood cell (RBC), plasma methylglyoxal (MG) levels, and ACS risk in South Indian T2DM patients.

METHODS

A total of 150 T2DM patients with ACS as cases and 150 T2DM patients without ACS as controls were recruited in a case-control study. The rs4746, rs1049346 and rs1130534 of the GLO1 gene were analysed using TaqMan allele discrimination assay. The RBC GLO1 activity and plasma MG levels were measured.

RESULTS

Significantly lower RBC GLO1 activity and higher plasma MG levels were found in cases compared to controls (p < 0.001 and p = 0.008, respectively). The genotype and allele frequencies of rs1049346 significantly differed between cases and controls (p < 0.001). For rs1130534 and rs1049346, no significant difference was found. For rs1049346, the TT and CC genotypes were associated with higher (p = 0.002) and lower (p = 0.001) ACS risk, respectively, in various genetic models. The TT genotype of rs1049346 was associated with lower RBC GLO1 activity (p = 0.004) and higher MG level (p = 0.010). In haplotype analysis, higher ACS susceptibility with the TAT haplotype (p < 0.001) and lower ACS susceptibility with the TAC haplotype (p < 0.001) were observed. Also, lower RBC GLO1 activity was associated with the TAT haplotype (p = 0.002).

CONCLUSIONS

The rs1049346 of the GLO1 gene may be associated with ACS risk in South Indian T2DM patients, and the T and C allele might be essential precipitating and protective factors, respectively.

Association Between Interleukin-6 Gene Polymorphism and Severity of Coronary Artery Disease in Patients with Diabetes

Introduction

Previous studies have identified diabetes as a risk factor for coronary heart disease. This study determined the correlation between the IL-6 gene -572 G/C polymorphism and the incidence and severity of coronary heart disease in patients with diabetes.

Methods

One hundred four patients with diabetes who were admitted to our hospital from January 2019 to December 2020 were retrospectively enrolled in the current study. These patients were divided into a diabetes only group (group A, 27 patients) and a diabetes complicated by coronary heart disease group (group B, 77 patients). Seventy patients in the latter group were further divided into low, medium, and high Syntax score groups based on coronary angiography results. A correlation analysis between IL-6, blood lipids, and the IL-6 -572 G/C gene levels was performed.

Results

The serum IL-6 level in patients with the IL-6-572G/C-GG genotype was higher than patients with the GC and CC genotypes. In patients with diabetes, the presence of the IL-6-572G/C-GG and GC genotypes was associated with a significantly increased risk of developing coronary heart disease. Patients with the IL-6-572G/C-GG genotype and diabetes were shown to have more severe coronary artery lesions compared to patients with the CC genotype. Moreover, the G allele of the IL-6-572G/C gene was linked to a higher risk of coronary heart disease and more severe coronary artery lesions in patients with diabetes compared to the C allele.

Conclusion

The IL-6-572G/C gene polymorphism is associated with the incidence and severity of coronary heart disease in patients with diabetes.

Disparities in diabetes prevalence and management by race and ethnicity in the USA: defining a path forward

Type 2 diabetes disparities in the USA persist in both the prevalence of disease and diabetes-related complications. We conducted a literature review related to diabetes prevention, management, and complications across racial and ethnic groups in the USA. The objective of this review is to summarise the current understanding of diabetes disparities by examining differences between and within racial and ethnic groups and among young people (aged <18 years). We also examine the pathophysiology of diabetes as it relates to race and ethnic differences. We use a conceptual framework built on the socioecological model to categorise the causes of diabetes disparities across the lifespan looking at factors in five domains of health behaviours and social norms, public awareness, structural racism, economic development, and access to high-quality care. The range of disparities in diabetes prevalence and management in the USA calls for a community-engaged and multidisciplinary approach that must involve community partners, researchers, practitioners, health system administrators, and policy makers. We offer recommendations for each of these groups to help to promote equity in diabetes prevention and care in the USA.

Polygenic Variants Linked to Oxidative Stress and the Antioxidant System Are Associated with Type 2 Diabetes Risk and Interact with Lifestyle Factors

Oxidative stress is associated with insulin resistance and secretion, and antioxidant systems are essential for preventing and managing type 2 diabetes (T2DM). This study aimed to explore the polygenic variants linked to oxidative stress and the antioxidant system among those associated with T2DM and the interaction of their polygenic risk scores (PRSs) with lifestyle factors in a large hospital-based cohort (n = 58,701). Genotyping, anthropometric, biochemical, and dietary assessments were conducted for all participants with an average body mass index of 23.9 kg/m2. Genetic variants associated with T2DM were searched through genome-wide association studies in participants with T2DM (n = 5383) and without T2DM (n = 53,318). The Gene Ontology database was searched for the antioxidant systems and oxidative stress-related genes among the genetic variants associated with T2DM risk, and the PRS was generated by summing the risk alleles of selected ones. Gene expression according to the genetic variant alleles was determined on the FUMA website. Food components with low binding energy to the GSTA5 protein generated from the wildtype and mutated GSTA5_rs7739421 (missense mutation) genes were selected using in silico analysis. Glutathione metabolism-related genes, including glutathione peroxidase (GPX)1 and GPX3, glutathione disulfide reductase (GSR), peroxiredoxin-6 (PRDX6), glutamate-cysteine ligase catalytic subunit (GCLC), glutathione S-transferase alpha-5 (GSTA5), and gamma-glutamyltransferase-1 (GGT1), were predominantly selected with a relevance score of >7. The PRS related to the antioxidant system was positively associated with T2DM (ORs = 1.423, 95% CI = 1.22-1.66). The active site of the GASTA proteins having valine or leucine at 55 due to the missense mutation (rs7739421) had a low binding energy (<-10 kcal/mol) similarly or differently to some flavonoids and anthocyanins. The PRS interacted with the intake of bioactive components (specifically dietary antioxidants, vitamin C, vitamin D, and coffee) and smoking status (p < 0.05). In conclusion, individuals with a higher PRS related to the antioxidant system may have an increased risk of T2DM, and there is a potential indication that exogenous antioxidant intake may alleviate this risk, providing insights for personalized strategies in T2DM prevention.

Decoding the genetic relationship between Alzheimer's disease and type 2 diabetes: potential risk variants and future direction for North Africa

Introduction

Alzheimer's disease (AD) and Type 2 diabetes (T2D) are both age-associated diseases. Identification of shared genes could help develop early diagnosis and preventive strategies. Although genetic background plays a crucial role in these diseases, we noticed an underrepresentation tendency of North African populations in omics studies.

Materials and methods

First, we conducted a comprehensive review of genes and pathways shared between T2D and AD through PubMed. Then, the function of the identified genes and variants was investigated using annotation tools including PolyPhen2, RegulomeDB, and miRdSNP. Pathways enrichment analyses were performed with g:Profiler and EnrichmentMap. Next, we analyzed variant distributions in 16 worldwide populations using PLINK2, R, and STRUCTURE software. Finally, we performed an inter-ethnic comparison based on the minor allele frequency of T2D-AD common variants.

Results

A total of 59 eligible papers were included in our study. We found 231 variants and 363 genes shared between T2D and AD. Variant annotation revealed six single nucleotide polymorphisms (SNP) with a high pathogenic score, three SNPs with regulatory effects on the brain, and six SNPs with potential effects on miRNA-binding sites. The miRNAs affected were implicated in T2D, insulin signaling pathways, and AD. Moreover, replicated genes were significantly enriched in pathways related to plasma protein binding, positive regulation of amyloid fibril deposition, microglia activation, and cholesterol metabolism. Multidimensional screening performed based on the 363 shared genes showed that main North African populations are clustered together and are divergent from other worldwide populations. Interestingly, our results showed that 49 SNP associated with T2D and AD were present in North African populations. Among them, 11 variants located in DNM3, CFH, PPARG, ROHA, AGER, CLU, BDNF1, CST9, and PLCG1 genes display significant differences in risk allele frequencies between North African and other populations.

Conclusion

Our study highlighted the complexity and the unique molecular architecture of North African populations regarding T2D-AD shared genes. In conclusion, we emphasize the importance of T2D-AD shared genes and ethnicity-specific investigation studies for a better understanding of the link behind these diseases and to develop accurate diagnoses using personalized genetic biomarkers.

Prevalence of Cognitive Decline in Type 2 Diabetes Mellitus Patients: A Real-World Cross-Sectional Study in Mysuru, India

The goal of this research is to study the prevalence of cognitive impairment in diabetes mellitus (DM) patients and establish the necessity of detecting and treating it early in these patients. A cross-sectional study was conducted at a tertiary care hospital in Mysuru for 4 months examined diabetic patients (test) and nondiabetic subjects (control) for cognitive decline using the Montreal Cognitive Assessment (MoCA) tool. Cognitive functions such as visuospatial/executive function, naming, attention, language, abstraction, delayed recall, and orientation were assessed in both groups. The diabetic group showed a significantly lower total MoCA score than the non-diabetic group (18.99 ± 0.48 and 26.21 ± 0.46, respectively; p < 0.001). Assessment of scores in diabetic patients demonstrated the significant influence of age demographics on cognitive impairment (p-value < 0.001). Furthermore, a higher proportion of diabetic patients displayed cognitive impairment despite a higher score in a single subdomain, making it evident that diabetes is diverse and multifactorial in origin, where oxidative stress and inflammatory responses play a predominant role. This study suggested that the local T2DM population residing in Mysuru (India) has a high prevalence of cognitive impairment, evident from poor performance in almost all cognitive domains assessed by MoCA. Future studies could examine the generalizability of cognitive function findings in diabetic patients across diverse geographic regions and ethnic groups, as well as investigate interventions such as lifestyle modifications and medication to prevent or delay cognitive decline in those with diabetes.

Geospatial analysis of type 2 diabetes mellitus and hypertension in South Sulawesi, Indonesia

The spatial variation of type 2 diabetes mellitus (T2DM) and hypertension and their potential linkage were explored in South Sulawesi Province, Indonesia. The Global Moran's I and regression analysis were utilized to identify the characteristics involved. The methods were performed based on T2DM and hypertension data from 2017 and 2018 acquired from Social Health Insurance Administration in Indonesia. The spatial variation of T2DM and hypertension showed that the prevalence rate of T2DM and hypertension tends to occur randomly (p = 0.678, p = 0.711, respectively). By utilizing Generalized Poisson Regression Analysis, our study showed a significant relationship between T2DM and hypertension (p ≤ 0.001). This research could help policy makers to plan and support projects with the aim of overcoming the risk of T2DM and hypertension.

Genetic heterogeneity in cardiovascular disease across ancestries: Insights for mechanisms and therapeutic intervention

Cardiovascular diseases (CVDs) are complex in their aetiology, arising due to a combination of genetics, lifestyle and environmental factors. By nature of this complexity, different CVDs vary in their molecular mechanisms, clinical presentation and progression. Although extensive efforts are being made to develop novel therapeutics for CVDs, genetic heterogeneity is often overlooked in the development process. By considering molecular mechanisms at an individual and ancestral level, a richer understanding of the influence of environmental and lifestyle factors can be gained and more refined therapeutic interventions can be developed. It is therefore expedient to understand the molecular and clinical heterogeneity in CVDs that exists across different populations. In this review, we highlight how the mechanisms underlying CVDs vary across diverse population ancestry groups due to genetic heterogeneity. We then discuss how such genetic heterogeneity is being leveraged to inform therapeutic interventions and personalised medicine, highlighting examples across the CVD spectrum. Finally, we present an overview of how polygenic risk scores and Mendelian randomisation can foster more robust insight into disease mechanisms and therapeutic intervention in diverse populations. Fulfilment of the vision of precision medicine requires more exhaustive leveraging of the genetic variability across diverse ancestry populations to improve our understanding of disease onset, progression and response to therapeutic intervention.

Ionically cross-linked alginate-chitosan core-shell hydrogel beads for oral delivery of insulin

Here, core-shell hydrogel beads for oral insulin delivery at intestine was reported, which was a target site for insulin absorption. The core-shell hydrogel beads were prepared using naturally derived alginate and chitosan polysaccharides by simple dropping technique. In order to effectively control leakage of insulin from core-shell hydrogel beads, insulin was embedded into the layered double hydroxides (LDHs). LDH/insulin-loaded complexes were firstly coated with chitosan, and then coated with alginate to generate core-shell hydrogel beads. The biocompatibility and angiogenic response of core-shell hydrogel beads were evaluated by direct contact of the beads with chick embryo chorioallantoic membrane, which indicates safety of the core-shell beads. The beads successfully retained the insulin within the core-shell structure at pH 1.2, indicating that insulin had a good protective effect in harsh acidic environments. Interestingly, insulin release starts at the simulated intestinal fluid (pH 6.8) and continue to release for 24 h in a sustained manner.

Glucose sensor modeling based on Fano resonance excitation in titania nanotube photonic crystal coated by titanium nitride as a plasmonic material

The brilliant optical properties of plasmonic metal nitrides improve many applications. Modeling of light-confining Fano resonance based on a titanium nitride (TiN)-coated titanium oxide one-dimensional photonic crystal is investigated as a glucose sensor. There is a cavity layer filled with a glucose solution between the TiN thin layer and photonic crystals. The reflection spectrum is calculated numerically by using Bruggeman's effective medium approximation and transfer matrix method. The effect of plasmonic layer thickness, cavity layer thickness, and the thicknesses of the titanium oxide nanotube layers are optimized to achieve a high performance sensor. The result shows that the Fano resonances shift to higher wavelengths with increasing glucose concentration. The best sensitivity of the optimized biosensor is about 3798.32 nm/RIU. Also, the sensor performance parameters such as the limit of detection, figure of merit, and quality factor are discussed. The proposed sensor can be of potential interest due to its easy fabrication and higher performance than many previous reported sensors in the sensing field.

Role of eNOS and TGFβ1 gene polymorphisms in the development of diabetic nephropathy in type 2 diabetic patients in South Indian population

Background

Diabetic nephropathy is known to be a leading complication of diabetes mellitus, characterized by diverse aspects such as high urinary albumin level, elevated blood pressure, and genetic susceptibility leading to end-stage renal disease. The current study was carried out to investigate the association of eNOS and TGFβ1 gene polymorphisms in the progression of diabetic nephropathy among type 2 diabetic patients in the South Indian population. The eNOS and TGFβ1 genetic variants were genotyped in 280 T2DM patients, 140 with DN, 140 without DN, and 140 controls. Genotyping was performed using ARMS PCR and the genomic variants were confirmed by the Sanger sequencing method.

Results

A significant (p < 0.05) association was observed in the genotypic frequencies of eNOS (G > T) polymorphism in the T2DM patients with diabetic nephropathy when compared to controls. The frequency of TT (heterozygous) genotype was observed to increase in patients with type 2 diabetes and DN when compared to the diabetic patients without DN and controls. This indicates that diabetic patients with TT genotype are at an increased risk to develop DN. However, TGFβ1 (G > C) polymorphism did not show any association in the allele and genotypic frequencies with DN when compared with T2DM and controls.

Conclusion

The results of the study propose a strong influence of TT genotype of eNOS gene be significantly linked with diabetic nephropathy in T2DM patients. Whereas no association was examined concerning TGFβ1 gene polymorphism and DN. Nevertheless, large sample size studies are required to confirm the part of these genetic variants in the development of DN.

Association of TNF-α 308G/A and LEPR Gln223Arg Polymorphisms with the Risk of Type 2 Diabetes Mellitus

The objective of the present study was to identify the association of the TNF-α- 308G/A and leptin receptor (LEPR) Gln223Arg polymorphisms with the risk of development of type 2 diabetes mellitus (T2DM). Methods: A total of 160 volunteers were studied: 108 with T2DM and 52 participants as control, who served as the control group. Polymerase chain reaction–restriction fragment length polymorphism (PCR-RFLP) for the genomic region of TNF-α- 308G/A and LEPR Gln223Arg were carried out. Results: The frequency of LEPR Gln223Arg genotypes in T2DM and control groups showed significant differences in the distribution of genotypes (p < 0.05). The frequency also of TNF-α- 308G/A genotypes in T2DM and control subjects showed significant differences in the distribution of genotypes (p < 0.05). Conclusion: Our results indicate that there are significant differences in the distribution of genotypes and alleles between the individuals with T2DM and control subjects (p < 0.05).