Association study of leukocyte telomere length and genetic polymorphism within hTERT promoter with type 2 diabetes in Bangladeshi population

Intronic Variants of the Angiotensin-Converting Enzyme 2 Gene Modulate Plasma ACE2 Levels and Possibly Confer Protection against Severe COVID-19

Membrane-bound angiotensin-converting enzyme 2 (ACE2) receptor acts as the entry point for the novel coronavirus, SARS-CoV-2. Polymorphisms in the ACE2 gene may alter viral binding, regulate the expression of ACE2, and thus, affect disease severity. In this study, 68 COVID-19 patients with varying degrees of severity and 40 healthy controls were enrolled. The genetic landscape of the ACE2 gene was explored by whole exome sequencing of 29 individuals, and specific regions of ACE2 were analyzed for the rest of the participants via PCR, followed by barcode-tagged sequencing. The mean soluble ACE2 level in the plasma of healthy controls and patients did not vary significantly but was higher in the patient group (3.77 ± 1.55 ng/mL vs. 3.94 ± 1.42 ng/mL). Analysis of exon 1, exon 2, and exon 8 of the ACE2 gene revealed that these regions are highly conserved in our population. Investigation of exon 11 and its flanking intronic region revealed that deletions in a stretch of 18T nucleotides in the noncoding region significantly decrease ACE2 levels in plasma, as individuals harboring wild-type variants had higher plasma ACE2 levels compared to those harboring T1del, T2del, and T3del variants. However, the intronic variants were not found to be significantly associated with disease severity.

Genetic Variants of the TERT Gene and Telomere Length in Obstructive Sleep Apnea

Introduction: Obstructive sleep apnea (OSA) is a worldwide breathing disorder that has been diagnosed globally in almost 1 billion individuals aged 30−69 years. It is characterized by repeated upper airway collapses during sleep. Telomerase reverse transcriptase (TERT) is involved in the prevention of telomere shortening. This prospective, observational study aimed to investigate the relationship between single nucleotide polymorphisms (SNPs) of TERT and the severity of OSA, taking into account hypertension and diabetes prevalence. Methods: A total of 149 patients with OSA were diagnosed using one-night video-polysomnography based on the American Academy of Sleep Medicine guidelines. The TERT SNPs and telomere length (TL) were detected using real-time quantitative polymerase chain reaction. Results: Statistical analysis showed that there is no relationship between the rs2853669 and rs2736100 polymorphisms of TERT, and the severity of OSA (p > 0.05). Moreover, no relationship between TL and the severity of OSA was observed. The G allele in the locus of rs2736100 TERT was associated with hypertension prevalence and was more prevalent in hypertensives patients (46.00% vs. 24.49%, p = 0.011). The prevalence of hypertension was higher in patients with the C allele in the locus of rs2853669 than in patients without this allele (50.79% vs. 30.23%, p = 0.010). Moreover, a lower prevalence of diabetes was observed in homozygotes of rs2736100 TERT than in heterozygotes (5.63% vs. 15.38%, p = 0.039). Conclusion: This study showed no relationship between OSA and TERT SNPs. However, SNPs of the TERT gene (rs2736100 and rs2853669) were found to affect arterial hypertension and diabetes prevalence.

The polymorphic landscape analysis of GATA1 exons uncovered the genetic variants associated with higher thrombocytopenia in dengue patients

The current study elucidated an association between gene variants and thrombocytopenia through the investigation of the exonic polymorphic landscape of hematopoietic transcription factor—GATA1 gene in dengue patients. A total of 115 unrelated dengue patients with dengue fever (DF) (N = 91) and dengue hemorrhagic fever (DHF) (N = 24) were included in the study. All dengue patients were confirmed through detection of NS1 antigen, IgM, and IgG antibodies against the dengue virus. Polymerase chain reaction using specific primers amplified the exonic regions of GATA1 while Sanger sequencing and chromatogram analyses facilitated the identification of variants. Variants G>A (at chX: 48792009) and C>A (at chX: 4879118) had higher frequency out of 13 variants identified (3 annotated and 10 newly recognized). Patients carrying either nonsynonymous or synonymous variants had significantly lower mean values of platelets compared to those harboring the reference nucleotides (NC_000023.11). Further analyses revealed that the change in amino acid residue leads to the altered three-dimensional structure followed by interaction with neighboring residues. Increased stability of the protein due to substitution of serine by asparagine (S129N at chX: 48792009) may cause increased rigidity followed by reduced structural flexibility which may ultimately disturb the dimerization (an important prerequisite for GATA1 to perform its biological activity) process of the GATA1 protein. This, in turn, may affect the function of GATA1 followed by impaired production of mature platelets which may be reflected by the lower platelet counts in individuals with such variation. In summary, we have identified new variants within the GATA1 gene which were found to be clinically relevant to the outcome of dengue patients and thus, have the potential as candidate biomarkers for the determination of severity and prognosis of thrombocytopenia caused by dengue virus. However, further validation of this study in a large number of dengue patients is warranted.

Trial Registration: number SLCTR/2019/037.

Dengue, a mosquito-borne viral disease, caused by dengue virus (DENV) of the Flaviviridae family has been the source of a global epidemic for decades, and it has recently spread to all parts of the globe. Hemorrhagic manifestations in dengue are caused by increased vascular permeability and thrombocytopenia (150K cells/L). GATA1 is considered to be the master transcription factor for regulating the differentiation and maturation of megakaryocytes (MKs). The exonic polymorphism landscape of hematopoietic transcription factor—GATA1 in dengue patients was investigated in our study to see if there is an association between genetic variations and thrombocytopenia. Out of the 13 variations identified, variants G>A (chX:48792009) and C>A (chX:4879118) had the highest frequencies. Patients harboring either nonsynonymous or synonymous variants had significantly lower mean platelet counts compared to those having wild-type nucleotides. We have identified new GATA1 gene variations that were proven to be clinically related to the outcome of dengue patients and hence holds the potential to be candidate biomarkers for determining the severity and prognosis of dengue thrombocytopenia. However, this study needs to be replicated in a large number of dengue patients.

Association of telomere length with diabetes mellitus and idiopathic dilated cardiomyopathy in a South Indian population: A pilot study

Telomere shortening has been associated with ageing and with many age-related diseases including cancer, coronary artery disease, heart failure and diabetes. We sought to investigate the link between telomere shortening and age-related diseases like type 2 diabetes mellitus (DM) (without any complications: DM; with neuropathic complication: DN) and idiopathic dilated cardiomyopathy (IDCM) in south Indian population. We compared telomere lengths of blood lymphocytes taken from patients with associated age-related diseases, namely DM (n = 47), DN (n = 52) and IDCM (n = 34) and controls (n = 46). In addition, we evaluated the relationship between echocardiographic left ventricular ejection fraction (LVEF), left ventricular end diastolic and systolic diameters (LVEDd and LVESd) and telomere length in IDCM patients. Telomere length negatively correlated with age in the cohorts with diabetes and IDCM, and in controls. Average telomere length in diabetes and IDCM patients was significantly shorter than that of controls either before or after adjustments for age and sex. Duration of diabetes in patients with type 2 diabetes did not correlate with telomere length. No correlation was found between the length of telomeres and echocardiography parameters like LVEF, LVEDd and LVESd in IDCM patients. Though echocardiographic characteristics of IDCM did not correlate with telomere length, telomere shortening was found to be accelerated in diabetes (both DM and DN) and IDCM in a south Indian population. Neuropathic complication in diabetes had no effect on telomere shortening. While telomere shortening is a cause or a consequence of diabetic and cardiac pathology remains further investigation, the current study substantiates the usefulness of telomere length measurements as a marker in conjunction with other biochemical markers of age-related diseases.

MNS16A VNTR polymorphism of human telomerase gene: Elucidation of a gender specific potential allele associated with type 2 diabetes in Bangladeshi population

BACKGROUND

Type 2 diabetes (T2D) is a multifactorial disorder that affects multi-organ and can alter telomerase (encoded by hTERT gene) activity and thus, may affect telomere length. The variable number of tandem repeats MNS16A in hTERT gene facilitates extension of telomeres by regulating telomerase. In the present study, genetic analysis of MNS16A tandem repeats in hTERT gene was performed with the aim of finding out any association of allelic and genotypic variations with the risk of T2D in Bangladeshi population.

METHODS

A total of unrelated 395 individuals with T2D and 247 healthy individuals were included in the study. The genotypic and allelic frequencies were determined using allele specific polymerase chain reaction. The association of allelic and genotypic frequencies with risk of T2D was analyzed using logistic regression analysis on the basis of odds ratio at 95% confidence interval. Hardy-Weinberg equilibrium (HWE) test was performed to evaluate the uniformity of the genotypic frequencies and deviation from the HWE was tested using Chi-square test.

RESULTS

Logistic regression analyses revealed significant association of short allele containing 243 bp (OR: 1.37 and p = 0.03) with T2D, when the long alleles (commonly found) were considered as reference. The heterozygous genotype 272/302 was significantly associated with the decreased risk of T2D (OR: 0.33, p = 0.001). The combined results of genotypes indicated that the MNS16A polymorphism was significantly associated with the increased risk of T2D under the dominant model (LL vs SL + SS; OR: 2.62, p < 0.0001). Interestingly, short allele 243 was associated with the risk of disease only in male population (OR: 1.62, p = 0.02). The genotype 272/302 was also found to be associated with the decreased risk of T2D when respective data for male was analyzed individually.

CONCLUSIONS

We have identified four variable number of tandem repeats with varying patterns of association with T2D in Bangladeshi population and to extend our knowledge of understanding regarding these VNTRs, further large-scale studies are warranted.

Evaluation of D-loop hypervariable region I variations, haplogroups and copy number of mitochondrial DNA in Bangladeshi population with type 2 diabetes

The profound impact of mitochondrion in cellular metabolism has been well documented. Since type 2 diabetes (T2D) is a metabolic disorder, mitochondrial dysfunction is intricately linked with the disease pathogenesis. Mitochondrial DNA (mtDNA) variants are involved with functional dysfunction of mitochondrion and play a pivotal role in the susceptibility to T2D. In this study, we opted to find the association of mtDNA variants within the D-loop hypervariable region I (HVI), haplogroups and mtDNA copy number with T2D in Bangladeshi population. A total of 300 unrelated Bangladeshi individuals (150 healthy and 150 patients with T2D) were recruited in the present study, their HVI regions were amplified and sequenced using Sanger chemistry. Haplogrep2 and Phylotree17 tools were employed to determine the haplogroups. MtDNA copy number was measured using primers of mitochondrial tRNALeu (UUR) gene and nuclear β2-microglobulin gene. Variants G16048A (OR:0.12, p = 0.04) and G16129A (OR: 0.42, p = 0.007) were found to confer protective role against T2D according to logistic regression analysis. However along with G16129A, two new variants C16294T and T16325C demonstrated protective role against T2D when age and gender were adjusted. Haplogroups A and H showed significant association with the risk of T2D after adjustments out of total 19 major haplogroups identified. The mtDNA copy numbers were stratified into 4 groups according to the quartiles (groups with lower, medium, upper and higher mtDNA copy numbers were respectively designated as LCN, MCN, UCN and HCN). Patients with T2D had significantly lower mtDNA copy number compared to their healthy counterparts in HCN group. Moreover, six mtDNA variants were significantly associated with mtDNA copy number in the participants. Thus, our study confers that certain haplogroups and novel variants of mtDNA are significantly associated with T2D while decreased mtDNA copy number (though not significant) has been observed in patients with T2D. However, largescale studies are warranted to establish association of novel variants and haplogroup with type 2 diabetes.