http://reposit.library.du.ac.bd:8080/xmlui/xmlui/handle/123456789/158 2026-10-19T16:51:05Z http://reposit.library.du.ac.bd:8080/xmlui/xmlui/handle/123456789/4909 Elucidating Genetic and Epigenetic Mechanisms of Type 2 Diabetes Mellitus Pathogenesis Barman, Nilima Type 2 diabetes mellitus (T2DM) is a rapidly escalating public health crisis in Bangladesh, which now ranks seventh globally, with approximately 13.9 million adults living with the disease. T2DM is a multifactorial disorder arising from complex interactions among genetic susceptibility, epigenetic dysregulation, and environmental exposures. Despite the growing burden, molecular-level evidence from Bangladeshi populations remains scarce. This study aimed to investigate the genetic, environmental, and epigenetic factors associated with T2DM in the Bangladeshi population by examining genetic variations in the TCF7L2 rs12255372 and SLC30A8 rs13266634 genes, exploring the association between adverse childhood experiences (ACEs) and adult T2DM risk, characterizing genome-wide DNA methylation alterations in T2DM, and assessing the potential mediating role of DNA methylation in the relationship between ACE exposure and T2DM susceptibility. A case-control study was conducted among Bangladeshi T2DM patients and healthy controls. Clinical, anthropometric, biochemical, and psychosocial data were collected, and ACE exposure was assessed using the standardized ACE questionnaire. Candidate gene polymorphisms were analyzed by PCR amplification and Sanger sequencing. The Structural consequences of the SLC30A8 rs13266634 substitution were investigated via molecular dynamics simulation. Genome-wide DNA methylation profiling was performed using whole-genome enzymatic methyl sequencing on peripheral blood-derived genomic DNA, followed by bioinformatic analysis using the nf-core/methylseq pipeline and differential methylation analyses with edgeR and DMRcate. Pathway enrichment analysis was conducted using Ingenuity Pathway Analysis. High-dimensional mediation analysis (HDMAX2) was applied to explore the potential mediating role of DNA methylation in the association between ACE and T2DM. The study demonstrated that both genetic and environmental factors contribute significantly to T2DM susceptibility in the Bangladeshi population. The TCF7L2 rs12255372 T allele was significantly associated with increased T2DM risk, with individuals carrying either GT or GT-TT genotypes showing higher odds of disease. Similarly, the SLC30A8 rs13266634 wild-type CC genotype and major C allele were associated with increased T2DM susceptibility, whereas the variant TT genotype x appeared to confer a protective effect. Molecular dynamics simulations further suggested that the ZnT8 p.R325W substitution increased structural rigidity and reduced conformational flexibility, potentially affecting zinc transport and insulin granule physiology. In addition to genetic susceptibility, ACEs were strongly associated with T2DM, as individuals exposed to four or more ACEs had more than two-fold higher risk of developing the disease. Genome-wide DNA methylation profiling identified 608 differentially methylated CpG sites, the majority of which were hypermethylated. Pathway enrichment analyses revealed epigenetic dysregulation in neurotransmitter signaling, fatty acid metabolism, adiponectin signaling, insulin resistance pathways, and mitochondrial regulation. Furthermore, high-dimensional mediation analysis identified multiple methylated loci potentially involved in the association between ACE exposure and T2DM, while pooled mediation analysis indicated that the indirect effect through DNA methylation accounted for approximately 41.1% of the total ACE–T2DM association. These findings provide statistical evidence consistent with a potential epigenetic pathway through which early-life adversity may influence adult metabolic disease risk, rather than establishing a definitive causal relationship. In conclusion, this study provides integrated evidence that genetic susceptibility, adverse childhood experiences, and epigenetic dysregulation collectively contribute to T2DM in the Bangladeshi population. The findings enhance understanding of the molecular mechanisms underlying T2DM and may contribute to future strategies for early risk prediction, prevention, and personalized management of diabetes in Bangladesh. This thesis is submitted for the degree of Doctor of Philosophy. 2026-10-18T00:00:00Z http://reposit.library.du.ac.bd:8080/xmlui/xmlui/handle/123456789/4723 Molecular Basis of the Pelvi-Ureteric Junction Obstruction in Children with Hydronephrosis SHADRUL ALAM, MOHAMMED ABSTRACT: Background: Pelvi-Ureteric Junction Obstruction (PUJO) represents a significant cause of congenital hydronephrosis that can lead to progressive renal damage if untreated. While the condition is well-characterized clinically, its molecular pathogenesis remains poorly understood. This study aimed to identify key genetic alterations in PUJO through comprehensive transcriptomic analysis. Methods: We conducted a prospective study from January 2016 to December 2023 involving 9 pediatric patients (18 tissue samples) undergoing Anderson-Hynes pyeloplasty. Paired samples were collected from stenotic PUJ segments and adjacent normal ureteral tissue. RNA sequencing was performed followed by bioinformatic analysis to identify differentially expressed genes (DEGs) and pathway enrichment. Clinical parameters including demographics, presentation, and postoperative outcomes were systematically recorded. Results: The cohort showed male predominance (3.5:1 ratio) with mean age 40.22±32.61 months and left-sided predominance (77.8%). Key clinical presentations included abdominal distension (55.6%) and urinary tract infections (33.3%). Postoperative complications occurred in 22.2% cases. Transcriptomic analysis revealed 590 significant DEGs (292 upregulated, 298 downregulated), with notable enrichment in neuroactive ligand-receptor interactions (141 genes) and olfactory transduction pathways (50 genes). Chromosomal analysis identified 29 enriched regions, particularly on chromosomes 19, 17, and 9. Key dysregulated genes included KRT8 (upregulated) and SEMA3F (downregulated), implicating defects in smooth muscle differentiation and ureteral development. Conclusion: This first Bangladeshi transcriptomic study of PUJO identifies distinct molecular signatures involving neural signaling, ion transport, and developmental pathways. The findings provide novel insights into PUJO pathogenesis and potential biomarkers for early diagnosis. These results establish a foundation for developing targeted therapies to prevent renal damage in affected children. This thesis is submitted for the degree of Doctor of Philosophy. 2025-11-05T00:00:00Z http://reposit.library.du.ac.bd:8080/xmlui/xmlui/handle/123456789/4684 Impacts of pathogenic mutations and XmnI polymorphism on the severity of haemoglobin E β-thalassaemia patients in Bangladesh Aziz, Md. Abdul Background: Haemoglobin E β-thalassaemia is a common blood disorder in South Asia, especially Bangladesh. The disorder can range from mild and asymptomatic anemia to life-threatening anemia. Patients with asymptomatic anemia do not require blood transfusions in their lifetime. Mild Hb E beta thalassaemia patients require occasional blood transfusions. However, patients with life-threatening anemia need frequent blood transfusions. The presence of XmnI polymorphism with specific mutation led to a delay of blood transfusions, higher haemoglobin levels, better response to hydroxyurea treatment, and milder phenotypic presentation among Hb E β thalassaemia patients. Aims: The aim of this study is to examine how the HBB gene mutations and the XmnI polymorphism affect the severity and transfusion needs of haemoglobin E β thalassaemia patients. Methodology: In this study, a total of 360 Hb E β-thalassaemia patients were included. The seven common HBB mutations in Bangladesh were detected by amplification refractory mutation system (ARMS) method, and rare/novel mutations were detected by Sanger sequencing. Moreover, XmnI (PdmI) restriction site was detected by XmnI (PdmI) restriction enzyme digestion. Results: Among the subjects in this research, 62.5% (n=225) were regular transfusion dependent, 22.8% (n=82) were occasionally transfusion-dependent, 8.1% (n=29) were one-time transfusion patients, and 6.7% (n=24) were transfusion-independent patients. This study identified a total of thirteen pathogenic mutations among the 360 Hb E β thalassaemia patients. The most common mutation was IVS 1-5 (G>C), accounting for 57.8% (n=208) of cases, followed by Fr 41/42(-CTTT) 12.2% (n=44), codon 30 (G>C) 8.3% (n=30), Fr 8/9 (+G) 7.5% (n=27), codon 16 (-C) 3.9% (n=14), and codon 15 (G>A) 2.8% (n=10). The study also identified six rare mutations, including -90(C>T) 3.1% (n=11), IVS-I-130(G>A) 3.1% (n=11), IVS II-654 (C>T) 0.6% (n=2), and -30 (T>C) 0.3% (n=1), codon 14/15 (+G) 0.3% (n=1) and -29 (A>G) 0.3% (n=1). Of these, -29 (A>G) had not been reported previously in Bangladesh. Page | v This study found that those with codon 16 (-C) mutation required regular transfusions, while those with codon 30 (G>C) mutations had the least transfusion dependency (6.7%). Patients with codon 30 (G>C) mutations had the highest response to hydroxyurea therapy (76.7% (n=23)) (p=0.051), while patients with Codon 16 (-C) mutations had the lowest response (0% (n=14)) (p=0.057). Codon 16 (-C) mutation was associated with the least HbF (mean ± SD= 24.8±7.7%), while codon 30 (G>C) mutation was associated with the highest HbF (mean ± SD= 41.9±16.10%). Regarding XmnI polymorphism, Codon 16 (-C) mutation was associated with the highest wild type (-/-) (n=11) genotype (p=0.153), while codon 30 (G>C) mutation was associated with the highest homozygous mutated (+/+) (n=11) and the least wild type (-/-) (n=4) of XmnI polymorphism genotype (p=0.157). Conclusion: The outcomes of this study will be useful for developing treatment strategies involving HU therapy and for managing Hb E β-thalassemia patients in Bagladesh. This thesis is submitted for the degree of Doctor of Philosophy. 2025-07-07T00:00:00Z http://reposit.library.du.ac.bd:8080/xmlui/xmlui/handle/123456789/3591 Metabolomics Profiling for Amino Acidopathies of Infants in Hospital Based Settings in Bangladesh and Development of Easy-to-Use Kit for Disease Diagnosis and Monitoring Hossain, Md. Shawkat This study aimed to address the challenges associated with identifying inborn errors of metabolism (IEM) in resource-constrained environments, focusing on amino acid and galactose metabolism disorders in the Bangladeshi infant population. Liquid Chromatography Mass Spectrometry (LC-MS) is a robust diagnostic tool but faces limitations due to cost, complexity, and accessibility. Therefore alternative approaches, including enzyme assays, genetic testing, and metabolite profiling, were explored for effective IEM detection. In pursuit of an affordable diagnostic solution, a low-cost kit was developed for early detection and intervention of amino acid and galactose-related disorders. A validated HPLC-based method was established for accurate quantification of amino acids. The method exhibited strong linearity (R2 = 0.9999) and high accuracy (99.10% average recovery), establishing its suitability for amino acid analysis. Precision was confirmed through repeatability and intermediate precision tests, with low RSD values (0.30% to 1.53% and 0.23% to 0.66%, respectively). Amino acid cutoff ranges were determined for the Bangladeshi population using the validated HPLC method. Noteworthy variations in amino acid counts were observed in positive samples, emphasizing the importance of accurate cutoff values. A lateral flow paper-based diagnostic kit was designed for phenylalanine detection, offering a cost-effective means for phenylketonuria (PKU) monitoring. The kit demonstrated a minimum detection limit of 2 mg/dL, catering to PKU therapy needs. The study also concentrated on Galactosemia as a model disorder, underlining the necessity of early intervention. Molecular analysis of the GALT gene unveiled specific mutations in the Bangladeshi population, contributing to Galactosemia's molecular diversity. Evaluation of silent mutations' impact on splicing shed light on potential gene expression and protein function alterations, influencing Galactosemia outcomes. An easy-to-use lateral flow diagnostic kit for Galactosemia was developed, showing specificity for galactose and delivering rapid results within 5 minutes. Stability assessment revealed promising results at 2-8°C storage over a year, with signal degradation at higher temperatures, emphasizing proper storage conditions. The study highlights the potential of the HPLC method for amino acid detection, paving the way for accessible and cost-effective amino acidopathy detection facilities. The Galactosemia kit, with further refinement, holds promise for broader use. Insights into alternate GALT gene splicing patterns provide avenues for therapeutic exploration. Future research should fine-tune kits and establish precise phenylalanine and galactose cutoff ranges for the Bangladeshi population, contributing to improved IEM management. A DESSERTATION SUBMITTED TO THE UNIVERSITY OF DHAKA IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY IN GENETIC ENGINEERING AND BIOTECHNOLOGY. 2025-02-09T00:00:00Z