👤 Junaid Zafar

Pancreatic islets undergo coordinated cellular remodeling during obesity-induced insulin resistance (IR). However, the associated molecular changes across endocrine and non-endocrine compartments remain largely unexplored. Here, using longitudinal single-cell RNA sequencing (scRNA-seq) and single-cell ATAC sequencing (scATAC-seq) on islets from C57BL/6 mice subjected to high-fat diet (HFD) feeding for 8, 16, and 24 weeks, along with age-matched controls on regular chow, we mapped dynamic changes in islet cell composition and transcriptional states. Beta cells demonstrated pronounced stress-induced reprogramming, with the emergence of proliferative and dysfunctional subsets. Alpha and delta cell fractions declined under HFD, despite increased polyhormonal biosynthesis, suggesting functional rather than numerical adaptation. Immune profiling showed robust expansion of proinflammatory M1 macrophages and upregulation of NF-κB and chemotaxis pathways, particularly at 16 weeks. Notably, cell-cell communication analyses revealed diet-specific disruption in signaling networks. Under HFD conditions, intercellular communication among beta cells, macrophages, and delta cells was markedly altered, leading to the disruption of key signaling pathways such as the gastric inhibitory polypeptide receptor (GIPR) and major histocompatibility complex-I (MHC-I). Notably, C-C motif chemokine ligand 27A ( Show less

Liver cancer is the sixth most frequent malignancy and the fourth major cause of deaths worldwide. The current treatments are only effective in early stages of cancer. To overcome the therapeutic challenges and exploration of immunotherapeutic options, broad spectral therapeutic vaccines could have significant impact. Based on immunoinformatic and integrated machine learning tools, we predicted the potential therapeutic vaccine candidates of liver cancer. In this study, machine learning and MD simulation-based approach are effectively used to design T-cell epitopes that aid the immune system against liver cancer. Antigenicity, molecular weight, subcellular localization and expression site predictions were used to shortlist liver cancer associated proteins including AMBP, CFB, CDHR5, VTN, APOBR, AFP, SERPINA1 and APOE. We predicted CD8+ T-cell epitopes of these proteins containing LGEGATEAE, LLYIGKDRK, EDIGTEADV, QVDAAMAGR, HLEARKKSK, HLCIRHEMT, LKLSKAVHK, EQGRVRAAT and CD4+ T-cell epitopes of VLGEGATEA, WVTKQLNEI, VEEDTKVNS, FTRINCQGK, WGILGREEA, LQDGEKIMS, VKFNKPFVF, VRAATVGSL. We observed the substantial physicochemical properties of these epitopes with a significant binding affinity with MHC molecules. A polyvalent construct of these epitopes was designed using suitable linkers and adjuvant indicated significant binding energy (>-10.5 kcal/mol) with MHC class-I and II molecule. Based on in silico cloning, we found the considerable compatibility of this polyvalent construct with the E. coli expression system and the efficiency of its translation in host. The system-level and machine learning based cross validations showed the possible effect of these T-cell epitopes as potential vaccine candidates for the treatment of liver cancer. Show less

Congenital nephrotic syndrome of the Finnish type (CNF) is an autosomal recessive disorder resulting from mutations in the We describe the salient features of a newborn with CNF and multiple fetal anomalies based on clinical risk factors discovered by ultrasound (US) and X-rays, which include cardiomegaly, polycystic kidney disease, and renal dysplasia. Biochemical tests showed substantial proteinuria and excess protein in the urine detected at birth; this condition caused albuminuria, hypoalbuminemia, edema, and additional symptoms. The patient underwent treatment to reduce the risks of proteinuria, hypertension, infection, and other symptoms. The next generation sequencing (NGS) analysis revealed that the infant had five previously unreported heterozygous missense variants classified as VUS in The infant's illness may be related to changes in exonic splicing caused by Show less

Intellectual disability is a heterogeneous disorder, diagnosed using intelligence quotient (IQ) score criteria. Currently, no specific clinical test is available to diagnose the disease and its subgroups due to inadequate understanding of the pathophysiology. Therefore, current study was designed to explore the molecular mechanisms involved in disease perturbation, and to identify potential biomarkers for disease diagnosis and prognosis. A total of 250 participants were enrolled in this study, including 200 intellectually disabled (ID) subjects from the subgroups (mild, moderate, and severe) with age and gender matched healthy controls (n = 50). Initially, IQ testing score and biochemical profile of each subject was generated, followed by label-free quantitative proteomics of subgroups of IQ and healthy control group through nano-LC/MS- mass spectrometry. A total of 310 proteins were identified, among them198 proteins were common among all groups. Statistical analysis (ANOVA) of the subgroups of ID showed 142 differentially expressed proteins, in comparison to healthy control group. From these, 120 proteins were found to be common among all subgroups. The remaining 22 proteins were categorized as exclusive proteins found only in disease subgroups. Furthermore, the hierarchical cluster analysis (HCL) of common significant proteins was also performed, followed by PANTHER protein classification and GO functional enrichment analysis. Results provides that the datasets of differentially expressed proteins, belong to the categories of immune / defense proteins, transfer carrier proteins, apolipoproteins, complement proteins, protease inhibitors, hemoglobin proteins etc., they are known to involvein immune system, and complement and coagulation pathway cascade and cholesterol metabolism pathway. Exclusively expressed 22 proteins were found to be disease stage specific and strong PPI network specifically those that have significant role in platelets activation and degranulation, such as Filamin A (FLNA). Furthermore, to validate the mass spectrometric findings, four highly significant proteins (APOA4, SAP, FLNA, and SERPING) were quantified by ELISA in all the study subjects. AUROC analysis showed a significant association of APOA4 (0.830), FLNA (0.958), SAP (0.754) and SERPING (0.600) with the disease. Apolipoprotein A4 (APOA4) has a significant role in cholesterol transport, and in modulation of glucose and lipid metabolism in the CNS. Similarly, FLNA has a crucial role in the nervous system, especially in the functioning of synaptic network. Therefore, both APOA4, and FLNA proteins represent good potential for candidate biomarkers for the diagnosis and prognosis of the intellectual disability. Overall, serum proteome of ID patients provides valuable information of proteins/pathways that are altered during ID progression. Show less

Obesity is highly polygenic disease where several genetic variants have been reportedly associated with obesity in different ethnicities of the world. In the current study, we identified the obesity risk or protective association and BMI raising effect of the minor allele of adiponectin, C1Q and collagen domain containing (ADIPOQ), cholesteryl ester transfer protein (CEPT), FTO alpha-ketoglutarate dependent dioxygenase (FTO), leptin (LEP), and leptin receptor (LEPR) genes in a large cohort stratified into four BMI-based body weight categories i.e., normal weight, lean, over-weight, and obese. Based on selected candidate genetic markers, the genotyping of all study subjects was performed by PCR assays, and genotypes and allele frequencies were calculated. The minor allele frequencies (MAFs) of all genetic markers were computed for total and BMI-based body weight categories and compared with MAFs of global and South Asian (SAS) populations. Genetic associations of variants with obesity risk were calculated and BMI raising effect per copy of the minor allele were estimated. The genetic variants with higher MAFs in obese BMI group were; rs2241766 (G = 0.43), rs17817449 (G = 0.54), rs9939609 (A = 0.51), rs1421085 (C = 0.53), rs1558902 (A = 0.63), and rs1137101 (G = 0.64) respectively. All these variants were significantly associated with obesity (OR = 1.03-4.42) and showed a high BMI raising effect (β = 0.239-0.31 Kg/m2) per copy of the risk allele. In contrast, the MAFs of three variants were higher in lean-normal BMI groups; rs3764261 A = 0.38, rs9941349 T = 0.43, and rs7799039 G = 0.40-0.43). These variants showed obesity protective associations (OR = 0.68-0.76), and a BMI lowering effect per copy of the protective allele (β = -0.103-0.155 Kg/m2). The rs3764261 variant also showed significant and positive association with lean body mass (OR = 2.38, CI = 1.30-4.34). Overall, we report six genetic variants of ADIPOQ, FTO and LEPR genes as obesity-risk markers and a CETP gene variant as lean mass/obesity protective marker in studied Pakistani cohort. Show less

To investigate the association of -1131T>C polymorphism of apolipoprotein A5 (APOA5) with metabolic syndrome and associated traits. A cross-sectional comparative study. Department of Physiology, University of Health Sciences Lahore, from July 2016 to December 2017. Study population included 200 cases of metabolic syndrome and 200 controls. Cases were selected from Sheikh Zayed Hospital, Lahore according to the International Diabetes Federation guidelines. Fasting blood sample of 8 ml was taken for biochemical and genetic analysis, as per objective. Demographics, waist circumferance and blood pressure (BP) were also recorded. Subjects with metabolic syndrome had significantly higher waist circumference, BP, serum lipid and glycemic parameters as compared to the controls (p<0.001). The observed frequency of APOA5-1131T>C genotype TT was 180 (45%), 202 (50.5%) for TC and 18 (4.5%) for CC. Minor C allele frequency of APOA5-1131T>C variant was significantly higher in metabolic syndrome as compared to the controls (0.33 vs. 0.26: p = 0.031*). In the Dominant genotype model (TC+CC vs. TT), 'TC+CC' genotype was significantly associated with the increased risk of metabolic syndrome (OR: 1.50, CI: 1.01-2.23, p = 0.044*). Waist circumference and fasting triglyceride levels were significantly higher in 'TC +CC' genotype as compared to the 'TT' in metabolic syndrome and controls (p = <0.001 and 0.043; p = 0.022 and 0.006). There was significant association of the 'TC+CC' genotype of APOA5 -1131T>C with the increased risk of Met S and the association remained significant after controlling for age and gender. Show less

The present study aimed to determine the association of adrenergic receptor beta-3 (ADRB3) rs4994 T>C and liver X receptor alpha (LXR-α) rs12221497 G>A polymorphism with metabolic syndrome (Met S) and the related traits in Pakistanis. Patients of Met S were recruited from the Endocrinology and Diabetic Clinic of Sheikh Zayed Hospital Lahore, over the time span of 6 months from July to December 2016. Single-nucleotide polymorphism (SNP) of ADRB3 was determined by restriction fragment length polymorphism and of LXR-α by amplification refractory mutation system polymerase chain reaction. The frequency of TT variant of ADRB3 T>C in Met S was 69 (34.5%) and in controls 89 (44.5%), frequency of TC 103 (51.5%) and 96 (48%), and of CC 28 (14%) and 15 (7.5%), respectively. In the recessive model (CC: TT + TC), CC genotype was found to be associated with the increased risk of Met S (P = 0.027; odds ratio [OR] = 2.09; confidence interval [CI] =1.08-4.03) and the association remained significant after controlling for the confounders such as age and sex. The frequency of GG variant of LXR-α G>A in Met S was 35 (17.5%) and in controls 15 (7.5%), GA 129 (64.5%) and 137 (68.5%), and AA 36 (18%) and 48 (24%), respectively. In the recessive model (GG: GA + AA), GG genotype was found to be associated with the increased risk of Met S (P = 0.004; OR = 2.52; CI = 1.33-4.80) and the association remained significant after controlling for the confounders such as age and sex. It was concluded that SNP of ADRB3 (190 T>C) and LXR-α (-115 G>A) were associated with the risk of Met S and might increase the susceptibility to the obesity-related traits. Show less

Evidence is sparse about the genetic determinants of major lipids in Pakistanis. Variants (n=45 000) across 2000 genes were assessed in 3200 Pakistanis and compared with 2450 Germans using the same gene array and similar lipid assays. We also did a meta-analysis of selected lipid-related variants in Europeans. Pakistani genetic architecture was distinct from that of several ethnic groups represented in international reference samples. Forty-one variants at 14 loci were significantly associated with levels of HDL-C, triglyceride, or LDL-C. The most significant lipid-related variants identified among Pakistanis corresponded to genes previously shown to be relevant to Europeans, such as CETP associated with HDL-C levels (rs711752; P<10(-13)), APOA5/ZNF259 (rs651821; P<10(-13)) and GCKR (rs1260326; P<10(-13)) with triglyceride levels; and CELSR2 variants with LDL-C levels (rs646776; P<10(-9)). For Pakistanis, these 41 variants explained 6.2%, 7.1%, and 0.9% of the variation in HDL-C, triglyceride, and LDL-C, respectively. Compared with Europeans, the allele frequency of rs662799 in APOA5 among Pakistanis was higher and its impact on triglyceride concentration was greater (P-value for difference <10(-4)). Several lipid-related genetic variants are common to Pakistanis and Europeans, though they explain only a modest proportion of population variation in lipid concentration. Allelic frequencies and effect sizes of lipid-related variants can differ between Pakistanis and Europeans. Show less