👤 Alaa Abbas

Astrocytes are central regulators of neural homeostasis, synaptic function, and neuroinflammatory responses in the central nervous system (CNS). Upon pathological stimuli, astrocytes undergo reactive transformations, producing pro-inflammatory cytokines, reactive oxygen species (ROS), and chemokines, which exacerbate neuronal injury. Flavonoids, a diverse class of polyphenolic compounds found in fruits, vegetables, and medicinal plants, have emerged as potent modulators of astrocyte activity, promoting neuroprotection and cognitive enhancement. These compounds, including quercetin, hesperetin, rutin, casticin, and anthocyanins, attenuate astrocyte-mediated neuroinflammation by suppressing NF-κB, MAPK, TLR, and NLRP3 inflammasome signaling while activating antioxidant pathways such as Nrf2 and PI3K/Akt. Flavonoid-mediated modulation also enhances the synthesis and release of neurotrophic factors, including BDNF, GDNF, NGF, and TGF-β1, which support synaptic plasticity, dendritic spine formation, and network connectivity. By preserving astrocytic homeostasis, reducing gliosis, and regulating astrocyte-microglia crosstalk, flavonoids mitigate cytokine-mediated neuronal damage, restore synaptic integrity, and improve learning and memory in models of neurodegeneration, ischemia, and neuroinflammation. Preclinical evidence suggests that flavonoids can cross the blood-brain barrier, exhibit low toxicity, and synergize with other neuroprotective interventions. Understanding the molecular mechanisms of flavonoid-astrocyte interactions provides insight into precision therapeutic strategies aimed at alleviating neuroinflammation and enhancing CNS resilience, offering promising avenues for the prevention and treatment of cognitive and neurodegenerative disorders. Show less

Fluoroquinolones (FQs) are key components of World Health Organization (WHO)-recommended regimens for multidrug-resistant tuberculosis (MDR-TB). Accurate detection of FQ resistance is essential for optimizing treatment. This study evaluated the concordance between the Second-Line Line Probe Assay (SL-LPA) and Liquid Culture Drug Susceptibility Testing (LC-DST) for detecting FQ resistance in Mycobacterium tuberculosis isolates. In this retrospective study, 1402 non-duplicate clinical isolates of MDR TB were tested using SL-LPA and LC-DST at a reference laboratory. Genotypic resistance was identified through mutations in the gyrA and gyrB genes identified by SL-LPA, while phenotypic resistance was determined using MGIT-based LC-DST at critical concentrations for fluoroquinolones. Targeted nanopore sequencing was performed on a subset of isolates with discordant molecular and phenotypic results to investigate resistance-associated mutations. SL-LPA detected FQ resistance in 907 (64.7%) isolates, whereas LC-DST identified resistance in 852 (60.8%) isolates. Using LC-DST as the reference standard, SL-LPA showed a sensitivity of 93.2%, specificity of 98.6%, positive predictive value of 99.2%, and negative predictive value of 88.7%. Overall concordance between the two methods was observed in 1292 (92.2%) isolates. Discordant results occurred in 110 (7.8%) isolates, mainly involving low-level resistance mutations or inferred resistance due to missing wild-type bands on SL-LPA. Nanopore sequencing of 15 discordant isolates identified high-confidence mutations (Asp94Tyr, Asp94Gly, Asp94Asn) and interim or low-confidence mutations (Ala90Val, Ser91Pro, Asp94Ala, gyrB Asn499Asp, Asp461Asn). SL-LPA demonstrates excellent specificity and positive predictive value for detecting FQ resistance; however, discordance associated with low-confidence mutations and heteroresistance highlights the importance of integrating molecular assays with phenotypic DST and sequencing to improve MDR-TB resistance detection and guide treatment decisions. Show less

Familial dyslipidemia (FD), particularly familial hypercholesterolemia (FH), is a major contributor to premature cardiovascular disease (CVD), especially in regions with high consanguinity and underutilized genetic screening, such as Egypt. This study aimed to assess clinical, biochemical, and genetic factors that differentiate FD patients with and without CVD, and to develop a composite risk score for individualized stratification. A cross-sectional study was conducted on 60 Egyptian patients aged 15-25 years with genetically confirmed FD, equally divided based on CVD status. All participants underwent detailed clinical assessment, lipid profiling, and targeted next-generation sequencing of LDLR, APOB, and PCSK9 genes. Missense variants were evaluated using SIFT, PolyPhen-2, CADD, and ΔΔG stability scores, and classified according to ACMG criteria. Compared to non-CVD patients, those with CVD had significantly higher triglyceride levels (median: 356.5 vs. 236.5 mg/dL; p < 0.001) and a higher frequency of heterozygous pathogenic LDLR variants (30.0% vs. 3.3%; p = 0.006), while homozygous variants were more common in non-CVD patients (26.7% vs. 0%; p = 0.002). Deleterious missense variants were notably more frequent in the CVD group (56.7% vs. 10.0%; p < 0.001). A 10-variable composite risk score integrating clinical, lipid, and bioinformatic predictors effectively distinguished high- and moderate-risk cases (AUC = 0.742; p = 0.022), with 89.5% sensitivity and 81.8% negative predictive value. The study highlights the importance of combining clinical and genomic data for early risk stratification and introduces a pragmatic tool for identifying high-risk youth in resource-limited, consanguineous populations. Show less

Plant-derived compounds have recently gained attention owing to their better safety profile and multi-targeted actions. Charantin, a plant-based natural compound known for its diverse pharmacological properties, was investigated for its anti-hyperlipdemic activity using both in-silico and in-vivo approaches. A detailed network pharmacology analysis was used to predict charantin-related targets, cross-referenced with hyperlipidemia-associated genes from GeneCards, DisGeNET, and CTD. Shared targets were subjected to protein-protein interaction analysis and functional enrichment using STRING, Cytoscape, and ShinyGO. Molecular docking studies assessed charantin's binding interactions with key lipid-regulating proteins (HMGCR, PCSK9, LDLR, PPAR-α, PI3K). In-vivo efficacy of charantin (100 and 200 mg/kg) was evaluated in Sprague-Dawley rats fed with high-lipid diet (HLD) for 12 days. Lipid profiles, liver enzymes and transcript levels of lipid-regulating genes were analyzed. A total of 242 overlapping genes were identified between charantin targets and hyperlipidemia-associated genes, with enrichment analyses highlighting key lipid metabolic and inflammatory pathways. Molecular docking revealed that charantin exhibited stronger binding affinities than simvastatin across multiple targets. In HLD animal model, charantin significantly reduced total cholesterol, triglycerides, LDL, and VLDL, while increasing HDL levels in a dose-dependent manner. Liver function remained preserved, accompanied by downregulation of HMGCR, PCSK9, and APOB, and upregulation of LDLR and PPAR-α at both gene and protein levels. Charantin exerts potent lipid-lowering effects through modulation of multiple pathways, including cholesterol biosynthesis, lipoprotein metabolism, and nuclear receptor activation. Its efficacy and hepatoprotective properties reiterate its potential as a safe, effective alternative or adjunct to conventional therapies for hyperlipidemia. Show less

Coronary artery disease (CAD) is a multifactorial disorder influenced by both genetic and clinical risk factors. Lipid metabolism genes such as apolipoprotein B(APOB) (rs515135) and proprotein convertase subtilisin/kexin type 9 (PCSK9)(rs505151), have been associated with susceptibility to CAD. Study investigates the potential role of these genetic polymorphisms with risk of CAD in the Indian population. A case-control study including 150 CAD cases and 150 controls. Angiographically proven Cases were recruited from the Cardiology Unit, Department of Medicine, Era's Lucknow Medical College. Genotyping was done using specific primers and restriction digestion; statistical analysis included t-tests, odds ratios, and haplotype analysis. CAD cases(mean age 49.93   ±   9.13 years) had higher serum cholesterol and VLDL but lower systolic and diastolic BP compared to controls (mean age 56.47   ±   9.39 years). The APOB G allele showed a significant protective effect against CAD (OR: 0.431, The APOB G allele may serve as a protective factor against CAD, highlighting its potential role in genetic screening for lower disease risk. Further large-scale studies are required to confirm these findings. Show less

Type 2 diabetes (T2D) is a complex metabolic disorder driven by genetic and environmental factors. While genome-wide association studies (GWAS) have identified numerous T2D-associated variants, many remain functionally uncharacterized. Integration of GWAS with molecular phenotyping offers a path to revealing biological relevance. We investigated the influence of GWAS-variants, including sub-threshold T2D-associated variants (GWAS p-value ≤ 0.0001), on gene and protein expression to assign functional relevance. Genetic variants associated with T2D in the GWAS Catalog and present in our whole-genome sequencing (WGS) data were used to perform expression quantitative trait loci (eQTL) analysis in 242 whole-blood mRNA-sequenced samples. The same variants were used to perform protein quantitative trait loci (pQTL) analysis in a set of 362 plasma samples profiled on the Olink platform. For each analysis, the datasets were randomly split into discovery and validation subsets. Associations between variants and mRNA or protein levels were tested by multiple linear regression, and only QTLs that reached a false discovery rate adjusted p-value ≤ 0.05 in the discovery dataset and replicated in the validation dataset (p ≤ 0.05) with same direction of effect were carried forward. QTL-linked mRNAs and proteins were subsequently evaluated for their relationship with T2D status to connect them with T2D pathophysiology. We identified 1,291 eQTLs linked to 97 mRNAs and 1,273 pQTLs linked to 22 proteins. Among these, 10 mRNAs and 5 proteins were differentially expressed between non-diabetic and diabetic individuals. Notably, LPL, APOBR, APOM (lipid metabolism), NOTCH2, TREH (β-cell/endocrine regulation), and HLA-A, OAS3 (immune response) converged on three biological axes central to T2D pathophysiology. The directionality of molecular effects was consistent with known disease mechanisms, including insulin resistance (LPL, APOBR), β-cell stress (TREH, NOTCH2), and chronic inflammation (OAS3). Our findings indicate that variants falling below conventional GWAS significance thresholds can have demonstrable effects on gene expression and protein levels. This underscores the importance of prioritizing biological relevance alongside statistical significance, rather than relying solely on rigid p-value cutoffs. Show less

Crateva magna (Cm) was utilized as a folkloric medicine against neurological disorders. This study aimed to investigate the phytochemical profile of Cm leaf extract and its endophytic fungus, Nigrospora oryzae (No) extract. Additionally, the neuroprotective potential of their optimized bilosomes (BLs) will be assessed as an approach to Alzheimer's disease (AD) treatment. UPLC-ESI-MS/MS chemical profiling was performed. In vitro anti-Alzheimer activity of Cm and No extracts was evaluated against AChE and BACE1 enzymes. Cm-BLs and No-BLs were prepared using the thin-film hydration technique. In vivo anti-Alzheimer potential was assessed in a streptozotocin (STZ)-induced sporadic AD mouse model. Behavioral assays, neurochemical assays, RT-PCR analysis, histopathological examination, and immunohistochemical analysis were performed. Chemical profiling revealed diverse metabolites from various chemical classes. The major class identified in Cm extract was flavonoids, e.g., kaempferol-O-hexoside, whereas in No extract, it was alkaloids, e.g., phenazine carboxamide. The neuropathological markers (Aβ1-42, IL-6, and p-Tau protein) were reduced by ≈50% and 60% in mice receiving Cm-BLs and No-BLs, respectively, relative to the STZ group. Also, the BLs exhibited the greatest ability to downregulate the expression of p-JNK, p-P38, and p-ERK in the brain. Histopathological examination revealed that No-BLs showed the highest protection for the hippocampus and cerebral cortex regions. Also, it revealed a significantly decreased reaction for NFκB in cerebral cortex neurons. Cm-BLs and No-BLs exhibit considerable potential as novel adjuvant therapies for AD, utilizing natural bioactive compounds to improve the efficiency of targeted drug delivery and enhance therapeutic outcomes. Show less

Elevated lipoprotein(a) [Lp(a)] and low high-density lipoprotein-cholesterol (HDL-C) are established cardiovascular (CV) risk factors, but their combined impact on mortality and sex differences remains unclear. This retrospective study analyzed 97 396 patients with measured Lp(a) and HDL-C. Groups were stratified by Lp(a) (≥50 vs. <50 mg/dl) and HDL-C [low (<40), optimal (40-60), high (>60 mg/dl)]. Mortality was assessed using the Kaplan-Meier curve and Cox models. Over a median of 5.9 years, 7794 deaths occurred. Compared to optimal HDL-C/low Lp(a) (reference), high HDL-C/low Lp(a) had the lowest mortality [adjusted hazard ratio (aHR): 0.85; 95% confidence interval (CI): 0.80-0.91], while low HDL-C/high Lp(a) had the highest risk (aHR: 1.55; 1.41-1.71). High HDL-C protective effect was insignificant with elevated Lp(a) (aHR: 0.98; 0.89-1.08). Sex-stratified analyses revealed divergent effects: women with high HDL-C/high Lp(a) retained the HDL-C protective effect (aHR: 0.82; 0.72-0.93), whereas men faced increased risk (aHR: 1.22; 1.05-1.42). Elevated Lp(a) enhances mortality risk despite elevated HDL-C levels, with sex-specific differences: women retain mortality benefits from high HDL-C despite elevated Lp(a), whereas men with concurrent elevations in HDL-C and Lp(a) experienced mortality risks comparable to those with low HDL-C. Findings underscore sex-specific CV risk stratification incorporating HDL-C and Lp(a), challenging the HDL-C universal protective role. Show less

GNAS (guanine nucleotide-binding protein, alpha stimulating) is an imprinted gene that encodes G This review examines the structure and function of GNAS and provides an overview of the disorders that are caused by defects in this gene and may feature early-onset obesity. Moreover, it elucidates the potential molecular mechanisms underlying G G Show less

Alzheimer's disease (AD) is a progressive neurological disorder for which no effective cure currently exists. Research has identified β-Secretase (BACE1) as a promising therapeutic target for the management of AD. BACE1 is involved in the rate-limiting step and produces toxic amyloid-beta (Aβ) peptides that lead to deposits in the form of amyloid plaques extracellularly, resulting in AD. In this connection, 60 small peptides were evaluated for their The identified hit peptides were synthesized using Solid-Phase Peptide Synthesis (SPPS), and Electrospray Ionization Mass Spectrometry (ESI-MS) elucidated their structures and 1 1 HNMR spectroscopy. According to their According to the cytotoxicity study, peptide 21 was found to be noncytotoxic at 4.64 μM, 10 μM and 20 μM. The forthcoming target of this study is to evaluate further the effect of peptide 21 in an in-vivo mice model. Show less

Glycation is among the underlying mechanisms attributed to ageing and associated morbidities. There is no drug available to combat this deleterious phenomenon. The present study aimed to explore phloroglucinol (PHL) for its anti-glycation potential at preclinical level. The rats were treated with methylglyoxal (MGO, 17.25 mg/kg, i.p. for 14 days) to induce glvcative stress. The treatment groups received additional administration of test drug (PHL; 0.25mg/kg, 0.5mg/kg, and 1mg/kg) or standard aminoguanidine (AG, 50 mg/kg) or saline (control, 5ml/kg). During 14 days, the weight and food intake was noted. Afterwards, the cognitive function was evaluated using Morris Water Maze (MWM) while hepatic and renal functions were assessed through liver function test (bilirubin, alkaline phosphatase, SGPT, and SGOT) and creatinine respectively, using chemical analyzer. The carboxymethyllysine (CML) levels were quantified in the blood using ELISA technique. Histopathological study was performed on the brain, liver, and kidney using H&E staining. Additionally, the qPCR was used to quantify the expression of TNF-α, RAGE and BACE-1 (brain), RAGE, TNF-α, and glyoxalase-I (liver) and RAGE, TNF-α, and VEGF (kidney), while glyceraldehyde-3-phosphate dehydrogenase (GAPDH) was used as a reference housekeeping gene. The data regarding weight and food intake did not reveal significant alterations. In MWM, the MGO treatment caused significant increase in the time to reach target quadrant, while decrease in the time spent in target quadrant and number of crossings through platform position. All these effects were inhibited by both AG and PHL. The navigation maps also exhibit that the retention of spatial memory. Additionally, the MGO-induced alteration in hepatic and renal function indicators was ameliorated by both AG and PHL treatments. The plasma CML levels were found to be elevated following MGO treatment, while the concomitant administration of AG and PHL has resisted this raise. Histopathological assessment revealed no specific pathology in liver kidney and brain tissues. The qPCR data revealed enhanced expression of all genes, especially TNF-α and BACE, which were found to be reduced following both AG and PHL treatments. PHL prevented the brain, hepatic, and renal impairments caused by MGO induced glycative stress. Hence, the PHL, a clinically used anti-spasmodic drug, presents itself as a potential candidate to be repurposed as anti-glycation drug. Show less

This study aims to clinically and genetically assess 30 unrelated consanguineous Pakistani families from various ethnic backgrounds, all exhibiting features of neurodevelopmental disorders (NDDs). We conducted clinical, genetic, biochemical, and molecular analyses on 30 consanguineous families with NDDs enrolled from various regions of Pakistan. The likely molecular causes of primary microcephaly and NDDs were identified. Detailed clinical investigations and molecular diagnoses were performed using whole exome sequencing (WES) of the proband, followed by Sanger sequencing for validation and segregation in the available family members of the affected families. WES identified likely disease-causing homozygous variants in 30 unrelated consanguineous families. Six families presented newly described variants in known NDD-related genes: In the present study, we observed a high frequency of Show less

Several studies provide evidence for a role of serum cytokines imbalance including IL-10 and IL-27 in immune thrombocytopenia pathogenesis and prognosis. The aim of this study was designed to investigate the role of serum levels of IL-10 and IL-27 in prognosis the efficiency of treatment in thrombocytopenic Iraqi children. This case controls study was carried out at Department of Biochemistry, College of Medicine, University of Baghdad, during the period from October 2023 to March 2024. It included 88 children, 63 children previously diagnosed with immune thrombocytopenia, and 25 apparently healthy children who served as control group. The included immune thrombocytopenic children were sub-grouped according to their treatment into three groups: Romiplostim group (group 1), Prednisolone group (group 2), Prednisolone and intravenous immunoglobulin (IVIG) or Prednisolone and mycophenolate group (group 3). Investigations included serum level measurements of IL-10 and IL-27 by using enzyme linked immunosorbent assay ELISA. Platelet count of each included children was measured by Huma Count 30 TS Human, Germany. The mean (±SEM) values of serum IL-10 and IL-27 levels of immune thrombocytopenic children were insignificantly lower than that of controls. In addition, there was non- significant differences in serum levels of IL-10 and IL-27 among and between the three groups of patient children. The mean value of platelet count of patient children was significantly increased by all types of treatment in whole immune thrombocytopenic children (117.48±18.15*10⁹/L). Measurement of serum IL-10 and IL-27 are helpful biomarker in prognosis of thrombocytopenia irrespective of type of treatment. Show less

A cardiac condition marked by excessive growth of heart muscle cells, hypertrophic cardiomyopathy (HCM) is a complex genetic disorder characterized by left ventricular hypertrophy, microvascular ischemia, myocardial fibrosis, and diastolic dysfunction. Obstructive hypertrophic cardiomyopathy (oHCM), a subset of HCM, involves significant obstruction in the left ventricular outflow tract (LVOT), leading to symptoms like dyspnea, fatigue, and potentially life-threatening cardiac events. With advancements in genetic understanding and the introduction of novel pharmacologic agents, including cardiac myosin inhibitors like mavacamten and aficamten, there is a paradigm shift in the therapeutic approach to oHCM. The underlying mechanisms of HCM are closely tied to genetic mutations affecting sarcomere proteins, particularly those encoded by the MYH7 and MYBPC3 genes. These mutations lead to disrupted sarcomere function, resulting in hypertrophic changes and LVOT obstruction. While genetic heterogeneity is a hallmark of HCM, clinical diagnosis relies heavily on imaging techniques such as Echocardiography and cardiac magnetic resonance imaging to assess the extent of hypertrophy and obstruction. Current pharmacological management of obstructive HCM (oHCM) focuses on alleviating symptoms rather than modifying disease progression. Beta-blockers and calcium channel blockers are primary treatment options, although their effectiveness varies among patients. Recent clinical trials have highlighted the potential of novel cardiac myosin inhibitors, including mavacamten and aficamten, in enhancing exercise capacity, reducing LVOT obstruction, and improving overall cardiac function. These innovative agents represent a significant breakthrough in targeting the fundamental pathophysiological mechanisms driving oHCM. A comprehensive literature review was conducted, utilizing top-tier databases such as PubMed, Scopus, and Google Scholar, to compile an authoritative and up-to-date overview of the current advancements in the field. This review sheds light on the updated 2024 American Heart Association (AHA) guidelines for HCM management, emphasizing the treatment cascade and tailored management for each stage of oHCM. By introducing a new paradigm for personalized medicine in oHCM, this research leverages advanced genomics, biomarkers, and imaging techniques to optimize treatment strategies. The introduction of cardiac myosin inhibitors heralds a new era in the management of oHCM. By directly targeting the molecular mechanisms underpinning the disease, these novel therapies offer improved symptom relief and functional outcomes. Ongoing research into the genetic basis of HCM and the development of targeted treatments holds promise for further enhancing patient care. Future studies should continue to refine these therapeutic strategies and explore their long-term benefits and potential in diverse patient populations. This review makes a significant contribution to the field by synthesizing the most recent AHA guidelines, emphasizing the crucial role of tailored management strategies in optimizing outcomes for patients with oHCM, and promoting the incorporation of cutting-edge genomics and imaging modalities to enhance personalized care. Show less

Hypertrophic cardiomyopathy (HCM) is the most common inherited cardiomyopathy. It follows an autosomal dominant inheritance pattern in most cases, with incomplete penetrance and heterogeneity. It is familial in 60% of cases and most of these are caused by pathogenic variants in the core sarcomeric genes ( Show less

Bardet-Biedl syndrome (BBS), is an emblematic ciliopathy hallmarked by pleiotropy, phenotype variability, and extensive genetic heterogeneity. BBS is a rare (~1/140,000 to ~1/160,000 in Europe) autosomal recessive pediatric disorder characterized by retinal degeneration, truncal obesity, polydactyly, cognitive impairment, renal dysfunction, and hypogonadism. Twenty-eight genes involved in ciliary structure or function have been implicated in BBS, and explain the molecular basis for ~75%-80% of individuals. To investigate the mutational spectrum of BBS in Romania, we ascertained a cohort of 24 individuals in 23 families. Following informed consent, we performed proband exome sequencing (ES). We detected 17 different putative disease-causing single nucleotide variants or small insertion-deletions and two pathogenic exon disruptive copy number variants in known BBS genes in 17 pedigrees. The most frequently impacted genes were BBS12 (35%), followed by BBS4, BBS7, and BBS10 (9% each) and BBS1, BBS2, and BBS5 (4% each). Homozygous BBS12 p.Arg355* variants were present in seven pedigrees of both Eastern European and Romani origin. Our data show that although the diagnostic rate of BBS in Romania is likely consistent with other worldwide cohorts (74%), we observed a unique distribution of causal BBS genes, including overrepresentation of BBS12 due to a recurrent nonsense variant, that has implications for regional diagnostics. Show less

The prevalence of hypertension reported around the world is increasing and is an important public health challenge. This study was designed to explore the disease's genetic variations and to identify new hypertension-related genes and target proteins. We analyzed 22 publicly available Affymetrix cDNA datasets of hypertension using an integrated system-level framework involving differential expression genetic (DEG) analysis, data mining, gene enrichment, protein-protein interaction, microRNA analysis, toxicogenomics, gene regulation, molecular docking, and simulation studies. We found potential DEGs after screening out the extracellular proteins. We studied the functional role of seven shortlisted DEGs (ADM, EDN1, ANGPTL4, NFIL3, MSR1, CEBPD, and USP8) in hypertension after disease gene curation analysis. The expression profiling and cluster analysis showed significant variations and enriched GO terms. hsa-miR-365a-3p, hsa-miR-2052, hsa-miR-3065-3p, hsa-miR-603, hsa-miR-7113-3p, hsa-miR-3923, and hsa-miR-524-5p were identified as hypertension-associated miRNA targets for each gene using computational algorithms. We found functional interactions of source DEGs with target and important gene signatures including EGFR, AGT, AVP, APOE, RHOA, SRC, APOB, STAT3, UBC, LPL, APOA1, and AKT1 associated with the disease. These DEGs are mainly involved in fatty acid metabolism, myometrial pathways, MAPK, and G-alpha signaling pathways linked with hypertension pathogenesis. We predicted significantly disordered regions of 71.2, 48.8, and 45.4% representing the mutation in the sequence of NFIL3, USP8, and ADM, respectively. Regulation of gene expression was performed to find upregulated genes. Molecular docking analysis was used to evaluate Food and Drug Administration-approved medicines against the four DEGs that were overexpressed. For each elevated target protein, the three best drug candidates were chosen. Furthermore, molecular dynamics (MD) simulation using the target's active sites for 100 ns was used to validate these 12 complexes after docking. This investigation establishes the worth of systems genetics for finding four possible genes as potential drug targets for hypertension. These network-based approaches are significant for finding genetic variant data, which will advance the understanding of how to hasten the identification of drug targets and improve the understanding regarding the treatment of hypertension. Show less

Consanguinity increases the risk of hereditary diseases including disorders of sex development (DSD). There are minimal data on DSD in the highly consanguineous population of Saudi Arabia. This study reports the molecular genetics of a series of patients with different types of DSD. We enrolled 77 patients from 47 families with DSD. DNA was isolated from peripheral leucocytes. Genes of interest were amplified by polymerase chain reaction and subsequently sequenced. Overall, 77 patients from 47 families (44 of them are consanguineous) had a total of 29 mutations; 16 of them were described before and 13 were novel mutations. The most common condition was 5-α reductase (SRD5A2) deficiency (25 patients from 18 families) and the most common mutation was a splice site mutation in intron 1 (c.282-2A>G). The next most common condition was 11-β hydroxylase (CYP11B1) deficiency where 19 patients from 10 families had 8 mutations (7 of them are novel). Other mutations affected CYP17A1 with 2 novel and 2 known mutations in 7 patients; HSD3B2 with 2 known mutations in 11 patients of 4 families; StAR with 1 novel and 1 known mutations in 4 patients; NR0B1 with 1 novel mutation in 2 siblings; HSD17B3 with 1 known mutation in 3 siblings; LHCGR with 1 novel mutation in 2 siblings; and AR with 1 novel and 3 known mutations in 4 unrelated patients. In the highly consanguineous and homogeneous population of Saudi Arabia, SRD5A2 and CYP11B1 deficiencies are common causes of DSDs. Other DSDs occur less frequently but often with novel mutations. Show less

Osteoarthritis (OA) of the knee is a multifactorial degenerative disease typically defined as the 'wear and tear' of articular joint cartilage. However, recent studies suggest that OA is a disease arising from chronic low-grade inflammation. We conducted a study to investigate the relationship between chronic inflammatory mediators present in both the systemic peripheral blood system and localised inflammation in synovial fluid (SF) of OA and non-OA knees; and subsequently made direct comparative analyses to understand the mechanisms that may underpin the processes involved in OA. 20-Plex proteins were quantified using Human Magnetic Luminex® assay (R&D Systems, USA) from plasma and SF of OA (n = 14) and non-OA (n = 14) patients. Ingenuity Pathway Analysis (IPA) software was used to predict the relationship and possible interaction of molecules pertaining to OA. There were significant differences in plasma level for matrix metalloproteinase (MMP)-3, interleukin (IL)-27, IL-8, IL-4, tumour necrosis factor-alpha, MMP-1, IL-15, IL-21, IL-10, and IL-1 beta between the groups, as well as significant differences in SF level for IL-15, IL-8, vascular endothelial growth factor (VEGF), MMP-1, and IL-18. Our predictive OA model demonstrated that toll-like receptor (TLR) 2, macrophage migration inhibitory factor (MIF), TLR4 and IL-1 were the main regulators of IL-1B, IL-4, IL-8, IL-10, IL-15, IL-21, IL-27, MMP-1 and MMP-3 in the plasma system; whilst IL-1B, TLR4, IL-1, and basigin (BSG) were the regulators of IL-4, IL-8, IL-10, IL-15, IL-18, IL-21, IL-27, MMP-1, and MMP-3 in the SF system. The elevated plasma IL-8 and SF IL-18 may be associated with the pathogenesis of OA via the activation of MMP-3. Show less

A major goal of biomedicine is to understand the function of every gene in the human genome. Loss-of-function mutations can disrupt both copies of a given gene in humans and phenotypic analysis of such 'human knockouts' can provide insight into gene function. Consanguineous unions are more likely to result in offspring carrying homozygous loss-of-function mutations. In Pakistan, consanguinity rates are notably high. Here we sequence the protein-coding regions of 10,503 adult participants in the Pakistan Risk of Myocardial Infarction Study (PROMIS), designed to understand the determinants of cardiometabolic diseases in individuals from South Asia. We identified individuals carrying homozygous predicted loss-of-function (pLoF) mutations, and performed phenotypic analysis involving more than 200 biochemical and disease traits. We enumerated 49,138 rare (<1% minor allele frequency) pLoF mutations. These pLoF mutations are estimated to knock out 1,317 genes, each in at least one participant. Homozygosity for pLoF mutations at PLA2G7 was associated with absent enzymatic activity of soluble lipoprotein-associated phospholipase A2; at CYP2F1, with higher plasma interleukin-8 concentrations; at TREH, with lower concentrations of apoB-containing lipoprotein subfractions; at either A3GALT2 or NRG4, with markedly reduced plasma insulin C-peptide concentrations; and at SLC9A3R1, with mediators of calcium and phosphate signalling. Heterozygous deficiency of APOC3 has been shown to protect against coronary heart disease; we identified APOC3 homozygous pLoF carriers in our cohort. We recruited these human knockouts and challenged them with an oral fat load. Compared with family members lacking the mutation, individuals with APOC3 knocked out displayed marked blunting of the usual post-prandial rise in plasma triglycerides. Overall, these observations provide a roadmap for a 'human knockout project', a systematic effort to understand the phenotypic consequences of complete disruption of genes in humans. Show less

Dengue Viruses (DENVs) cause one of the most prevalent arthropod-borne viral diseases affecting millions of people worldwide. Identification of genes involved in DENV pathogenesis would help in deciphering molecular mechanisms responsible for the disease progression. Here, we carried out a meta-analysis of publicly available gene expression data of dengue patients and further validated the meta-profile using in-vitro infection in THP-1 cells. Our findings reveal that DENV infection modulates expression of several genes and signalling pathways including interferons, detoxification of ROS and viral assembly. Interestingly, we have identified novel gene signatures comprising of INADL/PATJ and CRTAP (Cartilage Associated Protein), which were significantly down-regulated across all patient data sets as well as in DENV infected THP-1 cells. PATJ and CRTAP genes are involved in maintaining cell junction integrity and collagen assembly (extracellular matrix component) respectively, which together play a crucial role in cell-cell adhesion. Our results categorically reveal that overexpression of CRTAP and PATJ genes restrict DENV infection, thereby suggesting a critical role of these genes in DENV pathogenesis. Conclusively, these findings emphasize the utility of meta-analysis approach in identifying novel gene signatures that might provide mechanistic insights into disease pathogenesis and possibly lead towards the development of better therapeutic interventions. 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

Heterochromatin is important for gene regulation and chromosome structure, but the genes that are occupied by heterochromatin proteins in the mammalian genome are largely unknown. We have adapted the DamID method to systematically identify target genes of the heterochromatin proteins HP1 and SUV39H1 in human and mouse cells. Unexpectedly, we found that CBX1 (formerly HP1beta) and SUV39H1 bind to genes encoding KRAB domain containing zinc finger (KRAB-ZNF) transcriptional repressors. These genes constitute one of the largest gene families and are organized in clusters in the human genome. Preference of CBX1 for this gene family was observed in both human and mouse cells. High-resolution mapping on human chromosome 19 revealed that CBX1 coats large domains 0.1-4 Mb in size, which coincide with the position of KRAB-ZNF gene clusters. These domains show an intricate CBX1 binding pattern: While CBX1 is globally elevated throughout the domains, it is absent from the promoters and binds more strongly to the 3' ends of KRAB-ZNF genes. KRAB-ZNF domains contain large numbers of LINE elements, which may contribute to CBX1 recruitment. These results uncover a surprising link between heterochromatin and a large family of regulatory genes in mammals. We suggest a role for heterochromatin in the evolution of the KRAB-ZNF gene family. Show less