Biology subjects

Amer, M.

Publications and source records attributed to Amer, M..

9 recordsLinked to original sources

bioRxiv2026

EGP1K: Whole-Genome Sequencing of 1,024 Egyptians Characterizes Population Structure and Genetic Diversity

Middle Eastern and North African populations remain underrepresented in genomic databases, comprising less than 1% of genome-wide association study participants despite representing approximately 6% of the global population. Here we present the Egypt Genome Project (EGP1K), in which we performed whole-genome sequencing on 1,024 unrelated Egyptian individuals originating from 21 of Egypts 27 governorates, recruited through eight clinical and research centers across Upper and Lower Egypt. We identified over 51.3 million variants, of which 17.1 million (33.4%) were absent from dbSNP. Allele frequency comparisons across 6.5 million shared variants showed the strongest concordance with Middle Eastern populations ({tau} = 0.977). Principal component analysis and ADMIXTURE modeling at K = 7 revealed that Egyptians share a dominant ancestry component (71.8%) with Middle Eastern populations and carry a smaller Egyptian-enriched component (18.5%) that distinguishes them from neighboring groups. Runs of homozygosity varied substantially across subregions, with Upper Egypt showing the highest burden, paralleling elevated consanguinity rates. Carrier frequency analysis identified MEFV (Familial Mediterranean Fever) at 9.1% as the most prevalent pathogenic carrier state; when adjusted for the national consanguinity rate, MEFV carrier status alone projects approximately 6,600 affected births per year. HLA class I typing identified allele frequencies placing Egyptians within the Levantine-Eastern Mediterranean cluster, providing baseline immunogenetic data currently absent from international databases. Analysis of polygenic risk score distributions revealed substantial differences in threshold-based risk stratification between Egyptians and European reference populations. When the Europeanderived 90th percentile threshold was applied, 83.3% of Egyptians were assigned to high-risk strata for stroke, 76.4% for chronic kidney disease, and 72.8% for gout, compared to the intended 10% high-risk proportion. These distributional shifts were observed across several cardiometabolic traits (Cohens d = 1.55-1.61), while other traits showed closer cross-population concordance, indicating that the degree of threshold miscalibration varies by trait. Together, these findings establish EGP1K as a genomic reference for Egypt and indicate that European-derived risk stratification thresholds may not be directly transferable to the Egyptian population, supporting the need for population-specific calibration of polygenic risk scores.

genomics↗

bioRxiv2025

Synthetic Mimetics of Exosomal Lipid Profile Enhance Gemcitabine Delivery in Pancreatic Cancer

Pancreatic cancer ranks fourth among cancer-related deaths. Despite decades of research, the cure rate of disease remains disappointingly low. This dismal prognosis is due to late detection and to resistance of tumors to all known systemic therapies. Here, we build upon our previous findings that highlighted the selective uptake of tumor-associated macrophage-derived exosomes by cancer cells. We hypothesize that the prominent lipid contents on the exosome surface play a crucial role in facilitating selective cellular interactions, offering a novel avenue for developing efficient drug delivery platforms for pancreatic cancer. Lipids affinity toward cancer cells was measured, following mass spectral lipidomic analysis for screening the lipidic composition of macrophages and their derived exosomes. Subsequently, optimized and characterized synthetic exosomes underwent detailed intracellular trafficking studies in human pancreatic cancer cells, demonstrating enhanced cellular uptake kinetics. Notably, gemcitabine-loaded synthetic exosomes exhibited superior efficacy in inducing programmed cell death compared to both the free drug and conventional liposome formulations. The biodistribution examination of these synthetic exosomes underscored their potential for tumor specificity. In vivo experiments further demonstrated that the treatment with gemcitabine-incorporated synthetic exosomes inhibited tumor growth by nearly 50% compared to the administration of the free drug, indicating a significantly enhanced treatment efficacy. Our findings indicate that leveraging the lipid membrane composition of exosomes could lead to breakthroughs in drug delivery efficiency. This innovative strategy offers a promising direction in the ongoing battle against pancreatic cancer, highlighting the potential of exosomal lipid profiles for cancer therapy.

cell biology↗

bioRxiv2025

AI-based decoding of long covid cognitive impairments in mice using automated behavioral system and comparative transcriptomic analysis

Long COVID (LC) following SARS-CoV-2 infection affects millions of individuals world-wide and manifests with a variety of symptoms including cognitive dysfunction also known as "brain fog". This is characterized by difficulties in executive functions, planning, decision-making, working memory, impairments in complex attention, loss of ability to learn new skills and perform sophisticated brain tasks. No effective treatment options currently exist for LC-related cognitive dysfunction. Here, we use the IntelliCage, which is an automated tracking system of cognitive functions, following SARS-CoV-2 infection in mice, measuring the ability of each mouse within a group to perform tasks that mimic complex human behaviors, such as planning, decision-making, cognitive flexibility, and working memory. Artificial intelligence and machine learning analyses of the tracking data classified LC mice into distinct behavioral categories from non-infected control mice, permitting precise identification and quantification of complex cognitive dysfunction in a controlled, replicable manner. Importantly, we find that brains from LC mice with cognitive dysfunction exhibit transcriptomic alterations similar to those observed in humans suffering from LC-related cognitive impairments, including altered expression of genes involved in learning, executive functions, synaptic functions, neurotransmitters and memory. Together, our findings establish a validated murine model and an automated unbiased approach to study LC-related cognitive dysfunction for the first time, and providing a valuable tool for screening potential treatments and therapeutic interventions.

neuroscience↗

bioRxiv2025

Translating brain anatomy and neurodegenerative disease from mouse to human through latent gene expression space

BackgroundThe mouse model is the most widely used animal model in neuroscience, yet translating findings to humans suffers from the lack of formal models comparing the mouse and the human brain. Here, we devised a novel framework using mouse and human gene expression to build a quantitative common space and apply it to models of neurodegenerative disease. MethodsWe trained a variational autoencoder on mouse spatial transcriptomics, and embedded mouse and human gene orthologs in the models latent space. We computed a latent cross-species similarity matrix for translation and compared translated maps to human ground truth evidence. FindingsWe established the validity of our model based on anatomical homology. Independent of species, brain areas with similar latent patterns clustered together, improving the homology of known anatomical pairs, and preserving principles of brain organisation. Importantly, brain alterations in mouse disease models predicted human patterns of brain changes in Alzheimers and Parkinsons diseases. We further determined the best mouse model for the AD patients, based on how well the translations matched the patient data, across multiple models and timepoints. InterpretationOur work provides i) a quantitative bridge across evolutionary divergence between the human and the predominant preclinical species, ii) a predictive framework to help design and evaluate disease models. By highlighting which models are best suited across stages of disease, we effectively support the understanding of disease mechanisms, assist in the workflow of clinical trials, and ultimately accelerate the transformation of findings into improved human outcomes. FundingSupported by the Biotechnology and Biological Sciences Research Coundil (BBSRC) UK, the Medical Research Council (MRC) UK, the European Research Council, and the NIHR Oxford Health Biomedical Research Centre. Research in ContextO_ST_ABSEvidence before this studyC_ST_ABSInferences on the human brain based on findings in the mouse are backed by broad neuroanatomical similarities between the two species. However, interventions that were successful in rodents rarely translate into successful outcomes to treat human diseases. One way to address this challenge is to quantify the boundaries of translational possibilities using cross-species common space approaches. Low-level embedding spaces have been used to quantitatively compare across species, but there is currently no framework for effective translation of disease maps between species, and no tool to establish the best animal model for a given patient population. Added value of this studyThis study is the first to quantitatively link mouse models of neurodegenerative disease with human patient data. After validating our novel VAE-based comparative framework on anatomical homology compared to existing methods, we determine which of three Alzheimers Disease (AD) mouse models, and at which timepoint, best models a human patient population with mild AD. In addition, we predicted human brain changes in human Parkinsons Disease, based on maps from mouse models of this disease. Implications of all the available evidenceThis approach allows one to directly evaluate mouse models based on the quality of their translation to the human. At the level of preclinical model design, the translation from human to mouse of diverse disease phenotypes will highlight the relevant targets for intervention in the mouse. This will justify the relevance of specific animal models and time courses, and therefore streamline clinical trials. By additionally translating the effect of treatment or intervention longitudinally, we can optimize human treatment plans and life-long disease management. Combined with patient population stratification, this takes an important step towards personalised translational medicine.

neuroscience↗

bioRxiv2022

A Coiled-Coil-Based Design Strategy for the Thermostabilization of G-Protein-Coupled Receptors

The most common methods for generating crystallizable GPCRs are scanning alanine mutagenesis and fusion to crystallization-facilitating partner proteins. The major goal of our work was to create a new GPCR tool that would provide receptor stability and additional soluble surface for crystallization. Towards this aim, we selected the two-stranded antiparallel coiled coil as a domain fold that satisfies both criteria. A selection of antiparallel coiled coils was used for structure-guided substitution of intracellular loop of the {beta}3 adrenergic receptor. Unexpectedly, only the two GPCR variants containing thermostable coiled coils were expressed. We showed that one GPCR chimera is stable upon purification in detergent, retains ligand-binding properties, and can be crystallized. However, the quality of the crystals was not suitable for structure determination. To supply additional surface for promoting crystal contacts, we replaced in a structure-based approach the loop of the antiparallel coiled coil by T4L. Although expression is currently not suitable for structural work, we found that the engineered GPCR is even more stable than the coiled-coil variant. Our approach should be of interest for applications that benefit from stable GPCRs.

biophysics↗

bioRxiv2020

Remembering immunity: Neuronal ensembles in the insular cortex encode and retrieve specific immune responses

Increasing evidence indicates that the brain regulates peripheral immunity. Yet, it remains unclear whether and how the brain represents the state of the immune system. Here, we show that immune-related information is stored in the brains insular cortex (InsCtx). Using activity-dependent cell labeling in mice (FosTRAP), we captured neuronal ensembles in the InsCtx that were active under two different inflammatory conditions (DSS-induced colitis and Zymosan-induced peritonitis). Chemogenetic reactivation of these neuronal ensembles was sufficient to broadly retrieve the inflammatory state under which these neurons were captured. Thus, we show that the brain can encode and initiate specific immune responses, extending the classical concept of immunological memory to neuronal representations of immunity.

neuroscience↗

bioRxiv2020

Synergistic Material-Topography Combinations to Achieve Immunomodulatory Osteogenic Biomaterials

Human mesenchymal stem cells (hMSCs) are widely represented in ongoing regenerative medicine clinical trials due to their ease of autologous implantation. In bone regeneration, crosstalk between macrophages and hMSCs is critical with macrophages playing a key role in the recruitment and differentiation of hMSCs. However, engineered biomaterials able to both direct hMSC fate and modulate macrophage phenotype have not yet been identified. A novel combinatorial chemistry-microtopography screening platform, the ChemoTopoChip, is used to identify materials suitable for bone regeneration by screening with human immortalized mesenchymal stem cells (hiMSCs) and human macrophages. The osteoinduction achieved in hiMSCs cultured on the "hit" materials in basal media is comparable to that seen when cells are cultured in osteogenic media, illustrating that these materials offer a materials-induced alternative in bone-regenerative applications. These also exhibit immunomodulatory effects, concurrently polarizing macrophages towards a pro-healing phenotype. Control of cell response is achieved when both chemistry and topography are recruited to instruct the required cell phenotype, combining synergistically. The large library of materials reveals that the relative roles of microtopography and material chemistry are similar, and machine learning identifies key material and topographical features for cell-instruction.

bioengineering↗

bioRxiv2019

Distributed Biomanufacturing of Liquefied Petroleum Gas

Liquefied Petroleum Gas (LPG) is a major domestic and transport fuel. Its combustion lessens NOx, greenhouse gas and particulates emissions compared to other fuels. Propane - the major constituent of LPG - is a clean, high value drop-in fuel that can help governments develop integrated fuels and energy policies with low carbon burden, providing solutions to the multi-faceted challenges of future energy supply. We show that bio-LPG (bio-propane and bio-butane) can be produced by microbial conversion of waste volatile fatty acids that can be derived from anaerobic digestion, industrial waste, or CO2 via photosynthesis. Bio-LPG production was achieved photo-catalytically, using biomass propagated from bioengineered bacteria including E. coli, Halomonas (in non-sterile seawater), and Synechocystis (photosynthetic). These fuel generation routes could be implemented rapidly in advanced and developing nations of the world to meet energy needs, global carbon reduction targets and clean air directives.

bioengineering↗

bioRxiv2019

Prophylactic TLR9 stimulation reduces brain metastasis through microglia activation

Brain metastases are prevalent in various types of cancer, and are often terminal given low efficacy of available therapies. Therefore, preventing them is of outmost clinical relevance and prophylactic treatments are perhaps the most efficient strategy. Here, we show that systemic prophylactic administration of a TLR9 agonist, CpG-C, is effective against brain metastases. Acute and chronic systemic administration of CpG-C reduced tumor cell seeding and growth in the brain in three tumor models in mice, including metastasis of human and mouse lung cancer, and spontaneous melanoma-derived brain metastasis. Studying mechanisms underlying the therapeutic effects of CpG-C, we found that in the brain, unlike in the periphery, NK cells and monocytes are not involved in controlling metastasis. Next, we demonstrated that the systemically administered CpG-C is taken up by endothelial cells, astrocytes, and microglia, without affecting blood-brain barrier integrity and tumor brain extravasation. In vitro assays pointed to microglia, but not astrocytes, as mediators of CpG-C effects through increased tumor killing and phagocytosis, mediated by direct microglia-tumor contact. In vivo, CpG-C-activated microglia displayed elevated mRNA expression levels of apoptosis-inducing and phagocytosis-related genes. Intravital imaging showed that CpG-C-activated microglia cells contact, kill, and phagocytize tumor cells in the early stages of tumor brain invasion more than non-activated microglia. Blocking in vivo activation of microglia with minocycline, and depletion of microglia with a colony-stimulating factor 1 inhibitor, indicated that microglia mediate the anti-tumor effects of CpG-C. Overall, the results suggest prophylactic CpG-C treatment as a new intervention against brain metastasis, through an essential activation of microglia. SummaryBrain metastases are prevalent and often terminal. Thus, reducing their occurrence could markedly improve cancer outcome. We show that systemic prophylactic and perioperative administration of a TLR9 agonist, CpG-C, reduced metastatic growth in experimental and spontaneous brain metastasis models, employing mouse and human tumors. CpG-C was taken up in the brain, without affecting blood-brain barrier integrity and tumor extravasation. In vitro assays, imaging flow cytometry, and intravital imaging pointed to microglia as mediators of CpG-C effects through contact-dependent tumor killing and phagocytosis; corresponding with in vivo mRNA profile. In vivo depletion studies proved that microglia, but not NK cells or monocytes, mediated the beneficial effects of CpG-C; Also hindered by blocking microglial activation. In-toto, perioperative treatment with CpG-C should be considered clinically relevant. SignificancePreventing brain metastases is paramount, as they are considered incurable and their incidence is on the rise due to prolonged survival of cancer patients. Here, we demonstrate that systemic prophylactic treatment with CpG-C reduces peripheral and brain metastasis of mouse and human lung cancers. While traditional therapies are halted during the perioperative period, we found systemic CpG-C treatment during this time frame beneficial in a model of spontaneous brain metastases following excision of a primary melanoma tumor, comprehensively mimicking the clinical setting. Mechanistically, we show microglia activation with CpG-C results in tumor cell eradication, pointing to microglia as potential therapeutic targets. Importantly, CpG-ODNs have negligible toxicity in humans. Therefore, CpG-C may be used prophylactically and during the perioperative period in high-risk cancers.

neuroscience↗