Biology subjects

Abbas, M.

Publications and source records attributed to Abbas, M..

At least 19 recordsLinked to original sources

bioRxiv2026

Evolutionary diversification of lipid logistics shapes synaptic maturation in primates

The prolonged developmental trajectory of the human brain (neoteny) is a defining feature of human evolution. Yet, the cellular mechanisms underlying this delay remain poorly understood. Here, comparing human and chimpanzee induced neurons and cerebral organoids, we we show that human neurons form fewer excitatory synapses and synchronize network activity later. Electron microscopy further revealed reduced synaptic vesicle docking and clustering near release sites, identifying altered presynaptic assembly as a prominent feature of human neuronal development. Unexpectedly, human neurons accumulate more, not less, membrane lipids, revealing a dissociation between lipid abundance and synaptic maturation. Transcriptomics and synaptosome proteomics resolve this paradox: chimpanzee neurons preferentially engage lipid metabolism and synaptic-maturation programs, whereas human neurons upregulate intracellular lipid transport and trafficking pathways. Together, our findings identify membrane organization as a previously unrecognized regulatory layer that controls neuronal neoteny. These results also suggest that evolutionary divergence can arise through changes in the spatial deployment of membrane lipids rather than their abundance, providing a molecular framework for understanding the evolution of human brain neoteny.

evolutionary biology↗

bioRxiv2026

Primate Astrocyte Evolution Controls the Tempo of Neuronal Development

Prolonged neuronal maturation, also referred to as neoteny, constitutes a hallmark of human brain evolution. Yet, the mechanisms controlling neotenic brain development remain poorly understood, and have been defined as neuron-intrinsic. Astrocytes shape synapse formation, activity, and elimination, and have changed substantially between humans and other species. Yet, whether the evolutionary divergence in astrocytes shapes the timing of neuronal maturation is unknown. Here, we show that astrocytes from humans and their closest living relatives, chimpanzees, exert contrasting effects on neuronal maturation: chimpanzee astrocytes accelerate it, whereas human astrocytes delay it, without affecting neuronal survival. Through comparative transcriptomics and epigenomics, we find that evolutionarily reduced APOE expression in human astrocytes underlies the observed delay in neuronal maturation: restoring APOE levels in human astrocytes accelerates neuronal development. We further establish that the Hippo-TEAD signaling represses APOE expression in human astrocytes, revealing a link between the enhanced morphological complexity of human astrocytes and the observed reduced tempo of neuronal development in their presence. Strikingly, neuronal genes differentially impacted by human and chimpanzee astrocytes are associated with schizophrenia, Alzheimers disease, and epilepsy, linking astrocyte evolution to disease vulnerability. Altogether, these findings establish that brain neoteny is partly a glial phenomenon, revealing that understanding the pace of human brain development requires understanding how astrocytes, not only neurons, have evolved.

neuroscience↗

bioRxiv2026

Regulatory Genomics of Preeclampsia-Specific Risk Variants Highlights Immune and Endothelial Mechanisms

BackgroundPreeclampsia (PE) is a complex hypertensive disorder of pregnancy characterized by endothelial dysfunction, immune dysregulation, and systemic vascular injury. Multiple genome-wide association studies (GWAS) have revealed genetic signals shared with hypertension and blood pressure traits, potentially obscuring biological mechanisms that are more specific to PE pathogenesis. Furthermore, the functional consequences of most PE-associated variants remain poorly understood. In addition, GWAS relies on short-read sequencing and array-based analyses, limiting the ability to identify insertions, deletions, and other structural variants that may contribute to disease-associated regulatory mechanisms. In this study, we investigated the regulatory architecture of PE-specific genetic variants and evaluated their potential linkage disequilibrium (LD) with structural variants. MethodsWe integrated GWAS, transcriptomic, and long-read sequencing data to investigate the regulatory architecture of PE-specific genetic variants. Summary statistics for PE, hypertension, systolic and diastolic blood pressure were obtained from the GWAS Catalog, and variants uniquely associated with PE (P [≤] 1x10-4) were prioritized. Cis-expression quantitative trait locus (cis-eQTL) analyses were performed in whole-blood RNA-sequencing data from 180 African American women. Significant associations were replicated in biologically relevant tissues from the GTEx Project, including vascular, renal, and immune-related tissues. Long-read sequencing-derived structural variants (SVs) were subsequently evaluated for LD with replicated eQTL loci. ResultsA total of 10,843 PE-specific variants, present in whole-genome sequencing data of the 180 women, were evaluated. Cis-eQTL analyses identified 480 significant eQTL-gene associations involving 277 unique variants and 192 genes (FDR [≤] 0.05). Replication analyses supported 69 eQTL-gene associations across five GTEx tissues, involving 35 variants and 14 genes. Replicated signals were enriched in vascular tissues, particularly artery tibial and artery aorta. Several prioritized genes converged on immune and vascular pathways, including MICA, HLA-DPB1, SEMA4D, JUP, ZFP57, and TMEM204. Integration of GWAS and eQTL effects demonstrated consistent regulatory shifts associated with PE-risk alleles, including downregulation of immune-related loci and upregulation of select vascular-associated genes. Long-read sequencing analyses identified 66 high-LD (r2 [≥] 0.80) SNP-SV-gene associations, including 12 replicated eQTL variants, 8 candidate SVs, and 3 replicated genes, suggesting that structurally complex genomic regions may contribute to the observed regulatory signals. ConclusionsThe tissues enriched in the regulatory signal highlight the importance of systemic endothelial biology in PE susceptibility. The findings of this study support a model in which PE-specific genetic susceptibility converges predominantly on interconnected immune and vascular regulatory mechanisms. The integration of eQTL analyses with long-read structural variant discovery provides additional insight into the complex genomic architecture underlying PE and highlights candidate regulatory loci that may not be adequately captured through conventional GWAS approaches alone. The study also emphasizes the importance of conducting functional genomic analyses in diverse populations to improve understanding of disease biology and advance precision medicine efforts. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=105 SRC="FIGDIR/small/728031v1_ufig1.gif" ALT="Figure 1"> View larger version (40K): org.highwire.dtl.DTLVardef@1caf4a5org.highwire.dtl.DTLVardef@1839b4eorg.highwire.dtl.DTLVardef@14922c3org.highwire.dtl.DTLVardef@894040_HPS_FORMAT_FIGEXP M_FIG C_FIG Regulatory Genomics of Preeclampsia-Specific Risk Variants Highlights Immune and Endothelial Mechanisms. GWAS summary statistics for preeclampsia, hypertension, SBP, and DBP were integrated to identify 10,843 preeclampsia-specific variants that were subsequently evaluated in cis-eQTL analyses using whole-blood RNA-sequencing data from 180 African American women (left). Cis-eQTL analyses identified 480 significant associations involving 277 variants and 192 genes (FDR [≤] 0.05), of which 69 eQTL-gene associations involving 35 variants and 14 genes replicated across five GTEx tissues, with strongest enrichment observed in vascular tissues, particularly artery tibial and artery aorta (center). Prioritized genes, including MICA, HLA-DPB1, SEMA4D, JUP, ZFP57, and TMEM204, converged on interconnected immune and endothelial pathways associated with systemic vascular dysfunction, impaired placentation, and inflammatory dysregulation in preeclampsia. Integration of long-read sequencing data further identified 66 high-LD SNP-SV-gene associations involving 12 replicated eQTL variants, 8 candidate structural variants, and 3 replicated genes, suggesting that structurally complex genomic regions may contribute to regulatory mechanisms not fully captured through conventional GWAS approaches alone. eQTL indicates expression quantitative trait locus; FDR, false discovery rate; GTEx, Genotype-Tissue Expression project; SBP, systolic blood pressure; DBP, diastolic blood pressure; LD, linkage disequilibrium; SV, structural variant.

genomics↗

bioRxiv2026

Development and validation of a multilocus sequence typing scheme for Fasciola hepatica using next-generation deep amplicon sequencing

Fasciolosis caused by Fasciola hepatica is an economically important disease in sheep and cattle. Knowledge of the population genetic structure of F. hepatica is important for understanding gene flow and informing disease control. In the present study, we designed, developed, and validated a multilocus sequence typing (MLST) scheme based on six markers. These markers were selected by aligning newly sequenced whole-genome sequence (WGS) data with available reference genomes and selecting variable regions with five or more single-nucleotide polymorphisms SNPs from different scaffolds of the F. hepatica reference genome Fasciola 10x pilon (GCA_900302435.1). Twenty markers were initially identified, of which 12 were multiplexed for deep amplicon sequencing after validation on worm and faecal eggs DNA; six markers were ultimately retained for downstream population genetics analysis. These markers were used to investigate population genetic structure in 15 cattle- and 27 sheep-derived F. hepatica populations in UK. A total of 53 unique alleles from six MLST markers were identified from 30 faecal (cattle = 13, sheep = 17) and 12 adult worm (cattle = 2, sheep = 10) populations. Shared alleles were observed in sheep- and cattle-derived populations. The highest allelic variation was observed in the Scottish Borders, Southern Scotland, and South-West England, and the lowest in North-West England. Minimal genetic differentiation was observed between cattle- and sheep-derived populations, with most genetic structuring within rather than between populations. Five markers showed high allelic polymorphism, whereas one marker showed low levels of allelic polymorphism, highlighting the importance of multilocus approaches. Overall, this six MLST-marker panel provides a tool for population genetic studies, revealing high gene flow and clonal expansion of F. hepatica across hosts and regions in the UK.

genetics↗

bioRxiv2026

Extracellular Vesicles From Metabolically Healthy Obesity Convey Distinct Molecular Signals That Initiate Endothelial Dysfunction: A Multi-Omics Study in Adults of African Ancestry

BackgroundMetabolically healthy obesity (MHO) is unstable, with up to 80% of individuals progressing to metabolically abnormal obesity (MAO), yet mechanisms underlying this transition remain unclear. African Americans bear a disproportionate burden of obesity-related cardiovascular disease. Circulating extracellular vesicles (EVs) mediate inter-organ communication and may drive MAO-related vascular dysfunction. MethodsAdults of African ancestry were classified as metabolically healthy lean (MHL, n=14), MHO (n=9), or MAO (n=16). Plasma-derived EVs were characterized and their microRNA cargo profiled. Human coronary artery endothelial cells were treated with EVs from each group to assess nitric oxide signaling, oxidative stress, inflammatory activation, and mitochondrial dynamics. ResultsMHO participants exhibited preserved insulin sensitivity and lower inflammation compared with MAO despite comparable adiposity. EVs from MHO carried a distinct microRNA signature enriched in miR-148a-5p, miR-181c-5p, and miR-1255a, linked to antioxidant and matrix regulatory pathways. MAO EVs were enriched in miR-3613-3p, miR-6842-3p, and miR-326, targeting inflammation and insulin resistance pathways. Compared with both MHL and MHO EVs, MAO EVs suppressed endothelial nitric oxide synthase phosphorylation and reduced nitric oxide bioavailability, with increased reactive oxygen species and ICAM-1 expression. MHO EVs induced an intermediate phenotype with disrupted mitochondrial morphology, supporting a graded continuum of endothelial stress. ConclusionsMHO represents a biologically active intermediate state. Circulating EVs from MHO individuals convey molecular signals that impair endothelial and mitochondrial function, predisposing to vascular injury and progression toward MAO. EV-associated microRNAs are mechanistic mediators and candidate biomarkers of metabolic and vascular deterioration in obesity. CLINICAL PERSPECTIVEO_ST_ABSWhat Is New?C_ST_ABSO_LIThis study systematically investigated extracellular vesicles derived from metabolically healthy obese individuals to define direct vesicle effects on endothelial function using integrated omics coupled to functional outputs. C_LIO_LIExtracellular vesicles from metabolically healthy obesity convey a distinct molecular and biological signature that distinguishes lean and metabolically abnormal obesity. C_LIO_LIMetabolic health status, rather than obesity alone, drives extracellular vesicle-mediated endothelial nitric oxide signaling, oxidative stress, inflammation, and mitochondrial dynamics. C_LI What Are the Clinical Implications?O_LIThese findings explain why some individuals with obesity exhibit preserved vascular function while others develop early endothelial dysfunction. C_LIO_LIStratifying obesity by metabolic health status improves cardiovascular risk assessment beyond body mass index alone. C_LIO_LITargeting extracellular vesicle signaling pathways represents a novel strategy to prevent metabolically healthy individuals from progressing to metabolically abnormal obesity. C_LI

molecular biology↗

bioRxiv2026

Limited genetic structure and high gene flow in Fasciola hepatica populations infecting ruminants in different geographic areas in the UK

The liver fluke, Fasciola hepatica, is a major parasitic threat to ruminant health and productivity worldwide, with important implications for food security, animal welfare, and zoonotic risk. This study developed and validated a multiplex deep amplicon sequencing assay targeting the mitochondrial NADH dehydrogenase 1 (mt-ND1) and cytochrome c oxidase subunit 1 (mt-COX1) loci for high-throughput genotyping of F. hepatica. DNA was extracted from eggs sedimented from sheep and cattle faeces (n = 78) received from farms and from adult worm pools (n = 12) isolated at abattoirs from diverse regions across the UK. Following high-throughput sequencing, bioinformatics analysis was performed to demultiplex Illumina sequence reads and extract amplicon sequence variants (ASVs). A total of 11 ASVs were identified at each locus (mt-ND1: 264-279 bp; mt-COX1: 312-319 bp), with two or three predominant ASVs per locus, along with rare variants. Network and PCA analyses revealed two distinct clusters at the mt-ND1 locus: one primarily associated with sheep and another shared between sheep and cattle. In contrast, mt-COX1 sequence reads formed a single dominant cluster. Population analyses revealed extensive ASV sharing across regions, indicating high gene flow, likely facilitated by livestock movement and parasite adaptation.

evolutionary biology↗

bioRxiv2025

Plasmodium falciparum aquaglyceroporin (PfAQP) orchestrates glycerol-dependent lipid metabolism, membrane biogenesis, metabolomic flux, parasite growth and stress adaptation

Aquaglyceroporins (AQPs) are integral membrane channel proteins that facilitate transport of water and other solutes such as glycerol, thereby playing vital roles in cellular homeostasis. Here, we functionally characterized Plasmodium falciparum aquaglyceroporin (PfAQP) through localization, inducible knockdown, and comprehensive metabolomic analyses revealing its key role in lipid homeostasis and metabolomic flux. PfAQP localizes to the parasite plasma membrane and food vacuole membrane, at critical interfaces for nutrient and metabolite exchange. A glmS-ribozyme mediated inducible knock-down of PfAQP severely impairs parasite development from trophozoite to schizont, leading to marked suppression in parasite growth. Ultra-Expansion Microscopy (UExM) analyses show profound defects in membrane biogenesis, along with disruption in cytokinesis under PfAQP knock-down conditions. Detailed lipidomic analyses suggests that PfAQP disruption cause altered lipid homeostasis, characterized by reduced membrane phospholipid biosynthesis, impaired lipid scavenging, and accumulation of storage lipids. Metabolomic analyses further indicate metabolic dysregulation characterized by reduction in amino acid levels and dysregulated mitochondrial metabolism, including impaired tricarboxylic acid (TCA) cycle. Strikingly, PfAQP expression gets transiently upregulated under nutrient starvation condition, and its ablation drastically compromise parasite recovery, highlighting its role in adaptive responses. Overall, these results establish PfAQP as a critical regulator of glycerol-dependent metabolic pathways, orchestrating membrane biogenesis, energy metabolism, and stress resilience--functions indispensable for parasite growth and survival.

microbiology↗

bioRxiv2025

Multi-omics Integration with GWAS Unveils Molecular Mechanistic Insights for Type 2 Diabetes

BackgroundType 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. MethodsGenetic 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. ResultsWe 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 ({beta}-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), {beta}-cell stress (TREH, NOTCH2), and chronic inflammation (OAS3). ConclusionsOur 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.

genomics↗

bioRxiv2025

LFA-1 Interaction with GBP-130 on Plasmodium falciparum-infected Red Blood Cells mediates NK Cell Activation and Parasite Control

Natural Killer (NK) cells contribute to early immunity against Plasmodium falciparum by recognizing and eliminating infected red blood cells (iRBCs), a process mediated in part by the integrin LFA-1. However, the cognate parasite ligand for LFA-1 has remained unknown. Here, we identify Glycophorin Binding Protein-130 (PfGBP-130) as a surface-expressed ligand on iRBCs that binds the I-domain of LFA-1 (LFA-1 I). Using an LFA-1 I-Fc fusion protein, we demonstrate stage-specific binding to iRBCs, and LC-MS/MS analysis of immunopreciptates of I-Fc bound to iRBC revealed PfGBP-130 as a high-confidence interactor. Recombinant PfGBP-130 binds NK and THP-1 cells in an LFA-1-dependent manner. Co-culture assays show that PfGBP-130 promotes NK cell activation, degranulation, and facilitates contact-dependent killing of iRBCs. Neutralizing antibodies against PfGBP-130 significantly impair these responses. Our findings establish PfGBP-130 as the LFA-1 ligand on iRBCs, providing new insight into NK cell-mediated immunity in malaria and identifying a potential target for host-directed interventions.

immunology↗

bioRxiv2025

Development of a qPCR assay and tremabiome deep amplicon sequencing method for differentiation of fluke species in livestock

BackgroundTrematode parasites, or flukes, are a significant economic threat to ruminant production worldwide. Traditional diagnostic methods rely on egg sedimentation from faeces, a time-consuming methodology lacking sensitivity and specificity. This study aimed to develop and validate two diagnostic methods: firstly, qPCR for accurate identification of Fasciola spp, and secondly, tremabiome, deep amplicon sequencing technique for identifying fluke species using faecal egg DNA. MethodologyTo detect fluke infection primers targeting mitochondrial DNA were repurposed to develop a SYBR Green qPCR diagnostic. For the identification of fluke species, a tremabiome approach was developed. A reference sequence library and taxonomy file were generated for 21 fluke species, enabling species sequence read separation and extracting amplicon sequence variants (ASVs). To validate the qPCR and tremabiome approach, 402 faecal samples were collected from cattle and sheep across the UK. Fluke eggs were isolated by sedimentation, detected by microscopy and qPCR, and tremabiome used to identify fluke eggs to species level. ResultsqPCR demonstrated high analytical sensitivity, detecting Fasciola hepatica DNA down to 19.2fg and F. gigantica down to 6.4fg, with no cross-amplification of other flukes. Tremabiome was able to detect as few as five F. hepatica and Calicophoron daubneyi eggs and identify mixed infections. High levels of co-infection (14.4%) of F. hepatica and C. daubneyi were observed in faecal samples, followed by single infections with C. daubneyi (12.6%) and F. hepatica (3.2%). Notably, tremabiome detected F. hepatica in 20 samples missed by qPCR. Data analysis identified 55 and 32 ASVs for F. hepatica and C. daubneyi, respectively, with phylogenetic clustering within their respective clades. ConclusionThis study developed qPCR assay for Fasciola detection and validated a tremabiome deep amplicon sequencing for fluke species differentiation. These approaches have improved capacity to identify fluke species compared to microscopy and are valuable tools for enhancing fasciolosis surveillance and control. Author SummaryFlukes are flatworm parasites that cause disease domestic and wild animals and humans. The main species infecting cattle and sheep globally are the liver flukes F. hepatica and F. gigantica, with other species including the rumen fluke Calicophoron daubneyi locally important or emerging. Infections result in serious economic losses. The traditional method of diagnosing fluke infection involves observation of eggs in faecal samples under the microscope, but this can be time-consuming and error prone, since the eggs of different species often look similar. In this study, we developed and validated two methods to improve detection: qPCR, a sensitive DNA-based test to identify Fasciola infections, and tremabiome, a DNA sequencing technique that can accurately differentiate between different fluke species. We tested these methods using faecal samples collected from cattle and sheep across the UK. The qPCR could detect small amounts of Fasciola DNA, while tremabiome was more sensitive, identifying different fluke species from as few as five eggs. Our study found that co-infections of F. hepatica and C. daubneyi are common in the UK. The approaches we have developed could be valuable tools for to improve fluke diagnosis and enable better control of this important parasitic disease.

molecular biology↗

bioRxiv2025

Effects of hCG or GnRH Treatment on Embryonic Mortality and Reproductive Performance in Buchi sheep of Cholistan Desert, Pakistan

The present study was conducted on Buchi sheep at Government livestock farm, Jugaitpeer, district Bahawalpur. The objectives of this study were to investigates the genetic potential, birth and adult body weights, growth and turnover rates, and seasonal reproductive performance, the effect of Dalmazin (PGF2) on synchronization, the effect of GnRH and hCG treatment given on the mating day on pregnancy rate, and embryonic mortality after plasma hormone concentrations and embryo development to improve litter size. Male lambs exhibited significantly higher (P<0.05) birth (3.40 {+/-} 0.16 kg) and adult weights (61.67 {+/-} 0.95 kg) compared to females (3.00 {+/-} 0.00 kg and 39.67 {+/-} 0.41 kg, respectively), along with faster growth and higher turnover rates. Seasonal variations showed superior pregnancy rates in spring (62.83%) but higher reproductive efficiency and lower mortality in autumn. In a second experiment, 30 ewes divided into hCG, GnRH, and control groups. hCG and GnRH groups were mated to ram at synchronized estrus by two injections of 2ml PGF2 analogue (Dalmazin) given at 11 days apart. The control group received only saline. The blood samples were collected from jugular venipuncture (3ml) with a disposable syringe from day 2 to 16 after treatment. Plasma progesterone concentrations detected by ELISA were higher (P<0.05) in sheep as compared with saline treated controls and improved reproductive outcomes. The hCG group showed the best performance with a litter size of 1.28%, no embryonic mortality, and increased twinning and fecundity rates. The GnRH group also demonstrated enhanced reproductive efficiency with a litter size of 1.25% and no embryonic loss. The control group had the lowest reproductive outcomes, including a higher embryonic mortality rate. Overall, hCG proved more effective than GnRH in enhancing progesterone levels, fecundity, and prolificacy in Buchi sheep.

zoology↗

bioRxiv2025

Lipopolysaccharides nanodiscs, a biomimetic platform to study bacterial surface.

Lipopolysaccharides (LPS) are essential components of the outer membranes of Gram-negative bacteria, playing a crucial role in antimicrobial resistance, virulence, and the hosts immune response. Self-assembled particles displaying LPS are essential for biophysical studies addressing the behavior of bacterial surfaces under specific biomimetic conditions. Styrene-maleic acid (SMA) copolymers were employed to form LPS nanodiscs, either from extracted LPS or directly from purified outer membranes. These nanodiscs, derived from pathogenic O157:H7 or laboratory E. coli strains, are well-defined in size and yield high-resolution nuclear magnetic resonance (NMR) spectra. They have been successfully used to investigate molecular recognition by a human C-type Lectin Receptor (CLR) of the immune system and interaction with polymyxin antibiotics using various biophysical methods. This study high-lights the significance of LPS nanodiscs as bacterial surface mimetics and opens promising avenues for further research into LPS structure and interactions. The ability to generate well-defined LPS nanodiscs offers a powerful tool for studying the molecular mechanisms underlying bacterial pathogenesis and immune response.

biophysics↗

bioRxiv2025

Intersecting Transcriptomic Landscapes of Hypertension and Kidney Function in African American Women

BackgroundHypertension is a major risk factor for chronic kidney disease (CKD) and disproportionately affects African American women, contributing to disparities in kidney health outcomes. The biological mechanisms connecting hypertension to reduced kidney function, particularly in understudied populations, remain poorly understood. This study leverages transcriptomic analyses to uncover shared molecular signatures associated with hypertension and kidney function, focusing on female-specific profiles. MethodsThe study analyzed whole-blood mRNA sequencing data from a cohort of 344 African American women, divided equally into discovery (n = 172) and validation (n = 172) datasets, along with 147 African American men. Differential expression (DE) analyses were performed to identify mRNAs associated with hypertension and kidney function (measured as eGFR). Female-specific findings were determined by comparing results between females and males. Pathway enrichment analyses were subsequently conducted to link the identified mRNAs to key biological mechanisms. ResultsComparative analyses revealed unique transcriptomic profiles in females, underscoring the role of sex-specific factors in disease progression. DE analyses identified 95 female-specific genes associated with both hypertension and eGFR. Subsequent pathway enrichment analysis with the 95 genes revealed key pathways related to fibrosis, inflammation, lipid metabolism, and endothelial dysfunction. The list of 95 includes TGF-{beta}1 and PNPLA2 implicated in fibrotic and metabolic dysregulation, and immune system players such as IL32 and TNFSF12 that amplify inflammation and kidney injury. ConclusionsThis study provides novel insights into the transcriptomic mechanisms underlying hypertension and kidney function in African American women. The findings emphasize the importance of addressing sex-specific and population-specific molecular mechanisms to inform precision medicine approaches and reduce health disparities hypertension-related impaired kidney function. Future research should prioritize experimental validation and longitudinal studies to further elucidate these pathways.

genomics↗

bioRxiv2024

Changes in Proteome Profiles Linked to Hormonal Contraceptive Use Among African American Women with untreated high blood pressure

BackgroundHypertension is a leading contributor to cardiovascular disease in reproductive-age women, with African American women experiencing disproportionate risk and severity. Oral contraceptive (OC) use has been implicated in elevating blood pressure, but the underlying molecular mechanisms remain unclear. Understanding the proteomic alterations associated with OC use may provide novel insights into the biological pathways contributing to OC-related hypertensive risk. ObjectiveTo identify proteomic signatures associated with oral contraceptive use among premenopausal African American women with stage 2 hypertension and elucidate pathways that may contribute to blood pressure regulation in this population. Study DesignWe evaluated 2,941 serum proteins measured on the Olink platform to assess associations with oral contraception use in 51 pre-menopausal women with untreated stage 2 hypertension (13 OC users and 38 non-users). A generalized linear model was fitted for each protein, adjusting for age, body mass index, alcohol consumption, level of education, and physical activity. Pathway enrichment analysis was carried out to identify common pathways among the proteins associated with oral contraceptive use. Gene Ontology enrichment analysis was conducted to gain insight into the functional characteristics of the proteins and the underlying biology. ResultsWe identified 44 proteins significantly associated with OC use (FDR [≤] 0.05), including known and novel candidates. Among these, 13 proteins were elevated in OC users, including SERPINA6, SERPINA7, and TNFSF13, markers implicated in hormone transport, RAAS activation, and chronic inflammation. Proteins such as PLAU and PLAUR were enriched in sympathetic nervous system signaling and coagulation pathways, while SCG3 suggested neuroendocrine involvement. Enrichment analysis revealed overrepresentation of pathways related to complement and coagulation cascades, cholesterol metabolism, and the renin-angiotensin-aldosterone system.. ConclusionsOC use among premenopausal African American women, with stage 2 untreated hypertension, is associated with alterations in circulating proteins involved in neurohormonal signaling, immune modulation, lipid regulation, and vascular remodeling. The findings provide novel insights into the proteomic landscape associated with oral contraceptive in these women.

genomics↗

bioRxiv2024

Regulatory Roles of Long Non-Coding RNAs in Arterial Stiffness and Hypertension: Insights from Two African American Studies

BackgroundArterial stiffness, commonly assessed via pulse wave velocity (PWV), is marked by reduced arterial elasticity and serves as a significant risk factor for cardiovascular disease and an early indicator of hypertension. This study investigated the regulatory roles of long non-coding RNAs (lncRNAs) in modulating mRNAs associated with arterial stiffness and hypertension, with a particular focus on African Americans, a population disproportionately impacted by hypertension. MethodsWe utilized whole-blood transcriptome sequencing data from two African American (AA) cohorts with high hypertension prevalence: the GENE-FORECAST study (436 subjects) and the MH-GRID study (179 subjects). Our objectives were to: (1) identify lncRNAs and mRNAs differentially expressed (DE) between the upper and lower tertiles of PWV, (2) determine DE lncRNAs associated with the expression levels of each DE mRNA, and (3) link the lncRNA-modulated mRNAs to hypertension across both datasets. ResultsDifferential expression analysis revealed 1,035 DE mRNAs and 31 DE lncRNAs between upper and lower PWV groups. Then lncRNA-mRNA pairs significantly associated were identified, involving 31 unique lncRNAs and 1,034 unique mRNAs. Finally, 22 of the lncRNA-modulated mRNAs initially linked to PWV were found associated with hypertension, in both datasets. Interestingly, 30 lncRNAs were linked to the expression of UCP2 (Uncoupling Protein 2), a gene implicated in oxidative stress and endothelial function. ConclusionsOur findings underscore the significant roles of lncRNAs in regulating gene expression associated with arterial stiffness and hypertension. The differential expression of UCP2 in relation to PWV and hypertension, along with its potential regulation by lncRNAs, offers valuable insights into the molecular mechanisms underlying arterial stiffness and its connection with hypertension.

genomics↗

bioRxiv2024

Co-localized SNPs Affecting the Expression of Taste Perception Genes are linked to Alzheimer's Disease

BackgroundWhile previous research has shown the potential links between taste perception pathways and brain-related conditions, the area involving Alzheimers disease remains incompletely understood. Taste perception involves neurotransmitter signaling, including serotonin, glutamate, and dopamine. Disruptions in these pathways are implicated in neurodegenerative diseases. The integration of olfactory and taste signals in flavor perception may impact brain health, evident in olfactory dysfunction as an early symptom in neurodegenerative conditions. Shared immune response and inflammatory pathways may contribute to the association between altered taste perception and conditions like neurodegeneration, present in Alzheimers disease. MethodsThis study consists of an exploration of expression-quantitative trait loci (eQTL), utilizing whole-blood transcriptome profiles, of 28 taste perception genes, from a combined cohort of 475 African American subjects. This comprehensive dataset was subsequently intersected with single-nucleotide polymorphisms (SNPs) identified in Genome-Wide Association Studies (GWAS) of Alzheimers Disease (AD). Finally, the investigation delved into assessing the association between eQTLs reported in GWAS of AD and the profiles of 741 proteins from the Olink Neurological Panel. ResultsThe eQTL analysis unveiled 3,547 statistically significant SNP-Gene associations, involving 412 distinct SNPs that spanned all 28 taste genes. In 17 GWAS studies encompassing various traits, a total of 14 SNPs associated with 12 genes were identified, with three SNPs consistently linked to Alzheimers disease across four GWAS studies. All three SNPs demonstrated significant associations with the down-regulation of TAS2R41, and two of them were additionally associated with the down-regulation of TAS2R60. In the subsequent pQTL analysis, two of the SNPs linked to TAS2R41 and TAS2R60 genes (rs117771145 and rs10228407) were correlated with the upregulation of two proteins, namely EPHB6 and ADGRB3. ConclusionsOur investigation introduces a new perspective to the understanding of Alzheimers disease, emphasizing the significance of bitter taste receptor genes in its pathogenesis. These discoveries set the stage for subsequent research to delve into these receptors as promising avenues for both intervention and diagnosis. Nevertheless, the translation of these genetic insights into clinical practice requires a more profound understanding of the implicated pathways and their pertinence to the diseases progression across diverse populations.

genomics↗

bioRxiv2023

Molecular signature of primate astrocytes reveals pathways and regulatory changes contributing to the human brain evolution

Astrocytes contribute to the development and regulation of the higher-level functions of the brain, the critical targets of evolution. However, the molecular signature of foetal astrocyte evolution in primates is unknown. Here, to address this question, we use human, chimpanzee, and macaque induced pluripotent stem cell-derived foetal astrocytes (iAstrocytes). Human iAstrocytes are bigger and more complex than the non-human primate iAstrocytes. We find loci related to the regulation of cell size with increased expression in the human lineage. Likewise, we uncover that genes and mechanisms implicated in long-range intercellular signalling are activated in the human iAstrocytes. Strikingly, loci downregulated in the human lineage frequently relate to intellectual disability raising new questions on the trade-offs associated with the evolution of the human mind. Using our system, through a multilevel regulome analysis and machine learning, we uncover that functional activation of enhancers coincides with a previously unappreciated, pervasive gain of binding sites of stripe transcription factors. In summary, we shed new light on a mechanism driving the acquisition of the regulatory potential of enhancers.

neuroscience↗

bioRxiv2023

The unique three-dimensional arrangement of Macrophage Galactose Lectin enables E. coli LipoPolySaccharides recognition through two distinct interfaces

LipoPolySaccharides are a hallmark of Gram-negative bacteria and their presence at the cell surface is key for bacterial integrity. As surface exposed components, they are recognized by immunity C-type lectin receptors present on Antigen Presenting Cells. Human Macrophage Galactose Lectin binds E. coli surface that presents a specific glycan motif. Nevertheless, this high affinity interaction occurs regardless of the integrity of its canonical calcium-dependent glycan binding site. Nuclear Magnetic Resonance of MGL carbohydrate recognition domain and complete extracellular domain revealed a new glycan binding site opposite to the canonical site. A model of trimeric Macrophage Galactose Lectin was determined based on a combination of Small Angle X-ray scattering and Alphafold. A disulphide bond positions the Carbohydrate Recognition Domain perpendicular to the coiled-coil domain. This unique configuration for a C-type lectin orients the six glycan sites of MGL in an ideal position to bind LipoPolySaccharides at the bacterial surface with high avidity.

biophysics↗