Biology subjects

Ibrahim, H.

Publications and source records attributed to Ibrahim, H..

15 recordsLinked to original sources

bioRxiv2026

Non-Invasive Embryo Quality Assessment via Matrix-Optimized Untargeted LC-MS Metabolomics of Spent Embryo Culture Media and Weighted Ensemble Machine Learning

BackgroundNon-invasive embryo quality assessment is a critical unmet need in assisted reproductive technology (ART). Preimplantation genetic testing for aneuploidy (PGT-A) is effective but requires invasive biopsy that may compromise embryo viability. Metabolomics of spent embryo culture media (SECM) offers a non-invasive alternative, yet analytical challenges--limited sample volume, high salt content, and abundant proteins--have hindered standardization and clinical translation. ResultsWe systematically optimized sample preparation for untargeted LC-MS metabolomics of SECM using human serum as a reference. Optimal conditions were highly matrix-dependent: SECM required 7x volume of 50% acetonitrile for extraction and 40% acetonitrile for reconstitution, whereas serum required 10x volume of 100% methanol and 100% water--reflecting that SECM contains more non-polar species than serum. Applying the optimized workflow to 120 clinical SECM samples (72 euploid, 48 aneuploid), we identified 102 differential metabolites between euploid and aneuploid embryos, with prominent enrichment of lipid pathways (fatty acid metabolism, {beta}-oxidation, sphingolipid metabolism) and involvement of amino acid (methionine, tryptophan) and TCA cycle metabolism. A weighted ensemble machine learning model discriminated aneuploid from euploid embryos with an AUC of 0.977, 100.0% specificity, and 89.6% sensitivity. Among 72 euploid embryos stratified by morphological grading (good, fair, poor), metabolic alterations progressed from mitochondrial energy deficiency (good vs. fair) to broader lipid dysregulation (fair vs. poor), with the ensemble model achieving AUCs of 0.944, 0.889, and 0.943, respectively. ConclusionsThis study establishes a rigorously optimized and validated SECM metabolomics workflow that overcomes key analytical barriers in this challenging matrix. Our findings demonstrate that metabolic signatures--particularly in lipid and energy metabolism--are strongly associated with both embryo ploidy and morphological quality, providing biological insights into the metabolic underpinnings of embryo developmental competence. The high predictive performance of the ensemble model supports the feasibility of non-invasive embryo assessment as a complementary tool to existing methods, with potential to reduce reliance on invasive biopsy in ART. External validation in prospective multi-center cohorts is warranted to further assess clinical utility and generalizability. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=122 SRC="FIGDIR/small/741666v1_ufig1.gif" ALT="Figure 1"> View larger version (59K): org.highwire.dtl.DTLVardef@10fbe40org.highwire.dtl.DTLVardef@936273org.highwire.dtl.DTLVardef@246e5dorg.highwire.dtl.DTLVardef@1c9d115_HPS_FORMAT_FIGEXP M_FIG C_FIG

genetics↗

bioRxiv2026

Toxic Effects of Solanum sisymbriifolium Extracts on Meloidogyne hapla and Meloidogyne chitwoodi

Plant-parasitic nematodes (PPNs) are among the most destructive agricultural pests worldwide, causing significant economic losses across diverse cropping systems. Soil fumigation, the most common management strategy, is costly, detrimental to soil health, and increasingly restricted due to environmental and regulatory concerns. As a result, there is a critical need for alternative, sustainable approaches for PPN control. Solanum sisymbriifolium is resistant to several Meloidogyne species and represents a promising source of natural nematicidal compounds. In this study, we evaluated the effects of S. sisymbriifolium extracts on Meloidogyne chitwoodi and M. hapla, two economically important nematodes. Compounds were extracted using solvents of increasing polarity and then reconstituted in water. The water-solubilized extracts were then used in bioassays to assess their effects on nematode egg hatching, egg viability, and second-stage juvenile (J2) survival. Egg hatching and J2 viability of both Meloidogyne species were consistently affected by compounds in the 1-butanol fraction. Further characterization of these compounds may enable the development of novel, environmentally sustainable alternatives to conventional nematode management strategies.

Plant Biology↗

bioRxiv2026

GAPVD1 regulates CSNK1D-dependent PER2 FASP phosphorylation

The mammalian circadian clock relies on precisely timed transcriptional and post-translational events to generate [~]24-hour rhythms. A key post-translational mechanism is phosphorylation of PER2 by CSNK1D, governed by a phosphoswitch that integrates stabilizing and destabilizing phosphorylation marks at the FASP and Degron sites to control PER2 stability and circadian period. Here, a novel role for the PER complex protein GAPVD1 in regulating CSNK1D-mediated FASP site phosphorylation is revealed. GAPVD1 associates with PER2 and CSNK1D via a distinct helical bundle domain, weakening PER2-CSNK1D association and attenuating PER2 FASP phosphorylation in cells and in vitro. Mechanistically, this helical bundle interacts with the PER2 casein kinase binding domain and is contacted by the adjacent VPS9 region in GAPVD1, providing a structural explanation for how flanking GAPVD1 domains can control access of binding proteins to the helical bundle. Notably, a minimal GAPVD1 helical bundle fragment is sufficient for binding to PER2 and CSNK1D but not for robust attenuation of PER2 FASP phosphorylation, indicating that additional regions of GAPVD1 are required. GAPVD1-mediated inhibition of PER2 FASP phosphorylation also turned out to be independent of the CSNK1D C-terminal tail, pointing to mechanisms such as displacement of PER2 FASP from the CSNK1D active site or allosteric regulation of CSNK1D substrate engagement. Together, these findings identify GAPVD1 as a PER-complex scaffold that modulates the PER2-CSNK1D control node and introduce an additional regulatory layer into the circadian phosphoswitch. A GAPVD1 helical bundle domain binds the PER2 CKBD and CSNK1D to weaken PER2-CSNK1D interaction and attenuate PER2 FASP phosphorylation.

molecular biology↗

bioRxiv2025

Ghrelin and relamorelin alleviate hypoglycaemia in humanised mice with congenital hyperinsulinism

KATP-channel related hyperinsulinism (KATPHI) is a genetic disorder of the pancreatic beta cells, manifesting as life-threatening hypoglycaemia in neonates due to dysregulated insulin secretion. Management of the severe diffuse form of KATPHI currently lacks treatment options, as the first-line therapy octreotide is often insufficiently effective, necessitating radical pancreatectomy in many patients. In this study, we applied stem cell derived islets carrying KATPHI-causing mutation KCNJ11-/- to develop new pharmaceutical therapies for KATPHI. We tested seven candidate molecules in vitro, identifying three that reduced insulin secretion in KCNJ11-/- stem cell derived islets. Of these, we tested acyl-ghrelin and its long-acting analogue relamorelin in mice that became hypoglycaemic due to carrying human KCNJ11-/- stem cell derived grafts. Acyl-ghrelin and relamorelin alone increased fasting glycaemia. Combining relamorelin with octreotide increased blood glucose more than the sum of each drug alone, reversing hypoglycaemia to normoglycaemia. In conclusion, we show that ghrelin receptor agonists have acute anti-hypoglycaemic effects in a humanised mouse model of KATPHI, especially when combined with octreotide. Relamorelin has been tested in >650 diabetic adults with little side effects, leading us to propose relamorelin - octreotide combination as a novel therapeutic candidate for severe KATPHI patients.

physiology↗

bioRxiv2025

A compendium of adipocyte morphologies across different breast pathologies

Adipocytes are abundant in the breast tissue microenvironment. In breast cancer, they can change morphologically according to their proximity to tumour cells, with the closest becoming cancer-associated adipocytes (CAAs). It remains unclear whether breast cancer risk factors, including menopausal status, body mass index (BMI), and mammographic density (MD), influence CAAs morphology in breast carcinogenesis. This study aimed to quantify morphological differences in adipocytes across breast cancer pathologies and associated risk factors. Whole slide images of hematoxylin and eosin stained cancer (n = 149) and normal (n = 182) breast tissue samples were analysed. Parameters representative of adipocyte morphology: perimeter, area, concavity, and aspect ratio, were measured using ImageJ. Adipocytes were considered close ([≤] 2 mm) or distant (>2 mm) to cancer cells in cancer samples or breast epithelial cells in normal samples. Close adipocytes in cancer samples were designated CAAs. CAAs decreased in size compared to distant adipocytes (p [≤] 0.0001). A similar trend was observed between close and distant adipocytes in normal (p [≤] 0.0001). CAAs size increased post menopause (p [≤] 0.0001). CAAs size positively correlated with BMI (p [≤] 0.0001). In cancer cases, distant adipocyte size increased and concavity decreased with increasing MD (p [≤] 0.01). Smaller CAAs were associated with poorer survival (p [≤] 0.05). Morphological differences were identified in adipocytes dependent on location within the breast, tissue, pathology and risk factors. Understanding what drives these morphological differences could provide mechanistic insight into whether risk factor-induced alterations in adipocytes influence their role in breast carcinogenesis.

cancer biology↗

bioRxiv2025

Resources for molecular studies of unculturable obligate biotrophic fungal plant pathogens using their saprotrophic relatives

Obligate biotrophic plant pathogens like the powdery mildew fungi commit to a closely dependent relationship with their plant hosts and have lost the ability to grow and reproduce independently. Thus, at present, these organisms are not amenable to in vitro cultivation, which is a prerequisite for effective genetic modification and functional molecular studies. Saprotrophic fungi of the family Arachnopezizaceae are the closest known extant relatives of the powdery mildew fungi and may hold great potential for studying genetic components of their obligate biotrophic lifestyle. Here, we established telomere-to-telomere genome assemblies for two representatives of this family, Arachnopeziza aurata and A. aurelia. Both species harbor haploid genomes that are composed of 16 chromosomes at a genome size of 43.1 and 46.3 million base-pairs, respectively, which, in contrast to most powdery mildew genomes that are transposon-enriched, show a repeat content below 5% and signs of repeat-induced point mutation (RIP). Both species could be grown in liquid culture and on solid standard media and were sensitive to common fungicides such as hygromycin and fenhexamid. We successfully expressed a red fluorescent protein and hygromycin resistance in A. aurata following polyethylene glycol-mediated protoplast transformation, demonstrating that Arachnopeziza species are amenable to genetic alterations that may include gene replacement, gene modification, and gene complementation. With this work, we established a potential model system that promises to sidestep the need for genetic modification of powdery mildew fungi by using Arachnopeziza species as a proxy to uncover the molecular functions of powdery mildew proteins.

genomics↗

bioRxiv2024

Intracellular accumulation of free cholesterol in macrophages triggers a PARP1 response to DNA damage and PARP1 impairs lipopolysaccharide-induced inflammatory response

The formation of macrophage (M{varphi}) foam cells is a hallmark of atherosclerosis, yet how the process of lipid loading can modulate M{varphi} inflammatory responses by rewiring their intracellular metabolic circuits is not well understood. Our previous studies have shown that the accumulation of oxidized LDL (oxLDL) or free cholesterol in M{varphi}s impaired their inflammatory response by suppressing HIF-1-mediated glycolysis and upregulating NRF2 antioxidative response. However, it remains unclear if other metabolic processes are also contributory. In this study, we found that the accumulation of free cholesterol, but not oxLDL, in primary murine thioglycolate-elicited peritoneal M{varphi}s (PM{varphi}s) enhanced a PARP1-dependent response associated with repair of DNA damage, which was characterized by poly ADP-ribosylation of proteins, phosphorylation of histone 2A.X and consumption of NAD+. Both oxLDL and cholesterol enhanced the PARP1 response after LPS stimulation. Treatment of PM{varphi}s with mitoTEMPO, a specific mitochondrial reactive oxygen species (mtROS) scavenger, alleviated mtROS during cholesterol loading, blocked the PARP1 response and partially restored LPS-induced inflammatory gene expression. In contrast to inhibition of PARP1 enzymatic activity, knockdown of PARP1 expression in RAW264.7 M{varphi}s with siRNA elevated LPS-induced inflammatory gene expression. Overall, our study suggests that cholesterol accumulation triggers a PARP1 response to DNA damage in M{varphi}s and that PARP1 inhibits LPS-mediated inflammation through a non-enzymatic function.

immunology↗

bioRxiv2023

Quantifying stem cell derived islet graft volume and composition with FDOPA positron emission tomography

Stem cell derived islets (SC-islets) are being developed as a novel source of beta cells that would enable large scale cell replacement therapy for insulin dependent diabetes. Therapeutic use of SC-islets carries an inherent risk of unwanted growth; and multiple strategies are being explored for optimizing long-term SC-islet graft effectiveness. However, a method for noninvasive in vivo monitoring for SC-islet graft safety and efficacy is lacking, as current insulin secretion measurements are inadequate. Here, we demonstrate the potential of positron emission tomography (PET) for monitoring SC-islet grafts using two tracers: GLP1-receptor binding [18F]F-DBCO-exendin and dopamine precursor [18F]FDOPA. We could detect and longitudinally monitor human SC-islet grafts in calf muscles of immunocompromised mice. Importantly, graft volume quantified with PET strongly correlated with actual graft volume (r2=0.91 for [18F]F-DBCO-exendin). PET using [18F]F-DBCO-exendin allowed delineation of cystic structures and its uptake correlated with graft beta cell proportion, enabling study of SC-islet graft purity noninvasively. [18F]FDOPA performed similarly to [18F]F-DBCO-exendin, but with slightly weaker sensitivity. Uptake of neither tracer was biased in SC-islet grafts genetically rendered hyper- or hypoactive. Insulin secretion measurements under fasted, glucose-stimulated or hypoglycemic conditions did not correlate with graft volume. In conclusion, [18F]F-DBCO-exendin and [18F]FDOPA PET constitute powerful approaches to noninvasively assess SC-islet graft volume and composition regardless of their functionality. PET imaging could therefore be leveraged for optimizing safety and effectiveness of SC-islet grafts in patients with insulin dependent diabetes.

cell biology↗

bioRxiv2023

RFX6 haploinsufficiency predisposes to diabetes through impaired beta cell functionality

Regulatory factor X 6 (RFX6) is indispensable for pancreatic endocrine development and differentiation. The RFX6 protein-truncating variant p.His293LeufsTer7 is significantly enriched in the Finnish population with almost 1:250 individuals as a carrier. Importantly, the FinnGen study indicates a high predisposition for heterozygous carriers to develop type 2 diabetes (T2D) and gestational diabetes. To understand the role of this variant in {beta}-cell development and function, we generated allelic series of isogenic pluripotent stem cell models and directed them into pancreatic islet lineages (SC-islets). Expectedly, in-vitro models of the homozygous RFX6-/- variant failed to generate pancreatic endocrine cells, recapitulating the phenotype in Mitchell-Riley syndrome. Notably, heterozygous RFX6+/- derived SC-islets showed reduced {beta}-cell maturation markers and calcium oscillations, resulting in defective insulin secretion, without affecting {beta}-cell number or insulin content. The reduced insulin secretion is sustained during in-vivo implantation studies, consistent with the susceptibility of the carriers to develop diabetes. TeaserModeling RFX6-assocciated neonatal and type-2 diabetes using allelic series stem cell-derived islets in-vitro and in-vivo.

cell biology↗

bioRxiv2023

Mechanosensing and Sphingolipid-Docking Mediate Lipopetide-Induced Immunity in Arabidopsis

Bacteria-derived lipopeptides are immunogenic triggers of host defenses in metazoans and plants. Root-associated rhizobacteria produce cyclic lipopeptides that activate systemically induced resistance (IR) against microbial infection in various plants. How these molecules are perceived by plant cells remains elusive. Here, we reveal that immunity activation in Arabidopsis thaliana by the lipopeptide elicitor surfactin is mediated by docking into specific sphingolipid-enriched domains and relies on host membrane deformation and subsequent activation of mechanosensitive ion channels. This mechanism leads to host defense potentiation and resistance to the necrotroph B. cinerea but is distinct from host pattern recognition receptor-mediated immune activation and reminiscent of damage-induced plant immunity.

plant biology↗

bioRxiv2023

Long noncoding RNAs emerge from transposon-derived antisense sequences and may contribute to infection stage-specific transposon regulation in a fungal phytopathogen

The genome of the obligate biotrophic phytopathogenic barley powdery mildew fungus Blumeria hordei is inflated due to highly abundant and possibly active transposable elements (TEs). In the absence of the otherwise common repeat-induced point mutation transposon defense mechanism, noncoding RNAs could be key for regulating the activity of TEs and coding genes during the pathogenic life cycle. We performed time-course whole-transcriptome shotgun sequencing (RNA-seq) of total RNA derived from infected barley leaf epidermis at various stages of fungal pathogenesis and observed significant transcript accumulation and time point-dependent regulation of TEs in B. hordei. Using a manually curated consensus database of 344 TEs, we discovered phased small RNAs mapping to 104 consensus transposons, suggesting that RNA interference contributes significantly to their regulation. Further, we identified 5,127 long noncoding RNAs (lncRNAs) genome-wide in B. hordei, of which 823 originated from the antisense strand of a TE. Co-expression network analysis of lncRNAs, TEs, and coding genes throughout the asexual life cycle of B. hordei points at extensive positive and negative co-regulation of lncRNAs, subsets of TEs and coding genes. Our work suggests that similar to mammals and plants, fungal lncRNAs support the dynamic modulation of transcript levels, including TEs, during pivotal stages of host infection. The lncRNAs may support transcriptional diversity and plasticity amid loss of coding genes in powdery mildew fungi and may give rise to novel regulatory elements and virulence peptides, thus representing key drivers of rapid evolutionary adaptation to promote pathogenicity and overcome host defense.

plant biology↗

bioRxiv2022

Back to the Future: Unleashing your cytometers spectral potential

With the recent growth in spectral flow cytometry many laboratories are investing in new spectral flow cytometers in order to maximise the information gathered about every cell. This study hypothesised that traditional cytometers already within many laboratories may be used as spectral cytometers and have shown using a range of different cytometers that data acquired may be unmixed after acquisition.

bioengineering↗

bioRxiv2022

The type 1 diabetes gene TYK2 regulates β-cell development and its responses to interferon-α

Type 1 diabetes (T1D) is an autoimmune disease that results in the destruction of insulin producing pancreatic {beta}-cells. One of the genes associated with T1D is TYK2, which encodes a Janus kinase with critical roles in type-I interferon (IFN) mediated intracellular signaling. To study the role of TYK2 in human pancreatic {beta}-cell development and response to IFN, we generated TYK2 knockout human iPSCs and directed them into the pancreatic endocrine lineage. Here we show that loss of TYK2 compromised the emergence of endocrine precursors by regulating KRAS expression while mature stem cell-islets (SC-islets) function was not affected. In the maturing SC-islets, the loss or inhibition of TYK2 prevented IFN-induced antigen processing and presentation, including MHC Class I expression in pancreatic endocrine and progenitor cells. Furthermore, in a CD8+ cytotoxic T-cell co-culture model, the survival of {beta}-cells was enhanced by a selective TYK2 inhibitor. These results identify an unsuspected role for TYK2 on {beta}-cell development and support TYK2 inhibition in adult {beta}-cells as a potent therapeutic target to halt T1D progression.

molecular biology↗

bioRxiv2021

Functional, metabolic and transcriptional maturation of stem cell derived beta cells

Transplantation of pancreatic islet cells derived from human pluripotent stem cells is a promising treatment for diabetes. Despite progress in stem cell-derived islet (SC-islet) generation, detailed characterization of their functional properties has not been conducted. Here, we generated functionally mature SC-islets using an optimized protocol and comprehensively benchmarked them against primary adult islets. Biphasic glucose stimulated insulin secretion developed during in vitro maturation, associated with cytoarchitectural reorganization and increased alpha cells. Electrophysiology and exocytosis of SC-islets were comparable to adult islets. Glucose-responsive insulin secretion was achieved despite differences in glycolytic and mitochondrial glucose metabolism. Single-cell transcriptomics of SC-islets in vitro and throughout 6 months of murine engraftment revealed a continuous maturation trajectory culminating in a transcriptional landscape closely resembling that of primary islets. Our thorough evaluation of SC-islet maturation highlights their advanced degree of functionality and supports their use in further efforts to understand and combat diabetes.

developmental biology↗

bioRxiv2019

CHCHD10 OR CHCHD2 ARE NOT REQUIRED FOR HUMAN MOTOR NEURON DIFFERENTIATION IN VITRO BUT MODIFY SYNAPTIC TRANSCRIPTOMES

Mitochondrial intermembrane space proteins CHCHD2 and CHCHD10 have roles in diseases affecting motor neurons such as amyotrophic lateral sclerosis, spinal muscular atrophy and axonal neuropathy and in Parkinsons disease, and form a complex of unknown function. Here we address the importance of these two proteins in human motor neurons. We show that gene edited human induced pluripotent stem cells (iPSC) lacking either CHCHD2 or CHCHD10 are viable and can be differentiated into functional motor neurons that fire spontaneous and evoked action potentials. Knockout iPSC and motor neurons sustain mitochondrial ultrastructure and show reciprocal compensatory increases in CHCHD2 or CHCHD10. Knockout motor neurons have largely overlapping transcriptome profiles compared to isogenic control line, in particular for synaptic gene expression. Our results show that absence of CHCHD2 or CHCHD10 does not disrupt functionality, but induces similar modifications in human motor neurons. Thus pathogenic mechanisms may involve loss of synaptic function.

neuroscience↗