Biology subjects

Ibrahim, O.

Publications and source records attributed to Ibrahim, O..

5 recordsLinked to original sources

bioRxiv2026

Nanoparticle mediated delivery of PD-L1 inhibitor enhances γδ T cell immunotherapy against metastatic ovarian cancer cells

IntroductionImmune checkpoint inhibitors (ICIs) have only shown limited efficacy for patients with ovarian cancer (OC), partly due to the immune suppressive tumour microenvironment (TME) and platelet cloaking of the cancer cells. We tested a nanomedicine strategy to enhance {gamma}{delta} T cell immunotherapy by conjugating the PD-L1 inhibitor (BMS202) to nanodiamonds (NDs). MethodsPatient-derived ascites cells were exposed to activated platelets to model platelet cloaking and the immunosuppressive phenotype in metastatic OC. ND/BMS202 nanocomplexes were then applied to platelet-conditioned OC cells and co-cultured with expanded {gamma}{delta} T cells. Cytotoxicity and immune activation were assessed by quantifying Granzyme B, CD107a, {gamma}-H2AX, cleaved caspase-3, and cleaved caspase-8. ResultsND-mediated delivery of BMS202 significantly enhanced {gamma}{delta} T cell-mediated killing of platelet cloaked OC cells in a dose-dependent manner, with greater efficacy than free BMS202 This enhanced cytotoxicity was supported by increased degranulation (CD107a), Granzyme B release, tumour cell apoptosis (caspase cleavage) and DNA damage ({gamma}-H2AX staining). ConclusionsND-based delivery of the PD-L1 inhibitor (BMS202) enhances {gamma}{delta} T cell-mediated killing of platelet-cloaked metastatic OC cells. While our data support enhanced {gamma}{delta} T cell cytotoxicity following BMS202 delivery, direct evidence of PD-L1 target engagement or PD-1/PD-L1 binding inhibition was not demonstrated in this study. These findings nonetheless justify further validation in patient-derived organoid models to optimize this {gamma}{delta} T cell-based combination immunotherapy and advance its development as a precision therapeutic strategy for metastatic OC.

immunology↗

bioRxiv2026

BioReason-Pro: Advancing Protein Function Prediction with Multimodal Biological Reasoning

Protein function annotation is fundamental to understanding biological mechanisms, designing therapeutics, and advancing biomedical research. Current computational methods either rely on shallow sequence similarity or treat function prediction as isolated classification tasks, failing to capture the integrative reasoning across sequence, structure, domains, and interactions that expert biologists perform to infer function. We introduce BioReason-Pro, the first multimodal reasoning large language model (LLM) for protein function prediction that integrates protein embeddings with biological context to generate structured reasoning traces. A key input into BioReason-Pro is the set of GO term predictions made by GO-GPT, our autoregressive transformer that captures hierarchical and cross-aspect dependencies of GO terms. BioReason-Pro is trained via supervised fine-tuning on synthetic reasoning traces generated by GPT-5 for over 130K proteins and further optimized through reinforcement learning. It achieves 73.6% Fmax on GO term prediction and an LLM judge score of 8/10 on functional summaries, substantially outperforming previous methods. Evaluations with human protein experts show that BioReason-Pro annotations are preferred over ground truth UniProt annotations in 79% of cases. Remarkably, BioReason-Pro predicted a novel interaction partner for the renal cancer biomarker RCDG1, which we confirmed in the lab by co-immunoprecipitation. In other binding-partner predictions, its per-residue attention localized to the exact contact residues resolved in cryo-EM structures. Together, GO-GPT and BioReason-Pro establish a framework for protein function prediction that combines precise ontology modeling with interpretable biological reasoning.

molecular biology↗

bioRxiv2025

Lymphatic constraint of germinal centers optimizes protective antibody responses

Immunization strategies are central to pathogen control, where efficacy relies on antigen uptake, distribution, persistence, and inflammatory context. We recently demonstrated that dermal lymphatic capillaries regulate antigen presentation in lymph nodes (LN) by restraining fluid and virion transport following vaccinia virus (VACV) infection by skin scarification. Concurrently, a perifollicular, LN lymphangiogenic response encapsulates expanding B cell follicles. Given the important role of antigen transport and uptake on humoral immunity, we tested the hypothesis that lymphatic remodeling in the skin and LNs regulates germinal center (GC)-dependent antibody responses during infection. Using a model of lymphatic-specific VEGFR2 inhibition, we found that inhibiting viral-induced lymphatic remodeling in skin and LNs prompted significant GC expansion but paradoxically decreases protective VACV-specific class-switched antibodies. While the larger GC responses appeared structurally normal, they failed to support a proliferative burst consistent with clonal selection. Mathematical modeling revealed that this disconnect between GC size and function arises from impaired productive T follicular cell interactions in larger GC volumes and consistent with this finding, the optimal GC size was evolutionarily conserved across diverse mammals. Finally, we found that the presence of virus in the LN initiates these changes in GC function, inhibits LN lymphangiogenesis, increases B cell follicle size, and reduces selection efficiency. Therefore, protecting LN lymphatic vessels from virus-induced interferons rescues perifollicular lymphatic growth and follicle size, indicating that LN lymphangiogenesis directly constrains the follicular response. In summary, this study underscores the central role of lymphatic remodeling in compartmentalizing antigen and inflammatory signals to optimize GC fitness and protective antibody responses.

immunology↗

bioRxiv2025

The ZNF512B-NuRD complex co-ordinates a neural-specific gene expression program

The nucleosome remodelling and deacetylase complex (NuRD) plays a key role in chromatin regulation and a wide range of biological processes including development, haemopoiesis, immunity and neurogenesis. Its interaction with tissue-enriched and sequence-specific transcription factors (TFs) leads to distinct functional outputs in the given tissue by targeting a specific set of genes. However, how NuRD dynamically and specifically regulates gene expression in a tissue-specific manner is poorly understood. Here, we refine an N-terminal specific NuRD interaction motif which enables direct engagement with many transcriptional regulatory proteins. Using a series of structural modelling and biochemical techniques, we show that ZNF512B, a poorly characterised neuronal-expressed zinc finger protein, directly binds to the RBBP4 subunit of the NuRD complex. Subsequent knockdown of ZNF512B results in the downregulation of several neural-related molecular pathways suggesting that ZNF512B may play a regulatory role during neurogenesis. We also show that in NTERA-2 neural cells, the expression of ZNF512B is necessary for cell growth and survival, and is markedly enhanced during neural progenitor cell (NPC) differentiation. In summary, our data suggest that ZNF512B might regulate neural-specific transcriptional programs via engagement with the NuRD complex.

molecular biology↗

bioRxiv2020

Impact of Commiphora myrrha on bacteria (Streptococcus mutans and Lactobacillus species) related to dental caries

Dental caries is a chronic disease caused by the interaction of oral microorganisms, diet and host factors over time. Streptococcus mutans is considered as the main bacteria involve in dental decay, while the level of Lactobacillus spp. is directly related to the presence or onset of caries. Commiphora myrrha is an ancient plant which extracts are used as antiseptic and anti-inflammatory for mouth and throat due to it is antimicrobial activity. This study assessed the impact of Commiphora myrrha on two bacteria Streptococcus mutans and Lactobacillus spp. involved in dental caries. Three samples of Streptococcus mutans bacteria were collected randomly from patients with dental caries in Khartoum dental teaching hospital, while Lactobacillus spp. were obtained from fermented milk. Disk and well diffusion methods were used to test the effect of four concentration (100,50,25 and 12.5 mg/ml) of Myrrha volatile oil, extracted by hydro-distillation technique. The biochemical analysis of Commiphora myrrha oil was carried out using Gas Chromatography/Mass Spectrophotometric technique. The finding revealed that the four concentrations of oil were effective on Streptococcus mutans with the largest inhibition zone (18.7{+/-} 0.6 mm) through the well diffusion method and inhibition zone of (14.00 mm) with disc diffusion method regardless the two methods these inhibition zones were recorded at 100 mg/ml, with Minimum Bactericidal Concentration (MBC) at 3.125 mg/ml. While Lactobacillus spp. bacteria sensitive to three concentrations (100,50 and 25 mg/ml) and resistance to concentration 12.5 mg/ml, it is MBC found to be 25 mg/ml. In conclusion, this research revealed that Myrrh oil is effective on both S.mutans and Lactobacillus spp. Hence, Myrrha oil is a potential antibacterial product of interest in dental caries.

microbiology↗