Biology subjects

Al-Hasani, H.

Publications and source records attributed to Al-Hasani, H..

10 recordsLinked to original sources

bioRxiv2026

Systematic De-Risking of TCR-Mimic Therapeutics Through Proteome-Wide Off-Target Landscaping and a Generalizable Design Rule Framework

TCR-mimic (TCRm) antibodies targeting peptide-human leukocyte antigen (pHLA) complexes enable precision immunotherapy against intracellular antigens, including cancer-testis antigens (CTAs). Achieving high specificity, however, remains challenging because of the vast diversity of the human immunopeptidome and the associated risk of off-target recognition. Here, we introduce ValidaTe, a unified framework for the proteome-scale prediction, validation, and mitigation of off-target liabilities in pHLA-directed therapeutics. ValidaTe integrates rational target prioritization, peptide-centric binder selection, proteome-wide off-target prediction, and therapeutic engineering into a hierarchical de-risking workflow. Using the CTA MAGE-A4 as a proof-of-concept, we identify the TCRm antibodies VR-4 and VR-6 with superior specificity and demonstrate how this workflow enables the discovery of safer pHLA-targeted binders. Furthermore, ValidaTe establishes the basis for the WiFi (Widened Fingerprint) engineering principle, which rationally combines TCRms with complementary off-target fingerprints in trivalent T-cell engagers to minimize unintended interactions while preserving potent target-specific activity. Together, these findings establish a generalizable framework for the rational development of safer and more selective pHLA-targeted therapeutics. We further discuss how orthogonal proteomic characterization may complement this workflow as a final layer of translational safety assessment prior to clinical development. TeaserValidaTe accelerates safe pHLA-targeted immunotherapy through proteome-wide off-target mapping and WiFi design

immunology↗

bioRxiv2026

DLDN-Bench: A Benchmark Framework for Deep Learning de Novo Peptide Sequencing in Proteomics

De novo peptide sequencing is an essential approach for analyzing mass spectrometry data because it enables the identification of novel peptides without relying on protein sequence databases. Recent advances in deep learning have substantially improved the performance of de novo sequencing methods, but the rapid emergence of new models has led to heterogeneous evaluation practices and limited comparability. To address this, we introduce DLDN-Bench, a benchmark framework including a set of benchmark datasets derived from human muscle biopsy mass spectrometry data retrieved from PRIDE and annotated through consensus across multiple widely used database search engines. Using these datasets, we systematically benchmark recent deep learning-based de novo sequencing tools alongside traditional approaches. Performance is assessed using established metrics, including precision and coverage relative to a pseudo-ground truth defined by cross-engine agreement. To demonstrate the utility of DLDN-Bench, we benchmark four recent deep learning models and make all results publicly available. This benchmark framework provides a standardized basis for comparing state-of-the-art methods and offers an extensible resource for evaluating future tools in de novo peptide sequencing. Code availabilityhttps://github.com/ddz-icb/DLDN-Bench Data availabilityhttps://doi.org/10.5281/zenodo.19627459

bioinformatics↗

bioRxiv2026

Villin-SNAP25 interaction regulates insulin secretion downstream of ICA512 signaling

Pancreatic islet {beta}-cells step-up insulin production and secretion in response to the elevation of blood glucose levels. ICA512/PTPRN is a transmembrane cargo of the insulin secretory granules (SGs). Upon SG exocytosis, its Ca2+/calpain mediated cleavage at the plasma membrane generates an ICA512-cleaved cytosolic fragment (ICA512-CCF) which as a decoy phosphatase prolongs phospho-STAT5/3 activities, thereby enhancing the transcription of mRNAs for SG cargoes, including insulin and its own, to replenish SG stores. In addition, ICA512 positively regulates the expression of F-actin modifier villin. Villin, in turn, modulates the size of actin cages surrounding cortical SGs, hence regulating SG mobility and exocytosis. Here we show that villin controls the number of SG docking sites for exocytosis by directly interacting at low glucose with the t-SNARE SNAP-25, thus restricting in this condition SG access to fusion sites and insulin release. Replacement of ICA512-CCF N-terminal ubiquitin-acceptor lysine 609 (K609) with valine (V) stabilized ICA512-CCF in insulinoma cells and homozygous ICA512K609V mice and enhanced the levels of phospho-STAT5/3 and villin. In ICA512K609V female mice these molecular traits correlated with reduced body weight, improved insulin sensitivity, reduced basal insulin secretion and onset time for glucose stimulated insulin secretion. Taken together, these data demonstrates that SG exocytosis induced ICA512 retrograde signaling acts in concert with the novel SNARE complex regulator villin to plastically adapt {beta}-cell actin cytoskeleton and access to SG docking sites for optimal control of insulin secretion in response to variations in extracellular glucose levels. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=110 SRC="FIGDIR/small/699220v1_ufig1.gif" ALT="Figure 1"> View larger version (27K): org.highwire.dtl.DTLVardef@37d835org.highwire.dtl.DTLVardef@5389f1org.highwire.dtl.DTLVardef@855d98org.highwire.dtl.DTLVardef@1c3c639_HPS_FORMAT_FIGEXP M_FIG Graphical abstract Model of ICA512 and STAT3/5-dependent regulation of -cell function. At basal conditions, villin limits secretory granule (SG) docking by interacting with SNAP-25, restricting insulin release (1). Increased metabolic load triggers hyperglycemia-induced ICA512 processing and growth factor-mediated STAT3/5 phosphorylation (2-4), enhancing ISG mRNAs, granule biogenesis, and villin expression (5,6). Villin modulates SNARE protein availability, controlling SG docking and secretion. Together, ICA512 retrograde signaling and villin-mediated SNARE regulation dynamically remodel the -cell actin cytoskeleton, adjusting SG docking site access to ensure appropriate insulin secretion in response to fluctuating glucose levels. C_FIG

cell biology↗

bioRxiv2025

EpiTox: A Multi-Modular Framework for Population-Aware Off-Target Prediction Highlighting MAGE-A3 Cross-Reactivity

Targeting intracellular tumor antigens presented by peptide human leukocyte antigen (pHLA) complexes offers a promising immunotherapeutic strategy for patients with limited treatment options. However, development of pHLA-targeted drugs such as T-cell receptor (TCR) mimic antibodies (TCRm) and TCR-based therapeutics remains challenging due to severe offtumor and off-target toxicities arising from incomplete pHLA off-target profiling. The fatal neurological toxicities observed in the MAGEA3 TCR-T cell trial, potentially linked to unanticipated cross-reactivity with EPS8L2- and MAGEA12-derived peptides, underscore the urgent need for more comprehensive safety assessment. While current preclinical de-risking methods utilize sequence similarity searches, they lack the layered integration of genetic context, HLA binding profiles, and structured risk assessment needed to comprehensively evaluate peptide cross-reactivity. To address these limitations, we developed EpiTox, a computational multi-modular platform that systematically identifies and evaluates pHLA off-targets. EpiTox integrates proteome-wide sequence similarity, genetic context, HLA binding profiles, and layered risk assessment to provide a holistic evaluation of potential cross-reactive peptides. Using MAGEA3 as a model, EpiTox identified known toxic off-targets and predicted novel epitopes. Notably, an anti-MAGEA3 therapeutic TCRm antibody bound several newly predicted off-targets, including three SNP-derived peptides. By enabling comprehensive and predictive preclinical safety screening, Epi-Tox supports safer TCRm drug development and may help prevent future clinical failures.

bioinformatics↗

bioRxiv2025

Beyond Sequence Similarity: ML-Powered Identification of pHLA Off-Targets for TCR-Mimic Antibodies Using High Throughput Binding Kinetics

T-cell receptor mimic (TCRm) antibodies are an emerging class of tumor-targeting agents used in advanced immunother-apies such as bispecific T-cell engagers and CAR-T cells. Unlike conventional antibodies, TCRms are designed to recognize peptide-human leukocyte antigen (pHLA) complexes that present intracellular tumor-derived peptides on the cell surface. Due to the typically low surface abundance and high sequence similarity of pHLAs, TCRms require high affinity and exceptional specificity to avoid off-target toxicity. Conventional methods for off-target identification such as sequence similarity searches, motif-based screening, and structural modelling focus on the peptide and are limited in detecting cross-reactive peptides with little or no sequence homology to the target. To address this gap, we developed EpiPredict, a TCRm-specific machine learning framework trained on high-throughput kinetic off-target screening data. EpiPredict learns an antibody-specific mapping from peptide sequence to binding strength, enabling prediction of interactions with unmeasured pHLA sequences, including sequence-dissimilar peptides. We applied EpiPredict to two distinct TCRms targeting the cancer-testis antigen MAGE-A4. The model successfully predicted multiple off-targets with minimal sequence similarity to the intended epitope, many of which were experimentally validated via T2 cell binding assays. These findings establish EpiPredict as a valuable tool for lead optimization of TCRms, enabling the identification of antibody-specific off-targets beyond the scope of traditional peptide-centric methods and supporting the preclinical de-risking of TCRm-based therapies.

immunology↗

bioRxiv2024

High-resolution respirometry reveals altered mammalian tissue ketone body oxidation in different cardiometabolic diseases

Background and aimsReduced mitochondrial function has been implicated in metabolic disorders like type 2 diabetes (T2D), obesity, and metabolic dysfunction-associated steatotic liver disease (MASLD), which are tightly linked to insulin resistance and impaired metabolic flexibility. However, the contribution of the ketone bodies (KBs) {beta}-hydroxybutyrate (HBA) and acetoacetate (ACA) as substrates for mitochondrial oxidative phosphorylation (OXPHOS) in these insulin resistant states remains unclear. MethodsTargeted high-resolution respirometry protocols were applied to detect the differential contribution of HBA and ACA to OXPHOS capacity in heart, skeletal muscle, kidney, and liver of distinct human and mouse cohorts with T2D, obesity, and MASLD. ResultsIn humans with T2D, KB-driven mitochondrial OXPHOS capacity was [~]30% lower in the heart (p<0.05) and skeletal muscle (p<0.05) compared to non-diabetic controls. The relative contribution of KB to maximal OXPHOS capacity in T2D was also lower in both the heart ([~]25%, p<0.05) and skeletal muscle ([~]50%, p<0.05). Similarly, in kidney cortex from high-fat diet-induced obese mice, both the absolute and relative contribution of KB to OXPHOS capacity was [~]15% lower (p<0.05). Finally, hepatic HBA-driven mitochondrial OXPHOS capacity was 29% lower (p<0.05) in obese humans with MASLD compared to humans without MASLD. ConclusionsMitochondrial KB-driven OXPHOS capacity is impaired in insulin resistant states in various organs in absolute and relative terms, likely reflecting impaired mitochondrial metabolic flexibility. Our data suggest that KB respirometry can provide a sensitive readout of impaired mitochondrial function in diabetes, obesity, and MASLD.

cell biology↗

bioRxiv2024

A Novel 3D Imaging Approach for Quantification of GLUT4 Levels across the Intact Myocardium

Cellular heterogeneity is a well-accepted feature of tissues, and both transcriptional and metabolic diversity have been revealed by numerous approaches, including optical imaging. However, the high magnification objective lenses needed for high-resolution imaging provides information from only small layers of tissue, which can result in poor cell statistics. There is therefore an unmet need for an imaging modality that can provide detailed molecular and cellular insight within intact tissue samples in 3D. Using GFP-tagged GLUT4 as proof of concept, we present here a novel optical mesoscopy approach that allows precise measurement of the spatial location of GLUT4 within specific anatomical structures across the myocardium in ultrathick sections (5 mm x 5 mm x 3 mm) of intact mouse heart. We reveal distinct GLUT4 distribution patterns across cardiac walls and highlight specific changes in GLUT4 expression levels in response to high fat diet-feeding, and we identify gender-dependent differences in expression patterns. This method is applicable to any target that can be labelled for light microscopy, and to other complex tissues when organ structure needs to be considered simultaneously with cellular detail. SUMMARY STATEMENTHere we present a novel 3D optical mesoscopy approach that allows the study of both GLUT4 protein expression levels and structural distribution within ultrathick sections of intact murine hearts, in response to high fat diet-feeding.

cell biology↗

bioRxiv2024

Crosstalk between thrombospondin-1 and CD36 modulates platelet-RBC interaction limiting thrombosis and abdominal aneurysm formation

Red blood cells (RBCs) contribute to hemostasis and thrombosis by interaction with platelets via the FasL-FasR pathway to induce procoagulant activity and thrombin formation. Here, we identified a novel mechanism of platelet-RBC interaction via the CD36-thrombospondin-1 (TSP-1) signaling pathway, which is important in thrombus formation and the recruitment of RBCs to collagen-adherent platelets. Platelet-released TSP-1 can bind to CD36 at the RBC membrane to enhance procoagulant activity and to increase the activation of integrin IIb{beta}3, which represents an additional ligand for erythroid FasR, suggesting that both mechanisms of platelet-RBC interaction act in concert to propagate thrombus formation. In patients with abdominal aortic aneurysm (AAA), enhanced procoagulant activity of RBCs and platelets is accompanied by elevated exposure of TSP-1 and FasL at the platelet surface and accumulation of TSP-1 in the aortic wall and the intraluminal thrombus, suggesting that platelet-RBC interaction plays an important role in AAA pathology. TSP-1-deficient mice are protected against aortic diameter expansion in an experimental model of AAA, highlighting the crucial role of the CD36-TSP-1 axis in AAA. Thus, interfering with platelet-RBC interaction may be a promising therapeutic approach to reduce pro-coagulant activity and preserve AAA patients from surgery or rupture.

pathology↗

bioRxiv2023

Inhibition of proline-rich-tyrosine kinase 2 restores cardioprotection by remote ischemic preconditioning in type 2 diabetes mellitus

BackgroundEndothelial function and cardioprotection through remote ischemic preconditioning (rIPC) are severely impaired in type 2 diabetes mellitus (T2DM). Proline-rich tyrosine kinase 2 (Pyk2), a downstream target of the insulin receptor, reduces endothelial nitric oxide synthase (eNOS) activity. Therapeutic options to rescue cardioprotection in T2DM and improve outcomes after acute myocardial infarction (AMI) are lacking. We hypothesized that vascular endothelium contributes to rIPC, and that inhibition of Pyk2 restores cardioprotection in T2DM through modulation of eNOS, thus limiting infarct size. MethodsNew Zealand Obese (NZO) mice were used as a polygenic model of T2DM. Effects of Pyk2-inhibition on endothelial function, remote ischemic preconditioning (rIPC), and infarct size (IS) after ischemia/reperfusion (I/R) were compared in NZO, eNOS KO, and C57Bl/6 (Bl6) mice. Plasma derived from mice and individuals with or without T2DM at baseline and after rIPC was transferred to isolated hearts and aortic rings to assess the effects of Pyk2-inhibition on remote tissue protection. ResultsTransfer experiments with plasma drawn from non-diabetic humans and mice exposed to rIPC demonstrate that endothelium-dependent signals for remote tissue protection are conveyed by plasma. Key features reflecting the glucometabolic spectrum in T2DM were detected in NZO mice, including hyperinsulinemia, insulin resistance, obesity, and impaired glucose tolerance. Similar to T2DM patients, these mice also revealed endothelial dysfunction with decreased flow-mediated dilation (FMD), reduced circulating nitrite levels, elevated arterial blood pressure, and larger infarct size after I/R. Pyk2 increased the phosphorylation of eNOS on its inhibitory site (Tyr656). Cardioprotective effects by rIPC were lost in NZO mice. Inhibition of Pyk2 restored endothelial function and rescued endothelium-dependent cardioprotection after rIPC displayed by lower IS and improved LV function post I/R. ConclusionEndothelial function contributing to remote tissue protection is severely impaired in diabetes mellitus. Proline-rich tyrosine kinase 2 is a novel target to rescue cardioprotection through endothelium-dependent remote ischemic preconditioning, advocating its role in limiting infarct size in diabetes mellitus. Clinical perspective What is new?O_LIVascular endothelium contributes to remote tissue protection in ischemic preconditioning, which is severely impaired in diabetes C_LIO_LIProline-rich tyrosine kinase 2 reduces eNOS-activity, causes endothelial dysfunction, and impairs cardioprotection through ischemic preconditioning C_LIO_LIInhibition of proline-rich tyrosine kinase 2 restores eNOS activity, endothelial function, and cardioprotective effects of remote ischemic preconditioning limiting infarct size in an experimental model of diabetes. C_LI What are the clinical implications?O_LIProper endothelial function is cirtical to maintain cardiovascular health. Endothelial dysfunction contributes to impaired remote tissue protection in diabetes. C_LIO_LIThese data demonstrate for the first time that endothelium-dependent cardioprotection in myocardial ischemia/reperfusion through remote ischemic preconditioning can be restored in diabetes. C_LIO_LIProline-rich tyrosine kinase 2 is a novel target to restore endothelium-dependent remote cardioprotection to improve the outcome of diabetic patients with acute myocardial infarction. C_LI

physiology↗

bioRxiv2018

Ultra-parallel ChIP-seq by barcoding of intact nuclei

Chromatin immunoprecipitation followed by deep sequencing (ChIP-seq) is an invaluable tool for mapping chromatin-associated proteins. However, sample preparation is still a largely individual and labor-intensive process that hinders assay throughput and comparability. Here, we present a novel method for ultra-parallelized high-throughput ChIP-seq that addresses the aforementioned problems. The method, called RELACS (Restriction Enzyme-based Labeling of Chromatin in Situ), employs barcoding of chromatin within intact nuclei extracted from different sources (e.g. tissues, treatments, time points). Barcoded nuclei are pooled and processed within the same ChIP, for maximal comparability and significant workload reduction. The choice of user-friendly, straightforward, enzymatic steps for chromatin fragmentation and barcoding makes RELACS particularly suitable for implementation large-scale clinical studies and scarce samples. RELACS can generate ChIP-seq libraries from hundreds of samples within three days and with less than 1000 cells per sample.

genomics↗