Biology subjects

Prince, S.

Publications and source records attributed to Prince, S..

8 recordsLinked to original sources

bioRxiv2026

Clever-1 blockade disrupts lipid metabolism and mitochondrial fitness in acute myeloid leukemia

Therapy resistance in acute myeloid leukemia (AML) is linked to metabolic plasticity and mitochondrial fitness of leukemic stem and progenitor cells. Clever-1 is a scavenger receptor with established immunoregulatory functions, but its leukemia cell-intrinsic roles remain unclear. Here we identify Clever-1 as a regulator of mitochondrial integrity and lipid-dependent oxidative metabolism in AML. Using the anti-Clever-1 antibody bexmarilimab, we show that Clever-1 inhibition induces early mitochondrial transcriptional reprogramming, followed by suppression of oxidative phosphorylation (OXPHOS) in AML cell lines. Immunoelectron microscopy demonstrates mitochondrial localization of Clever-1, while proteomic analyses reveal altered association with mitochondrial-linked proteins, including ATAD3. Functionally, Clever-1 inhibition reduces mitochondrial delivery of lipoprotein-derived lipids, resulting in selective changes in mitochondrial lipid composition. These changes are accompanied by impaired respiratory complex IV assembly, disrupted cristae architecture, accumulation of dysfunctional mitochondria, and reduced spare respiratory capacity. AML models with high baseline OXPHOS activity are particularly sensitive to Clever-1 inhibition, with mitochondrial dysfunction exacerbated under lipid-restricted or metabolically stressful conditions. Together, these findings define Clever-1 as a regulator of mitochondrial bioenergetic resilience and a targetable metabolic vulnerability in AML.

cancer biology↗

bioRxiv2026

Deep learning models for chemical perturbation prediction do not yet utilise drug molecular features

Recent deep learning models for L1000 chemical perturbation prediction incorporate dedicated drug molecular encoders. We retrained seven such models from scratch with zeroed or shuffled drug inputs, and compared them with a multilayer perceptron that uses only cell-line basal expression. Under drug-blind evaluation, ablation caused negligible performance changes and the drug-free baseline matched all models. Current architectures do not yet utilise drug molecular features for generalisation to unseen compounds.

bioinformatics↗

bioRxiv2026

Experimental Data Driven AI Framework for Flexible Protein Conformational Reconstruction

Deep learning has revolutionized structural biology by prediction with near experimental accuracy static protein folds from amino acid sequence alone. However, proteins function as dynamic ensembles of protein conformation states, and current sequence-only models often fail to capture the specific conformational states and heterogeneity dictated by cellular environments or ligand binding. While recent generative models can sample broad conformational landscapes, they remain unconstrained by physical reality, often hallucinating plausible but experimentally invalid states. Here, we present AlphaSAXS, an end-to-end framework that constrains artificial intelligence (AI) inference using Small Angle X-ray Scattering (SAXS) experimental solution scattering data. By integrating real-space pair distance distributions (P(r)) directly into the AlphaFold architecture, AlphaSAXS effectively steers the structural hypothesis toward the experimentally observed structures. We demonstrate that AlphaSAXS resolves documented failure modes of sequence-only models in Apo-Holo transitions, successfully distinguishing between states with identical sequences but distinct scattering profiles. Furthermore, we introduce a hybrid inference protocol that couples deep learning with biophysical hydration modeling, enabling the reconstruction of solution state protein ensembles compatible with experimental data. This work establishes a paradigm for experimentally guided AI, bridging the gap between probabilistic sampling and biophysical measurement.

biophysics↗

bioRxiv2024

Secreted Clever-1 Modulates T Cell Responses and Impacts Cancer Immunotherapy Efficacy

Clever-1 functions as a scavenger and adhesion receptor, promoting tolerogenic activities in macrophages and subsets of endothelial cells, thereby contributing to cancer progression. High Clever-1 expression associates with resistance to immune checkpoint inhibitors and combined targeting of Clever-1 with anti-PD-1 enhances response in refractory mouse tumor models. A Clever-1-targeting humanized IgG4 antibody, bexmarilimab, is investigated in clinical trials as a macrophage-reprogramming therapy to treat solid tumors (NCT03733990) and hematological malignancies (NCT05428969). Here we describe a secreted form of (s)Clever-1 enriched in plasma of cancer patients, that was decreased upon bexmarilimab treatment. With the production of a recombinant sClever-1, mimicking the one found in human plasma, we show that sClever-1 can selectively bind activated T cells and disrupt T cell receptor signalling leading to impaired Th1 expansion. We demonstrate that sClever-1 binds to insulin growth factor 2 receptor (IGF2R) on T cells via its mannose-6-phosphate modification and further show that sClever-1 contributes to the immunosuppressive properties of macrophage-secreted extracellular vesicles, driving T cell tolerance and impairing anti-PD-1 efficacy. These findings suggest that Clever-1 exerts a systemic immunosuppressive effect independently of the cells it is expressed on, highlighting its potential as a target in cancer immunotherapy and a valuable biomarker for disease detection.

immunology↗

bioRxiv2024

Single-particle track colocalization using CoPixie reveals the impact of cancer-associated POT1 mutations on telomerase-telomere interactions

Single-particle imaging and tracking can be combined with colocalization analysis to study the dynamic interactions between macromolecules in living cells. Indeed, single-particle tracking has been extensively used to study protein-DNA interactions and dynamics. Still, identification and quantification of binding events at specific genomic loci remains challenging. Herein we describe CoPixie, a new software that identifies colocalization events between a theoretically unlimited number of imaging channels, including single-particle movies. We employed CoPixie with live cell single-molecule imaging of telomerase and telomeres to test the model that cancer-associated POT1 mutations facilitate telomere accessibility. We show that OB-fold mutants POT1-{Delta}OB, Y223C, D224N or K90E increase telomere accessibility for telomerase interaction and the cumulative dwell-time of telomerase at telomeres. However, unlike POT1-{Delta}OB or D224N mutants, the POT1 Y223C and K90E mutations also increase the duration of long-lasting telomerase interactions at telomeres. Our data reveal that telomere elongation in cells expressing cancer-associated POT1 mutants arises from the dual impact of these mutations on telomeres accessibility and telomerase retention at telomeres. CoPixie can be used to explore a variety of questions involving macromolecular interactions in living cells, including between proteins and nucleic acids, from multi-color single-particles tracks.

biochemistry↗

bioRxiv2022

Intracellular mechanics and TBX3 expression jointly dictate the spreading mode of melanoma cells in 3D environments

Cell stiffness and T-box transcription factor 3 (TBX3) expression have been identified as biomarkers of melanoma metastasis in 2D environments. This study aimed to determine how mechanical and biochemical properties of melanoma cells change during cluster formation in 3D environments. Vertical growth phase (VGP) and metastatic (MET) melanoma cells were embedded in 3D collagen matrices of 2 and 4 mg/ml collagen concentrations, representing low and high matrix stiffness. Mitochondrial fluctuation, intracellular stiffness, and TBX3 expression were quantified before and during cluster formation. In isolated cells, mitochondrial fluctuation decreased and intracellular stiffness increased with increase in disease stage from VGP to MET and increased matrix stiffness. TBX3 was highly expressed in soft matrices but diminished in stiff matrices for VGP and MET cells. Cluster formation of VGP cells was excessive in soft matrices but limited in stiff matrices, whereas for MET cells it was limited in soft and stiff matrices. In soft matrices, VGP cells did not change the intracellular properties, whereas MET cells exhibited increased mitochondrial fluctuation and decreased TBX3 expression. In stiff matrices, mitochondrial fluctuation and TBX3 expression increased in VGP and MET, and intracellular stiffness increased in VGP but decreased in MET cells. The findings suggest that soft extracellular environments are more favourable for tumour growth, and high TBX3 levels mediate collective cell migration and tumour growth in the earlier VGP disease stage but play a lesser role in the later metastatic stage of melanoma. Symbols O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=184 SRC="FIGDIR/small/495509v4_ufig1.gif" ALT="Figure 1"> View larger version (42K): org.highwire.dtl.DTLVardef@1444cf4org.highwire.dtl.DTLVardef@118427eorg.highwire.dtl.DTLVardef@1b56a0aorg.highwire.dtl.DTLVardef@144d41f_HPS_FORMAT_FIGEXP M_FIG C_FIG

biophysics↗

bioRxiv2020

Traceback of Core Transcription Factors for Soybean Root Growth Maintenance under Water Deficit

Some crops inhibit shoot growth but maintain root growth under water-deficit conditions. Unraveling the molecular mechanisms of root plasticity under water deficit conditions in plants remains a major challenge. We developed an efficient platform for identifying core transcription factors (TFs) that collectively regulate each other and/or themselves in response to water stress, and exploring their interconnected regulatory circuitry involved in root growth maintenance under water deficit in soybean. We performed multi-species phylogenetic footprinting combined with spatial-temporal transcriptome analysis of soybean (Glycine max) roots under water deficit to identify conserved motifs that function in the water-stress response. Using these functional conserved cis-motifs, we applied a new approach to trace back motifs-associated core TFs ingroup as signal mediators, which mediate signaling between abiotic and endogenous stimuli. We integrated a co-functional TF-TF network and conserved motif-centered TF-DNA networks to construct a core TF network defined by mutual cross-regulation among core TFs. We found that core TF ARG (Abscisic acid response element binding factor-like Root Growth regulator) represses BRG (Brassinosteroid enhanced expression-like Root Growth regulator) expression through binding to its promoter at a conserved binding site. ARG and BRG antagonistically regulate Phytochrome-interacting factor-like Root Growth regulator (PRG) and combinatorially regulate some other core TFs. These core TFs form complex regulatory circuits to integrate light and multiple hormone signaling pathways and maintain root growth in response to varying degrees of water stress. Our study provides valuable information to unravel the complicated mechanisms of molecular networks involved in the regulation of root growth under water deficit.

plant biology↗

bioRxiv2020

Cytoskeletal Tubulin Competes with Actin to Increase Deformability of Metastatic Melanoma Cells

The formation of membrane protrusions during migration is reliant upon the cells cytoskeletal structure and stiffness. It has been reported that actin disruption blocks protrusions and decreases cell stiffness whereas microtubule disruption blocks protrusion but increases stiffness in several cell types. In melanoma, cell migration is of concern as this cancer spreads unusually rapidly during early tumour development. The aim of this study was to characterise motility, structural properties and stiffness of human melanoma cells at radial growth phase (RGP), vertical growth phase (VGP), and metastatic stage (MET) in two-dimensional in vitro environments. Wound assays, western blotting and mitochondrial particle tracking were used to assess cell migration, cytoskeletal content and intracellular fluidity. Our results indicate that cell motility increase with increasing disease stage. Despite their different motility, RGP and VGP cells exhibit similar fluidity, actin and tubulin levels. MET cells, however, display increased fluidity which was associated with increased actin and tubulin content. Our findings demonstrate an interplay between actin and microtubule activity and their role in increasing motility of cells while minimizing cell stiffness at advanced disease stage. In earlier disease stages, cell stiffness may however not serve as an indicator of migratory capabilities.

cancer biology↗