Biology subjects

Paul, M.

Publications and source records attributed to Paul, M..

At least 19 recordsLinked to original sources

bioRxiv2026

Single-cell multi-omics identify OTP and NOVA1 as regulators of leptin action in hypothalamic feeding circuits

Leptin acts directly and indirectly on multiple neuronal populations to regulate feeding and numerous other physiologic functions. However, our understanding of how a single circulating signal coordinates diverse neuronal populations across multiple circuits is limited. To further elucidate how leptin reshapes molecular states in its direct and indirect neural targets, we combined time-resolved single-nucleus transcriptomics and chromatin accessibility profiling to map leptin-induced transcriptional and chromatin state changes across individual neurons in two key hypothalamic nuclei: the arcuate nucleus (ARC), which contains the majority of leptin receptor (LepR) neurons, and the paraventricular hypothalamic nucleus (PVH), an established downstream target of ARC LepR neurons. We found that leptin treatment of leptin-deficient ob/ob mice does not alter neuronal identity, but instead induces coordinated, cell-type-specific transcriptional and regulatory state changes that propagate hierarchically from the ARC to downstream PVH neurons. Integrating RNA velocity, cis-regulatory analysis, and cell-cell communication inference revealed that leptin modulates hypothalamic circuit architecture by selectively strengthening specific interactions while pruning broadly distributed, low-specificity signaling. Although leptin broadly activated STAT3 signaling across LepR neuronal subtypes, integrated multi-omic analyses revealed that activation of STAT3 engages distinct downstream regulatory programs in different neuronal populations, often with opposing physiological functions. Functional analyses identified the homeobox transcription factor OTP, a leptin-responsive regulator selectively induced in AGRP neurons, as a critical mediator of leptin-mediated inhibition of hunger-promoting AGRP neuronal activity and feeding. In parallel, unbiased analysis of PVH neuronal state transitions shows that NOVA1, an RNA-binding protein primarily expressed in inhibitory neurons, is regulated by leptin and alterations of NOVA1 expression bidirectionally control food intake and body weight. Together, these findings define a multi-layered regulatory framework through which leptin regulates hypothalamic feeding circuits to control energy balance.

neuroscience↗

bioRxiv2026

Radiotherapy-induced vascular dysfunction alters neutrophil phenotype to promote tumor cell colonization of mammary adipose tissue

Recurrence remains a significant clinical challenge for triple-negative breast cancer patients and radiotherapy (RT) is a key therapeutic tool that significantly reduces the risk of relapse. Despite this, patients with chronic lymphopenia and a high neutrophil:lymphocyte ratio (NLR) experience recurrence at significantly higher rates than those whose hematological biomarkers return to baseline post-RT, and there are currently no treatments to prevent this relapse. Here, we utilized in vivo mouse models of lymphocyte-deficiency to identify the mechanism behind systemic immune status and recurrence. Using a model of RT-induced circulating tumor cell (CTC) colonization, we found that neutrophils are sustained in the irradiated, lymphocyte-deficient mammary tissue up to 10 days post-RT. Persistent neutrophil accumulation was accompanied by excessive vascular remodeling and tumor cell colonization of the mammary tissue, both of which were abated upon systemic neutrophil depletion. Neutrophils in the colonization-permissive microenvironment exhibited a state of pathological activation consistent with a polymorphonuclear myeloid-derived suppressor cell (PMN-MDSC) phenotype that was not seen in systemic compartments, highlighting a microenvironment-induced phenotype shift. This phenotype was recapitulated in vitro when naive neutrophils were exposed to the secretome of RT-induced senescent endothelial cells (ECs). We found that these activated neutrophils then regulated the dysfunction of irradiated ECs in a canonical NF-kB-dependent manner, increasing their barrier permeability and activating downstream inflammatory signals. Our findings not only establish neutrophils as a critical component of tumor cell colonization in lymphocyte-deficient subjects but also uncover a positive feedback loop between neutrophils and irradiated vasculature that leads to aberrant tissue remodeling and ultimately tumor cell colonization. This work deepens our understanding of how systemic factors influence treatment-damaged microenvironments, which could ultimately lead to identification of molecular targets for prevention of RT failure.

cancer biology↗

bioRxiv2026

HR-FRGS: A Novel Biomarker Discovery Protocol using Dual Layer Hypergraph Learning for NGS RNA Sequence Data

Biomarker discovery from high-dimensional RNA sequencing data remains challenging. Conventional methods such as differential expression analysis, pairwise protein-protein interaction networks, and weighted gene co-expression network analysis suffer from false-positive interactions, transitivity-driven noise, and arbitrary thresholds for feature selection. Addressing these limitations, this study proposed a novel framework, Hypergraph Regularised Fuzzy Rough Gene Selection (HR-FRGS), for knowledge-driven biomarker discovery. This pipeline integrates information-rich protein clustering with entropy filtering and PPI-pruned co-expression interactions to form a dual-layer hypergraph. A hypergraph-based scoring method that combines Random Walk with Restart diffusion and Hypergraph Betweenness Centrality is used to identify genes that are central in the biological network. Furthermore an autonomous fuzzy rough set selection eliminates arbitrary threshold dependency for gene selection. HR-FRGS was applied to four TCGA cancer cohorts: Lung Adenocarcinoma, Head and Neck Cancer, Kidney Clear Cell Carcinoma, and Colon Cancer, which reduced over 60,000 transcripts to compact biomarker panels. Validation using classical Machine Learning algorithms with cross-validation demonstrated that biomarker panels matched or exceeded the classification performance of the full transcriptome (AUC > 0.99, MCC > 0.94) and confirmed generalizability (MCC $\geq$ 0.893). Benchmarking against baseline methods and an ablation study showed the contribution of major parts of the algorithm. Functional enrichment analysis captures established pan-cancer hallmarks and cohort-specific oncogenic mechanisms, confirming the biological relevance of the identified genes.

bioinformatics↗

bioRxiv2026

A mammary-specific microfluidic device for studying post-radiotherapy vascular-immune cell interactions

Radiotherapy (RT) significantly improves outcomes and reduces the risk of recurrence in breast cancer. However, in patients that experience recurrence despite treatment, the irradiated breast tissue may create a pre-metastatic niche that promotes tumor cell infiltration. Because current models of metastasis lack key physiological and microenvironmental cues, we developed a mammary vasculature-on-chip (MVoC) to model how the vasculature responds to RT and impacts immune and tumor cell behavior in mammary tissue. Murine and human MVoCs incorporated endothelial cells (ECs) cultured under physiologic shear stress and mammary-specific fibroblasts to mimic the vascular-fibrous stroma interface. MVoCs exhibited a transient, acute response to RT that led to a persistent phenotypic shift. Neutrophils, which play key roles in pre-metastatic niche formation, adhered more to irradiated ECs and induced persistent damage to the endothelial barrier, preventing recovery. Neutrophils also significantly increased tumor cell adhesion to the endothelium in MVoCs. These findings demonstrate that MVoCs can be used to study RT-induced pre-metastatic niche formation and suggest a positive feedback loop between damaged ECs and immune cell activation that may facilitate tumor cell colonization. MVoCs provide a biologically relevant approach to probe molecular and cellular interactions, improving translation toward developing novel therapies that improve patient outcomes.

cancer biology↗

bioRxiv2026

Identification of novel HDAC11 inhibitors: In silico & in vitro studies

Histone deacetylases (HDACs) are pivotal epigenetic regulators that modulate diverse cellular pathways by removing acetyl groups from lysine residues on both histone and non-histone proteins. Histone deacetylase 11 (HDAC11), the sole member of class IV HDACs, exhibits both deacetylation and fatty acid deacylation activities. Accumulating evidence implicates HDAC11 as a key epigenetic regulator of fundamental cellular processes, including metabolism, immune responses, and tissue development. Dysregulation of HDAC11 activity has been associated with inflammatory diseases, metabolic disorders, neurodegenerative conditions, and cancer, highlighting its potential as a therapeutic target. Although several HDAC11-specific inhibitors have been identified, none have progressed to clinical development. In this study, we aimed to discover HDAC11-selective inhibitors by integrating in silico and in vitro validation approaches. Homology modelling of the HDAC11 structure was conducted, followed by model validation, structure-based virtual screening, molecular dynamics (MD) simulations, and binding free energy calculations. We identified and validated three lead compounds and their intermediates using biochemical and cell-based assays. Fluorescence-based and HPLC-based enzymatic assays demonstrated potent inhibition of both the deacetylase and deacylase activities of HDAC11, with Inhibitor 6 and Inhibitor 3 exhibiting the strongest effects among the six compounds tested. Further, a decrease in lipid accumulation, reduced stability of the HDAC11 substrate SHMT2, as determined by immunoblot analysis and decreased cell viability, as assessed by MTT assay, confirmed HDAC11 inhibition in cellular models. The study shows that new HDAC11 inhibitors significantly reduce the viability of breast cancer cells and induce apoptosis; inhibitor 6, in particular, showed high potency, similar to the reference compound SIS-17. Flow cytometry showed that treated MDA-MB-231 cells exhibited cell-cycle arrest and increased apoptosis, a finding further confirmed by Annexin V/PI staining. Molecular analysis showed that BAX increased while BCL2 decreased, indicating that apoptotic pathways were activated in novel compound-treated MDA-MB-231 cells. The results suggest that inhibiting HDAC11 is an effective way to induce cancer cell death and provide a basis for further assessment of these compounds as potential treatments for breast cancer. Collectively, this study identifies novel zinc-chelating HDAC11 inhibitors containing a nitro-sp2 group, providing promising candidates for further therapeutic development.

bioinformatics↗

bioRxiv2026

SEPALLATA MADS transcription factors act as key regulators in fertilization efficiency, ovule outer integument growth and mucilage secretory cell differentiation in Arabidopsis

In angiosperms, ovule development requires the activity of the C, D and E classes of MADS genes, which encode key transcriptional regulators of reproductive development. The SEPALLATA (SEP) MADS transcription factors (MTFs), which belong to the E class, act as organizing hubs of MADS heterotetrameric complexes and play an essential role in the development of flower organs. However, the role of the SEP genes in ovule and seed development has been difficult to determine due to redundancy in the subclade, the lack of observable phenotypes in single and double sep1 sep2 mutants and the homeotic conversion of the carpel into sepal or leaf in higher order sep mutants. Here, we engineered a version of SEP3 (SEP3{Delta}M) that encodes a protein lacking the DNA-binding MADS-domain but retains the oligomerization domains needed for MADS protein heterotetramerization. In vitro experiments demonstrated the ability of SEP3{Delta}M to interact with the C and D classes of MTF, reducing the capability of such MADS complex to efficiently bind DNA. sep3{Delta}M plants showed a delay in flower opening and organ maturation and a reduced fertility. The ovules exhibited reduced outer integument growth, and the few seeds that developed showed impaired mucilage secretion upon imbibition. RNA-seq analysis of sep3{Delta}M demonstrated misregulation of genes involved in outer integument and seed coat development. Taken together, these data indicate the key role of SEP3-containing MADS complexes in proper ovule outer integument growth and seed coat development.

plant biology↗

bioRxiv2026

Pdgfrβ signaling orchestrates meningeal repair via the mobilization of arachnoid cells.

Zebrafish possess remarkable regeneration abilities, including the capacity to repair their central nervous system (CNS). Leveraging the optical accessibility of the zebrafish brain, we investigated the mechanisms underlying meningeal repair following laser-induced brain injuries to the optic tectum. In previous work, using live imaging of laser-induced surface injuries to the optic tectum in juvenile zebrafish, we identified a population of flat PDGFR{beta}+ cells that rapidly migrate to the wound site and contribute to meningeal repair. Here, using pharmacological inhibition or genetic perturbation of PDGFR{beta}, we show that recruitment of these PDGFR{beta}+ meningeal cells is strongly dependent on PDGFR{beta} signaling, unlike recruitment of PDGFR{beta}+ pericytes deeper in the wound. Furthermore, PDGFR{beta} inhibition diminishes neurite regrowth and macrophage recruitment. Using photoconversion assays, we traced the origin of PDGFR{beta}+ meningeal cells that migrated to the wound in response to injury, in the midbrain-forebrain and midbrain-hindbrain sulci. Our findings highlight PDGFR{beta}s pivotal role in orchestrating meningeal repair and reveal novel cellular dynamics during CNS regeneration. These results provide insights into potential therapeutic strategies for enhancing brain repair and mitigating fibrosis in mammals, where meningeal scarring remains a barrier to CNS regeneration. HighlightsPDGFR{beta} signaling orchestrates the rapid accumulation of meningeal cells at CNS injury sites to drive tissue remodeling. PDGFR activity acts as a critical regulator, co-recruiting PDGFR{beta}+ meningeal cells and mfap4+ macrophages to the lesion. Meningeal cells are essential for neural repair, with PDGFR inhibition leading to significantly reduced neurite density. Zebrafish maintain locomotor resilience post-injury, identifying a clear distinction between meningeal-driven axonal regrowth and basic motor circuitry recovery. Establishes a high-resolution zebrafish platform to identify conserved meningeal targets for mammalian CNS regeneration.

cell biology↗

bioRxiv2026

Leaves in Transition: Single nuclei RNA sequencing provides insights into sorghums juvenile and adult phases

The transition from juvenile to adult phase (JA) is a key developmental process in plants, driven by conserved pathways that shape growth and stress responses. In monocots such as sorghum, this transition influences traits linked to environmental resilience, yet the regulation of micro-anatomical features such as trichomes and bulliform cells remains poorly understood. Here, we use single-nucleus RNA sequencing (snRNA-seq) to generate high-resolution gene expression maps of juvenile and adult sorghum leaves. Contrary to the traditional developmental model, we find that trichomes are present in both juvenile and adult leaves, with stage-dependent differences in gene expression. We also observe that bulliform cells, typically considered adult-specific, are present in juvenile leaves. At the transcriptomic level, cell populations cluster more strongly by developmental stage than by cell type, with juvenile cells grouping with other juvenile cells and adult cells with adult counterparts, indicating a dominant effect of developmental state on gene expression. In addition, we identify enrichment of dhurrin biosynthetic genes in trichome-associated cells as well as elevated expression of aquaporin genes in these cells, pointing to a potential role for trichomes in coordinating defense and water-related processes. Together, these findings refine current models of sorghum development and suggest that key epidermal cells and their associated functions may be established earlier than previously known. Collectively, this study provides a single nucleus resolved framework for understanding how developmental stage shapes gene expression in sorghum leaves.

plant biology↗

bioRxiv2026

Dissecting the interactions of the ISG15-USP18-STAT2 inhibitory complex

The suppression of type I interferon (IFN) signalling by the ISG15-USP18-STAT2 inhibitory complex (ISG15 IC) is an established regulatory mechanism of the antiviral response. However, a molecular understanding of how the ISG15 IC forms to suppress IFN signalling is still emerging. Here, we use AlphaFold modelling in conjunction with biochemical and biophysical approaches to elucidate the interactions of this multiprotein assembly. Our analysis identified a unique STAT2 binding loop (SBL) in USP18, which is critical for the USP18-STAT2 association. Further biochemical characterisation through site-directed mutagenesis confirmed the importance of residues within and surrounding the SBL, enabling the design of mutants with both increased and decreased binding affinities. Moreover, several USP18 and STAT2 patient mutations severely disrupted this interaction. Lastly, using influenza B virus (IBV) and Zika virus (ZIKV) proteins, we investigated the influence of these viral effector proteins on these interactions. Taken together, these results provide much-needed insights into a key aspect of IFN signalling control.

biochemistry↗

bioRxiv2026

A combinatorial EVs-miRNA signature mediates the anti-tumoral activity of NFAT3-regulated extracellular vesicles in aggressive cancers.

Aggressive cancers such as triple-negative breast cancer (TNBC) and pancreatic cancer remain difficult to treat because their malignant behavior is driven by complex gene networks rather than single oncogenic targets. Here, we identify an extracellular vesicle (EV)-associated miRNA signature functionally linked to NFAT3 activity and demonstrate its ability to suppress tumor aggressiveness. Functional analyses revealed that a combination of fifteen miRNAs (miR-Comb 15) was required to fully reproduce the anti-tumoral effects of NFAT3-regulated EVs across TNBC and pancreatic cancer models, whereas individual miRNAs showed only partial activity. These effects were associated with coordinated regulation of validated target genes controlling proliferation and invasion, supporting a network-modulating mechanism of action. To facilitate therapeutic translation, we used EVs derived from HEK 293T cells, a non-tumoral, scalable, and readily engineerable EV source. Using an optimized exogenous pH-gradient loading strategy, miR-Comb 15 was efficiently incorporated into EVs without affecting vesicle integrity or intrinsic bioactivity. HEK 293T EVs loaded with miR-Comb 15 consistently showed the strongest anti-tumoral activity in vitro and in vivo among the delivery platforms evaluated. Together, these findings identify a functional NFAT3-dependent EV-miRNA program and support EV-mediated delivery of combinatorial miRNA therapeutics as a promising strategy for aggressive cancers.

cancer biology↗

bioRxiv2025

Pitavastatin counteracts venetoclax resistance mechanisms in acute myeloid leukemia

The BCL2 inhibitor venetoclax has therapeutic activity in several hematological malignancies. In acute myeloid leukemia (AML), venetoclax combined with hypomethylating agents is the standard of care for patients unfit for intensive chemotherapy, but intrinsic and acquired resistance are common. Loss of p53 function is strongly associated with venetoclax resistance, and adding venetoclax to 5-azacitidine provides no overall survival benefit in TP53-mutant AML. Other frequent mechanisms of venetoclax resistance in AML include FLT3 mutations, MCL-1 upregulation, and altered mitochondrial metabolism. Unfortunately, it has been challenging to develop agents that target these mechanisms directly and combinatorially. Here we report that pitavastatin, an inhibitor of HMG-CoA-reductase, promotes apoptosis and overcomes several venetoclax resistance mechanisms in human AML cells. At clinically achievable concentrations, pitavastatin treatment has potent cytotoxic activity in cells with mutations in TP53 or FLT3. The apoptotic mechanism involves p53-independent PUMA upregulation and reduced MCL-1 expression. Pitavastatin also suppresses mitochondrial gene expression and oxidative metabolism. The pro-apoptotic actions of pitavastatin depend on depletion of geranylgeranyl pyrophosphate (GGPP) and can be recapitulated by inhibiting GGPP synthase or geranylgeranyltransferase-1 enzymes. These results provide a mechanistic rationale for adding pitavastatin to AML regimens to prevent or overcome venetoclax resistance.

cancer biology↗

bioRxiv2025

Preservation and Clonal Behavior of Extrachromosomal DNA in Patient-Derived Xenograft Models of Childhood Cancers

Extrachromosomal DNA (ecDNA) is a powerful oncogenic driver linked to poor prognosis in pediatric cancers. Whole-genome sequencing of 338 patient-derived xenograft (PDX) samples and 127 matched primary tumors across multiple childhood cancer types was used to compare ecDNA prevalence, sequence conservation, and clonal dynamics. ecDNA in PDX models frequently mirrored oncogene amplifications observed in patient tumors (e.g., MYCN, MYC, MDM2) and showed high sequence conservation. Medulloblastoma and neuroblastoma PDXs exhibited significantly higher ecDNA prevalence, consistent with strong selection or de novo formation during tumor propagation. Although ecDNA copy numbers were generally preserved, some neuroblastoma PDXs displayed marked MYCN copy gains. Single-cell multiome profiling revealed that ecDNA-positive clones either persisted or expanded dramatically in PDXs, in one case growing from a minor subpopulation to nearly all tumor cells. These findings establish PDX models as valuable systems for ecDNA research and underscore the selective growth advantage conferred by ecDNA during tumor evolution.

genomics↗

bioRxiv2025

Non-catalytic and catalytic TREHALOSE-6-PHOSPHATE SYNTHASES interact with RAMOSA3 to control maize development.

Trehalose-6-phosphate (Tre6P) is the intermediate in the two-step pathway of trehalose biosynthesis mediated by Tre6P-synthases (TPSs) and Tre6P-phosphatases (TPPs). Plants harbor small families of TPS and TPP genes, however most plant TPSs lack enzymatic activity, suggesting they have regulatory functions. The classical mutant ramosa3 (ra3) increases inflorescence branching in maize, and RA3 encodes a catalytic TPP. We found that RA3 interacts with maize ZmTPS1, a non-catalytic TPS. Mutants in ZmTPS1 and its close paralog ZmTPS12 enhance ra3 phenotypes, suggesting their physical interaction is biologically significant. ZmTPS1 also interacts with the two catalytically active maize TPSs, ZmTPS11 and ZmTPS14, however zmtps11;zmtps14 double mutants fail to complete embryogenesis, suggesting that they are essential, as in arabidopsis. Interestingly, the non-catalytic ZmTPS1 protein stimulated the coupled activity of RA3 and ZmTPS14, suggesting that RA3, ZmTPS1, and ZmTPS14 form a complex, and we confirmed this by expressing and purifying the three proteins and by Alphafold predictions. Our results suggest that non-catalytic TPSs form a complex with catalytic TPSs and TPPs to stimulate catalytic activity and regulate plant development.

plant biology↗

bioRxiv2025

Conserved inter-domain interactions drive trans-Golgi network localisation and trafficking of homologous copper-ATPases

Polytopic transmembrane Copper-ATPases are central regulators of the essential, redox-active micronutrient copper in all organisms. The vertebrate Cu-ATPase homologs ATP7A and ATP7B facilitate excess copper efflux, in addition to metalating cuproproteins. ATP7A and ATP7B exhibit copper-responsive basolateral and apical trafficking polarity respectively, in polarized epithelia. To elucidate the role of conserved functional domains in copper-responsive trafficking and copper transport, we substituted the copper-binding amino-terminal, Nucleotide-Binding (NBD) and C-terminal domain of ATP7B with that of ATP7A either singly or in combinations. The six chimeric Cu-ATPases generated, although functionally active, exhibited altered trafficking phenotypes. Notably, the N-terminal-substituted ATP7B exhibited constitutive trafficking to the basolateral membrane; however, the N-terminal and NBD double-substituted chimera gained steady-state TGN localization, indicating a putative interaction between the two domains critical for its TGN-localization. We analyzed orthologous Cu-ATPase domain sequences from diverse organisms and found that the N-terminal domain and NBD showed similar evolutionary relationships, unlike that of C-terminal domain, suggesting their co-evolution. This study for the first time correlates evolutionary stringency imparted onto Cu-ATPase domains with their significance in proper trafficking regulation.

cell biology↗

bioRxiv2025

Highly pathogenic avian influenza management in high-density poultry farming areas

The continuous spread of highly pathogenic avian influenza H5 viruses poses significant challenges, particularly in regions with high poultry farm densities where conventional control measures are less effective. Using phylogeographic and phylodynamic tools, we analysed virus spread in Southwestern France in 2020-21, a region with recurrent outbreaks. Following a single introduction, the virus spread regionally, mostly affecting duck farms, peaking in mid-December with a velocity of 27.8 km/week and an effective reproduction number between farms (Re) of 3.8, suggesting the virus can spread beyond current control radii. Transmission declined after late December following preventive culling. Farm infectiousness was estimated around 9 days. Duck farm density was the main driver of virus spread and we identified farm density and proximity thresholds required to maintain effective control (Re < 1). These findings offer actionable guidance to support regional biosecurity and to improve the robustness of the poultry sector to mitigate future outbreaks.

evolutionary biology↗

bioRxiv2024

Universal Study Design for Instrument Changes in Pharmaceutical Release Analytics

Instrument changes in analytical methods of pharmaceutical quality control are required to maintain release analytics over decades, yet typically pose a challenge. We designed an efficient instrument comparability study to gain a comprehensive understanding of potential performance differences between instruments and therefore rationalize the risk assessment and decision process for a path forward. The results may either point out whether a full or partial re-validation is necessary or whether a science-based bridging can be pursued based on the data generated in the study. The study design is universally applicable to a substantial range of release analytical methods. In a straightforward setup of two experiments with the new instrument, a statistically meaningful data set is generated for comparison with available historical or validation data of the original instrument. In a Good Manufacturing Practice (GMP) environment, we realized the study design a first benchmark in imaged capillary isoelectric focusing (icIEF) analytics, comparing the ICE3 and Maurice C instruments. The core-study confirmed equal or better performance of Maurice C in all parameters and serves as a basis for seamless continuation of release measurements on Maurice C.

biochemistry↗

bioRxiv2024

The two crystal structures of unloaded and cargo-loaded Vacuolar Sorting Receptor 1 lumenal domain (VSR1-Nt) reveal two cargo binding sites and a mechanism of transport.

Vacuolar sorting receptors (VSRs) are type I membrane proteins crucial for seed germination and plant development. While VSR trafficking has been extensively studied, the mechanism of cargo binding and release by the N-terminal lumenal region is less understood. We have elucidated the crystal structures of unloaded and cargo-loaded forms of the lumenal region of VSR1 containing the protease-associated domain, the Central domain and epidermal growth factor-like repeats. Calcium coordination induces remodeling of the linkers between domains, triggering large conformational changes that expose two binding sites, one across the PA and Central domain and a second site in the Central domain. Our findings provide a mechanistic model for cargo binding in a calcium rich environment, where VSR is locked in a conformation exposing the cargo binding sites, while cargo release is favoured by lower calcium concentrations and trimer formation. These results advance our current knowledge on VSRs and will inform future studies on vacuolar trafficking and cargo binding/release.

plant biology↗

bioRxiv2024

ecPath detects ecDNA in tumors from histopathology images

Circular extrachromosomal DNA (ecDNA) can drive tumor initiation, progression and resistance in some of the most aggressive cancers and is emerging as a promising anti-cancer target. However, detection currently requires costly whole-genome sequencing (WGS) or labor-intensive cytogenetic or FISH imaging, limiting its application in routine clinical diagnosis. To overcome this, we developed ecPath (ecDNA from histopathology), a computational method for predicting ecDNA status from routinely available hematoxylin and eosin (H&E) images. ecPath implements a deep-learning method we call transcriptomics-guided learning, which utilizes both transcriptomics and H&E images during the training phase to enable successful ecDNA prediction from H&E images alone, a task not achievable with models trained on H&E images only. It is trained on more than 6,000 tumor whole-slide images from the TCGA cohort with the best performance in predicting ecDNA status in brain and stomach tumors (average AUC=0.78). ecPath revealed that ecDNA-positive tumors are enriched with pleomorphic, larger and high-density nuclei. Testing in an independent cohort, ecPath predicted ecDNA status of 985 pediatric brain tumor patients with an AUC of 0.72. Finally, we applied ecPath to identify ecDNA-positive tumors in the TCGA cohort for which no WGS data were available. Like WGS-based ecDNA-positive labels, the predicted ecDNA-positive status also identify poor prognoses for low grade glioma patients. These results demonstrate that ecPath enables the detection of ecDNA from routinely available H&E imaging alone and help nominate aggressive tumors with ecDNA to study and target it.

pathology↗