Biology subjects

Durand, S.

Publications and source records attributed to Durand, S..

At least 19 recordsLinked to original sources

bioRxiv2026

Effects of panitumumab on the proteome of treated EGFRvIII glioblastoma cells and on their extracellular vesicles

Glioblastoma (GB) is an aggressive brain tumor for which reliable biomarkers of therapeutic response are still needed. Extracellular vesicles (EVs) can carry molecular components derived from their parent cells, thereby providing information on changes associated with the tumor and treatments. Among potential biomarkers, epidermal growth factor receptor variant III (EGFRvIII), is found in more than 40% of GB patients and is associated with aggressive tumor behavior and therapeutic resistance. EGFRvIII has also been detected on the surface of EVs, suggesting its potential value for monitoring tumor-associated molecular changes. This study investigated the effects of panitumumab, an anti-EGFR monoclonal antibody, on the proteomic profiles of EVs derived from EGFRvIII cells. U87 and U87-EGFRvIII cells and their derived EVs were characterized before and after treatment. EGFRvIII expression in cells and EVs was assessed by Western blotting and flow cytometry. Proteomic analyses were performed on cell lysates and EVs before and after treatment. Our results demonstrate that panitumumab significantly reduced surface EGFRvIII on EVs derived from U87-EGFRvIII cells, whereas no significant decrease was observed in cell lysates. This suggests that treatment may affect EGFRvIII trafficking or its incorporation into EVs. The proteomic analysis highlighted much more changes in EVs than in their parental cells after treatment, particularly in proteins associated with extracellular matrix organization and collagen. Together, these results demonstrate that panitumumab treatment is associated with changes in protein profile from EVs derived from EGFRvIII cells suggesting that the panitumumab treatment might have an impact on cells that could be reflected on EVs released by glioblastoma cells. In conclusion, our results suggest that EVs derived from EGFRvIII cells could serve as a useful circulating biomarker for assessing treatment efficacy and for preventing treatment escape.

cancer biology↗

bioRxiv2026

Moving object generates topographic responses in the majority of entorhinal neurons

Vision is crucial in generating a complex array of responses in rodents during spatial exploration and in humans during memory tasks. These tasks involve other variables too, e.g. multisensory cues in rodents and complex memories in humans. Further, there are major differences between the medial and lateral entorhinal cortical (MEC and LEC) functional cell types. To understand the contribution of purely visual information to entorhinal responses, we presented a simple, moving vertical bar of light to head-fixed mice, without any task or reward. Surprisingly, 66% (2391/3601) of the MEC broad spiking neurons were significantly modulated by the bar position on the screen. Visual tuning in MEC had a pronounced dorsoventral topography --the tuning strength dropped from 79% in the dorsal most quartile to 40% in the ventral most quartile. Unlike major differences in spatial and other codes between MEC and LEC during free foraging experiments, LEC cells showed very similar visual tuning (392/606, 65%), including the dorso-ventral gradient in LEC5. Additionally, the majority of putative interneurons, from MEC as well as LEC, showed similar, widespread visual tuning, unlike spatial tasks. Neurons also encoded the object motion direction (naso-temporal vs. temporo-nasal visual motion) with changes in mean rate, tuning strength and/or tuning location. Such directional nature of visual tuning indicates significant history-dependence or sequence encoding. Consistently, replacing the continuous motion by randomly flashing bar of light abolished bar-tuning in two-thirds of continuous bar-tuned cells and substantially altered tuning in the rest. These results reveal the contribution of purely visual inputs in generating anatomically organized responses in the majority of entorhinal neurons. The prevalence and similarity of visual tuning across all layers of MEC as well as LEC exceeds that of other known functional cell types (like grid cells in MEC or egocentric object tuning/time-cells in LEC) during spatial navigation tasks and could be foundational in understanding entorhinal complexity.

neuroscience↗

bioRxiv2026

Bone regulates locomotion by sustaining motoneuronal mitochondrial function

Body-brain communication is crucial for optimal neuronal performance across the lifespan, yet whether peripheral organs regulate spinal cord motoneuron (MN) function through circulating molecules remains unknown. The expression of hormone receptors by spinal MNs raises the possibility that circulating cues allow the spinal cord to sense the body's energetic state and sustain motor activity. Here, we show that the bone-derived hormones osteocalcin (OCN) signals on spinal MNs via its receptor GPR158. GPR158 is selectively enriched in spinal cholinergic MNs, and its loss, globally or specifically in spinal MNs, or the one of OCN, impairs locomotor function and reduces choline acetyltransferase (ChAT) levels. Mechanistically, OCN signaling through GPR158 fine-tunes autophagy, mitophagy and mitochondrial activity in spinal MNs. Restoring any of these processes, by pharmacologically inducing mitophagy or chemogenetically activating mitochondria, is sufficient to rescue the locomotor deficits of Gpr158-deficient mice. Finally, OCN restoration in aged mice reverses age-related locomotor decline through a mechanism that requires MN autophagy and mitophagy. This study reveals that through OCN, the skeleton influences motor functions by fine-tuning motoneuronal mitochondria, and suggests that age-related motor decline is, at least in part, reversible.

neuroscience↗

bioRxiv2026

Glycometabolic, inflammatory and exocrine plasma proteins predict cancer in individuals with cardiovascular disease

Cancer development is preceded by systemic immune, metabolic and tissue perturbation. We asked whether a minimal circulating-protein signature anticipates incident cancer in patients with atheromatous cardiovascular disease (ACVD) exposed to tobacco. Discovery used a nested case-control set drawn from the longitudinal FLEMENGHO cohort (n=156; 38 incident lung cancers). Multi-omic profiling returned a two-step classifier: four proteins, smoking status, personal cancer history. Preprocessing constants, classifiers and both thresholds were fixed before transfer to PREVALUNG (n=397; 58 incident cancers, 26 of them lung). There, low O-GlcNAcase (OGA) with low interleukin-6 (IL-6) defined a very-low-risk stratum holding 1 of 58 cancers (sensitivity 98.3%, negative predictive value 98.8%); low chymotrypsin C (CTRC) with high beta microseminoprotein (MSMB) defined a high-risk stratum in which 15 of 28 participants developed cancer. No additional omic feature (metabolomic, immunophenotypic, clonal-haematopoietic or metagenomic) was retained as a reproducible improvement to the classifier under our selection framework. Discrimination was greater for cancers diagnosed more than 12 months after sampling than for near-term cancers (AUC 0.766, 95% CI 0.671-0.857, versus 0.589, 0.485-0.692), arguing against performance being driven principally by occult disease. These estimates are conditional on the cancer frequency of this population. They require prospective confirmation before any imaging schedule is changed.

cancer biology↗

bioRxiv2026

Psilocybin collapses visual change detection and drives cortical dynamics toward a state of surprise

Psilocybin profoundly alters visual perception, yet the neuronal mechanisms underlying these effects remain unclear. Here we combined large-scale Neuropixels recordings with cell-type specific optogenetics in head-fixed mice performing a visual change-detection task. Psilocybin severely impaired task performance without overt motor deficits. In cortex, the drug modestly suppressed activity of layer 5 neurons while preserving representations of image identity. By contrast, psilocybin imposed a 4-Hz oscillation on visually evoked activity that preferentially affected neurons encoding image change rather than image identity. Under psilocybin, expected image repetitions aberrantly recruited change-encoding ensembles and shifted cortical population dynamics towards trajectories normally evoked by genuine stimulus changes. These effects were strongest in somatostatin-expressing (SST) interneurons in visual cortex. The strength of this modulation depended on image structure and was greatest for images with clear, continuous contours, which preferentially recruited change-encoding ensembles. These findings demonstrate that psilocybin drives internally generated cortical surprise signals, providing a circuit mechanism for altered perception in the acute psychedelic state.

neuroscience↗

bioRxiv2026

RNase J2 is a specificity factor that governs global mRNA stability in Bacillus subtilis

Ribonucleases (RNases) play a key role in modulating gene expression at the post-transcriptional level, enabling bacteria to rapidly adapt to their environment. The B. subtilis genome encodes more than 20 RNases and understanding the role of each of these enzymes is crucial for a comprehensive knowledge of bacterial post-transcriptional adaptation mechanisms. Among these, RNase J1 and J2, belonging to the {beta}-lactamase enzyme family, form a heterodimer. While the primary function of RNase J1 as a 5'-exoribonuclease in B. subtilis has been known for some time, the role of RNase J2, encoded by the rnjB gene, has remained unclear. Indeed, it has been considered a minor degradation factor due its very weak 5'-exoribonuclease in vitro, the lack of a growth phenotype and the limited number of mRNAs with altered equilibrium levels in rnjB mutants. In this study, we demonstrate that the absence of RNase J2 influences pellicle and macro-colony biofilm formation, as well as swarming in B. subtilis. We show that RNase J2 plays a far more global role in governing mRNA half-lives than originally thought, by stimulating RNase J1-mediated degradation of a subset of RNase J1's mRNA substrates. An inter-subunit contact between RNase J1 and J2 is crucial for RNase J2 action. Altogether, our results suggest that RNase J2 acts primarily as a specificity co-factor for RNase J1 rather than as a ribonuclease per se.

microbiology↗

bioRxiv2026

CYCLON is a nucleolar protein that regulates pan-cancer cell fitness through ribosome biogenesis

Tumor progression is driven by cancer cell fitness, defined as the capacity of malignant cells to maintain growth, adapt to stress and withstand therapy Cellular fitness is fundamentally governed by nucleolar processes, which act as central regulators by integrating RNA processing with ribosome biogenesis to support protein synthesis and stress adaptation. The nuclear protein CYCLON, containing a large intrinsically disordered region (IDR) could be implicated in mediating biomolecular condensates and regulatory plasticity, which are key elements of nucleolar biology. CYCLON also emerged as a candidate regulator of cancer cell fitness, as it is frequently overexpressed across tumor types. Inducible silencing and cell biology approaches have shown that CYCLON maintains nucleolar integrity, controls nucleoli size and number, nucleolin and Ki-67 distribution and prevents nucleolar stress. CYCLON contributes to ribosome biogenesis by binding ribosomal RNA (rRNA) and regulating 32S and 21S pre-rRNA processing, ultimately influencing ribosomal subunit production and global protein synthesis. Its depletion impairs proliferation and clonogenic capacity by prolonging both interphase and mitosis, leading to slowed cell cycle progression. The impact of CYCLON on cellular fitness has been consistently observed across cancer models, reinforcing its essential role in the regulation of nucleolar biology.

cancer biology↗

bioRxiv2026

Combined inhibition of AIF/CHCHD4 interaction and GLS1 to exploit metabolic vulnerabilities in pediatric osteosarcoma

Osteosarcoma is a malignant bone tumor with a high risk of metastatic relapse and poor outcomes due to primary and acquired chemoresistance. This highlights the medical need to develop effective targeted approaches to overcome chemoresistance. Recent studies have revealed the roles of metabolic reprogramming and mitochondria-nucleus crosstalk in osteosarcoma progression, indicating the potential of these cellular processes as therapeutic targets. The complex formed by mitochondrial apoptosis-inducing factor (AIF) and coiled-coil-helix-coiled-coil-helix domain-containing protein 4 (CHCHD4) orchestrates the import and oxidative folding of cysteine-rich, nuclear-encoded proteins, thereby regulating key mitochondrial functions and metabolism. Here, we identified mitoxantrone as an inhibitor of the AIF/CHCHD4 mitochondrial import machinery and revealed a new mitoxantrone-induced metabolic vulnerability in some osteosarcoma cell line models, characterized by intracellular glutamine accumulation and an increase in nucleotide synthesis. As a result, synergy was found between mitoxantrone and the glutaminase inhibitor telaglenastat in both in vitro and in vivo osteosarcoma models. Collectively, our findings position the AIF/CHCHD4 complex as a druggable therapeutic target and provide a combination strategy for mitoxantrone/telaglenastat treatment to overcome metabolic adaptations and chemoresistance in osteosarcoma. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=126 SRC="FIGDIR/small/716303v1_ufig1.gif" ALT="Figure 1"> View larger version (22K): org.highwire.dtl.DTLVardef@1229e58org.highwire.dtl.DTLVardef@1c9af45org.highwire.dtl.DTLVardef@120d2borg.highwire.dtl.DTLVardef@11e8216_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2025

Translatome and translation dynamics analysis of a RiboCancer cell line panel reveals that leukemia-associated Rps15 mutations rewire translation through codon-specific tRNA accommodation defects.

Deletions and point mutations targeting ribosomal proteins (RPs) have been identified in cancer. Yet, their role in translational dysregulation remains poorly understood. We performed an integrated genome-wide translatome analysis (proteome, Ribo-seq and total RNA-seq) as well as RiboMethSeq on an isogenic cell line library modeling the most recurrent RP defects in cancer (Rpl5+/-, Rpl11+/-, Rpl22+/-, Rpl22-/-, Rpl10 R98S, Rps15 P131S and Rps15 H137Y). RP knock-out had minimal effects on translation, whereas RP point mutations induced a significant number of translation efficiency changes, affecting up to 10% of expressed genes in Rps15 mutants associated with Chronic Lymphocytic Leukemia (CLL). Cryo-electron microscopy and biochemical analyses revealed that the Rps15 mutations destabilize the C-terminal Rps15 domain, affecting the translation elongation cycle dynamics, and deregulating accommodation of aminoacylated tRNAs at the ribosomal A-site. Using Ribo-seq and translation reporter assays, we show that this accommodation defect shows codon specificity, explaining the reduced translation efficiency of genes enriched for these codons in Rps15 mutant cells, such as histones. Notably, genes with reduced translation efficiency in Rps15 mutated cells were enriched for transcriptional regulators such as transcription factor Runx3, resulting in downregulation of Runx3 target genes involved in immune regulation. Altogether, this study provides a comparative map of the translational rewiring driven by the most frequent somatic RP mutations. We provide unprecedented mechanistic insights in the translation defects induced by CLL-associated Rps15 mutations, and reveal an unappreciated cross-talk between translational and transcriptional dysregulation in these RP mutant cells. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=102 SRC="FIGDIR/small/687986v1_ufig1.gif" ALT="Figure 1"> View larger version (19K): org.highwire.dtl.DTLVardef@cd2846org.highwire.dtl.DTLVardef@10f3c49org.highwire.dtl.DTLVardef@13f1595org.highwire.dtl.DTLVardef@a212df_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

bioRxiv2025

Differential Immunomodulatory Properties of Langya and Nipah Virus Proteins

Langya virus (LayV) is a shrew-borne emerging parahenipavirus first identified in 2018 in 35 febrile patients in China. The closely related Nipah virus (NiV) is a highly pathogenic emerging bat-borne henipavirus that has caused numerous outbreaks with public health concerns in Asia. Among other symptoms, NiV causes severe acute respiratory syndrome and encephalitis, leading to high lethality. Thus, although closely related, infections with these two emerging and zoonotic viruses have distinct pathogenicity. Since the interplay with the hosts immune system is a key determinant of species barrier crossing and pathogenicity, we aimed at deciphering the ability of LayV to counteract the human intrinsic immunity using the better-characterised NiV as a prototype. NiV expresses the P, V, and W proteins, known to hinder the hosts innate immune response during infection. We thus compared the immunomodulatory properties of LayV and NiV proteins in human cells and showed that, similarly to NiV, the C-terminal domain of LayV V proteins inhibits the response to the activation of the pattern recognition receptor MDA5. However, although the N-terminal region of LayV P can inhibit the interferon signalling, it is not as efficient as its NiV counterpart. Moreover, only NiV W inhibits MDA5 and RIG-I signalling pathways. Similarly, unlike NiV, LayV W cannot efficiently block the activation of the NF-{kappa}B promoter after stimulation with IL-1{beta}. These results suggest that LayV is less efficient than NiV in counteracting the human intrinsic immunity, which may contribute to the difference in severity observed between NiV and LayV-infected patients. IMPORTANCELangya virus (LayV) is a shrew-borne emerging parahenipavirus recently identified in patients in China with symptoms such as fever, fatigue, cough, anorexia, headache, and vomiting. Since the interaction between a virus and its hosts immune system is an essential parameter influencing host adaptation and disease severity, we investigated the interplay between LayV and the human intrinsic immunity using as a prototype the better-characterized and closely related Nipah virus (NiV), a highly pathogenic henipavirus. We compared the immunomodulatory properties of LayV and NiV proteins in human cells and showed that, similarly to NiV, some of LayV proteins can inhibit human signalling pathways, while, unlike NiV, LayV W protein is unable to block essential immune pathways. This suggests that LayV is less efficient than NiV in counteracting the human intrinsic immunity, which may contribute to the difference in severity between NiV and LayV-infected patients.

microbiology↗

bioRxiv2025

Unlocking meiotic crossovers near plant centromeres

Crossovers (COs) ensure proper chromosome segregation during meiosis and generate genetic diversity. COs are non-uniformly distributed along chromosomes and almost universally suppressed in centromere-proximal regions, notably creating a significant bottleneck for plant breeding. The mechanism of this CO suppression is elusive, but chromatin state is a contributing factor. Here, we identify three factors that actively limit proximal CO in Arabidopsis, the cohesion establishment factor CTF18, the centromeric cohesin protector SGO2, and the deSUMOylase SPF2. The mutation of these factors allows both the formation of CO in centromere-proximal region where they were completely absent in the wild-type, and enhance their frequency where they were rare. COs can be further increased by combining these mutations together or with mutation in the DNA methylase CMT3, suggesting that multiple mechanism prevent proximal CO in parallel. The identification of the very conserved CTF18, SGO2 and SPF2 as suppressors of centromere-proximal CO highlights the importance of cohesin turnover in this process and opens up new possibilities for plant breeding.

genetics↗

bioRxiv2025

Monopolar orientation of kinetochores at meiosis is enforced by COHESINS and their regulators, CENP-C, and the deSUMOylase SPF2

The first division of meiosis is unique in its capacity to halve the ploidy of the future gametes. To this end, one key innovation compared to mitosis is the monopolar orientation of the pairs of sister kinetochores required for the proper separation of homologs at meiosis I. How monopolar orientation is imposed is unclear and seems to vary in eukaryotes. Here we performed a forward genetic screen in Arabidopsis thaliana, specifically designed to identify the molecular components imposing monopolar orientation, based on mutants ability to restore fertility in spo11 osd1 haploid plants. We show that monopolar orientation involves all four cohesin subunits (REC8, SCC3, SMC1, SMC3), the cohesion establishment factors CTF18 and DCC1, and the cohesin protectors SGO1/2 and PANS1, the inner kinetochore protein CENP-C, and the desumoylase SPF2. The mutants show bipolar orientation of achiasmatic chromosomes, but monopolar orientation is maintained in the presence of crossovers despite splitting of sister kinetochores at metaphase I and reduced levels of cohesin. Taken together, the findings demonstrate that cohesion establishment and protection, kinetochore function, and deSUMOylation, together with crossovers, enforce monopolar orientation in plants and support a cohesion-driven model of kinetochore orientation at meiosis I that is conserved across kingdoms.

cell biology↗

bioRxiv2025

A benchmarking workflow for assessing the reliability of batch correction methods

One of the most pervasive challenges in large-scale untargeted metabolomics is short and long-term analytical variability introducing the necessity of batch effect correction. In this context, several strategies and methods have been developed to limit those effects, either by monitoring the data generation process to maximize reproducibility or by applying post-analysis data correction. Different evaluation frameworks, either assessing the degree of bias in the data through visual tools or quantitative indicators, or evaluating the prediction performance of known biomarkers, were also proposed. However, there is currently no clear consensus on how to evaluate batch correction methods. This work offers a strategy to assess multiple dimensions of batch correction efficiency within a comprehensive and reliable framework, designed to assess the effectiveness and reliability of batch correction methods. Based on Mahalanobis Conformity Index (MCI), it provides a multivariate and covariance-aware metric to quantify within- and between-batch variability. Additionally, it combines visualization techniques (Principal Component Analysis (PCA) and Multivariate INTegrative (MINT) PCA) with numerical indicators (batch dispersion, Coefficient of Variation), supporting both multidimensional and metabolite-specific evaluations. Lastly, this novel approach integrates statistical tools alongside chemistry-based metrics for method overfitting and overcorrection assessment. Applied within a use case for comparing LOESS-based and ComBat correction methods, the present workflow provided a structured approach to systematically assess the reliability of batch corrections, ensuring both data intercomparability and biological relevance in metabolomics studies. Author summaryThe assessment of batch correction is a challenge in metabolomics, where there is no consensus for a define strategy, making it a complex task. However, knowing the impact of batch correction on the datasets and consecutive possible impact on downstream statistical analyses, providing a reliable framework for its assessment is a cornerstone for reproducible results. The objective of the present work was to provide a framework and a set of interpretation tools combining numerical indicators, as well as diagnostic plots, for assessing the reliability of batch correction methods. We introduced a robust evaluation framework centered on the Mahalanobis Conformity Index, providing a multivariate and covariance-aware metric to quantify within- and between-batch variability. By coupling this index with visual tools (based on Principal Component Analysis (PCA) and Multivariate INTegrative (MINT) PCA), as well as compound-level diagnostics, we enabled a fine-grained and interpretable comparison of correction strategies, highlighting their strengths and potential pitfalls.

bioinformatics↗

bioRxiv2025

Spatial tumour-immune ecosystems shape the efficacy of anti-PD1 immunotherapy in primary cutaneous melanoma

Intra-tumoral heterogeneity in melanoma arises from dynamic cancer cell plasticity and underlies various mechanisms of immune escape. Here, we combined high-plex immunofluorescence imaging with spatially resolved transcriptomics to map the architecture of melanoma cell states and their interactions with the immune microenvironment in primary cutaneous tumours prior to adjuvant anti-PD1 immune checkpoint inhibitor (ICI) treatment. Computational analyses showed that melanoma cells organise into spatially restricted patches, with a preferential organisation of undifferentiated cells associated with poor ICI efficacy. Neighbouring immune cell composition varied according to cancer cell states, with a crucial involvement of specific subsets of tumour-associated macrophages, driven by signalling pathways involving tumour-derived and microenvironmental cues such as IFN-{gamma} and hypoxia. Integrated spatial analyses further revealed tumour-immune ecosystems that stratify patient outcomes, delineating configurations either associated with ICI efficacy or metastatic relapse. These results uncover the spatial landscape of tumour ecosystems and identify signalling pathways as potential targets for improving the efficacy of ICI in melanoma. HighlightsO_LIMelanoma cell states spatial organization is associated with aPD1 therapy efficacy C_LIO_LISpatial organization of TAM subsets is a crucial determinant of ICI outcome C_LIO_LIMelanoma cells in different states co-localise with functionally distinct TAM subsets C_LIO_LIIdentification of cell-cell communication pathways that underlie tumour-TAM crosstalk C_LIO_LIA balance between tumour-immune ecosystems is associated with aPD1 therapy efficacy C_LI

cancer biology↗

bioRxiv2025

Taurine is a Natural Host Cytoadhesion Inhibitor in Asymptomatic Malaria Cases

The prolonged dry season in malaria-endemic regions of sub-Saharan Africa can be divided into periods of high and low transmission. The majority of symptomatic malaria cases are restricted to the short high transmission period that follows the rainy season. Shortly after, persistent asymptomatic malaria cases are more prevalent throughout the prolonged low transmission period. It is still unclear whether host metabolic alterations play a role in asymptomatic infections during seasonal malaria. In this study, we analyzed the blood plasma metabolome (n=199) of individuals in The Gambia, West Africa, capturing data from both high and low malaria transmission periods. Plasma samples from individuals (n=16) were collected monthly throughout the low transmission season, enabling a longitudinal analysis of metabolic alternations over six months. Our findings reveal that significant changes in host plasma metabolite composition are associated with seasonality and malaria pathogenicity. Notably, we observed elevated levels of taurine in asymptomatic malaria infections, especially during periods of low transmission. In vitro, this naturally occurring host molecule inhibits the cytoadhesion of malaria-infected red blood cells (iRBCs), which is key to malaria disease severity and mortality. Exogenous taurine can significantly reduce or reverse binding of iRBCs to the common adhesion receptor CD36 and the endothelial protein C receptor (EPCR), the later being associated with cerebral malaria. This study uncovers a mechanism by which elevated taurine plasma levels in asymptomatic infections could reduce cytoadhesion and lead to increased splenic clearance, thereby strengthening host resistance to symptomatic infections. In the absence of health strategies targeting dry season parasite reservoirs, our findings highlight taurine as a potential prophylactic or therapeutic agent to reduce symptomatic malaria in sub-Saharan Africa. One Sentence SummaryMetabolomics uncovers taurine as a natural host inhibitor of Plasmodium falciparum cytoadhesion in asymptomatic malaria carriers, offering new insights for disease control.

microbiology↗

bioRxiv2025

The epigenetic regulator TRIM24 controls melanoma cell dedifferentiation and resistance to treatment in melanoma

Cancer cell plasticity plays a key role in tumor progression and treatment resistance in melanoma. While the transcriptional programs enabling adaptative switching between melanocytic and mesenchymal phenotypes are well characterized, unravelling druggable epigenetic regulators that sustain melanoma cell adaptation and resistance remains crucial. Herein, we identified TRIM24, a bromodomain protein frequently upregulated during melanoma metastatic progression, as a crucial regulator of melanoma cell plasticity towards invasive/resistant states. shRNA-mediated knock-down of TRIM24 or degradation using a TRIM24-specific PROTAC decrease the migratory capacities and increase the sensitivity to BRAF inhibitors of melanoma cells. Integration of transcriptomic (RNA-seq) and epigenomic (ATAC-seq, CUT&Tag) analyses reveals that TRIM24 reprograms the epigenome of melanoma cells, promoting mesenchymal and repressing melanocytic transcriptional programs. We further define a TRIM24-specific transcriptional signature, that is consistently enriched in treatment-resistant mesenchymal subpopulations in melanoma single-cell RNA-seq datasets. Accordingly, analysis of TRIM24 protein expression in melanoma patients highlights that high TRIM24 expression correlates with relapse to adjuvant immunotherapy. Finally, TRIM24 knock-down in immunocompetent mouse models synergises with immune checkpoint inhibitors. Overall, our findings spotlight TRIM24 as a major epigenetic regulator driving melanoma cell dedifferentiation and resistance to therapy, representing a promising druggable target to reverse phenotype switching and resensitize to treatment.

cancer biology↗

bioRxiv2025

SnoBIRD: A tool to identify C/D box snoRNAs and refine their annotation across all eukaryotes

Small nucleolar RNAs (snoRNAs), a group of noncoding RNAs present amongst all eukaryotes, are most extensively characterized for their regulation of ribosome biogenesis and splicing. Despite their central roles, current snoRNA annotations remain incomplete. Several eukaryote genome annotations contain few or no snoRNAs, and none distinguish expressed snoRNAs from their pseudogenes--a recently characterized snoRNA subclass with distinct features and expression levels. To address this, we developed SnoBIRD, a BERT-based C/D box snoRNA predictor trained on snoRNAs spanning all eukaryote kingdoms. We show that SnoBIRD outperforms existing tools and is the only predictor capable of identifying snoRNA pseudogenes using biologically relevant signal. Applied on the fission yeast and human genomes, we demonstrate that only SnoBIRD scales well with genome size in terms of runtime, and we identify and experimentally validate several new SnoBIRD-predicted C/D box snoRNAs. By running SnoBIRD on multiple eukaryote genomes, we identify hundreds of novel snoRNA candidates and highlight SnoBIRDs usefulness to determine the evolutionary paths of snoRNAs distributed across different species. Overall, SnoBIRD represents a user-friendly and efficient tool for reliably predicting C/D box snoRNAs and their pseudogenes across any eukaryote genome. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=109 SRC="FIGDIR/small/646650v1_ufig1.gif" ALT="Figure 1"> View larger version (19K): org.highwire.dtl.DTLVardef@99b390org.highwire.dtl.DTLVardef@dbe375org.highwire.dtl.DTLVardef@32358aorg.highwire.dtl.DTLVardef@58fb3a_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2025

Fibrillarin-mediated ribosomal RNA maturation is a novel therapeutic vulnerability in triple-negative breast cancer

Triple-negative breast cancer (TNBC) remains one of the most challenging breast cancer subtypes to treat due to the lack of effective therapeutic options. Ribosome biogenesis has recently emerged as a promising therapeutic target across various cancers. Despite the current targeting of ribosome biogenesis through RNA polymerase I (RNA Pol I) inhibition, we speculated that other factors essential for ribosome assembly, such as rRNA maturation factors, may also represent therapeutic targets in TNBC. Here, we demonstrate that ribosome biogenesis-related genes are notably overexpressed in TNBC compared to other breast cancer subtypes, highlighting its critical role in TNBC progression. Accordingly, we show that RNA Pol I inhibition exerts potent anti-proliferative effects in pre-clinical models of TNBC, both in vitro and in vivo. However, the DNA-damaging activity of RNA Pol I inhibitors raises safety concerns, highlighting the need for alternative strategies to inhibit ribosome biogenesis. To this end, we show that targeting a downstream rRNA maturation step, specifically pre-rRNA cleavage, by inhibiting the maturation factor Fibrillarin, also inhibits tumor growth in TNBC models. Notably, ribosome biogenesis inhibition, through either RNA Pol I or Fibrillarin targeting, induces cell cycle arrest without triggering significant cell death. These findings establish ribosome biogenesis as a therapeutic vulnerability in TNBC and identify rRNA maturation, and Fibrillarin in particular, as novel targets for potential therapeutic intervention. SignificanceTargeting ribosome biogenesis, through inhibition of either rRNA synthesis or maturation, induces anti-tumoral effects in TNBC, representing a novel therapeutic vulnerability with potential to improve patient outcomes.

cancer biology↗