Biology subjects

Sharma, A.

Publications and source records attributed to Sharma, A..

At least 73 records · Page 4Linked to original sources

bioRxiv2026

Dynamic multimodal survival prediction in multiple myeloma integrating gene expression, longitudinal laboratories, and treatment history

Prognostic stratification in multiple myeloma (MM) relies on staging systems that assign patients to fixed categories at diagnosis and discard the temporal information that accumulates during treatment. We developed a dynamic multimodal framework that predicts residual overall survival using observation windows ranging from 1 to 18 months post-diagnosis. The model integrates DeepInsight-transformed gene expression representation, longitudinal laboratory measurement trajectories across 10 analytes, and treatment history for three drug classes through an adaptive fusion mechanism that accounts for missing clinical observations. On the MMRF CoMMpass cohort (n = 752), five-fold cross-validation yielded a concordance index (C-index) of 0.773 {+/-} 0.024 and a time-dependent AUC at a 1-year prediction horizon (tdAUC1yr) of 0.789 {+/-} 0.021, outperforming all evaluated baseline methods including DeepSurv (0.633 {+/-} 0.095) and random survival forests (0.636 {+/-} 0.024) on matched cross-validation splits. Modality ablation identified longitudinal laboratory measurements as the strongest individual contributor (C-index 0.693); the DeepInsight spatial encoding of gene expression yielded higher discrimination than a multilayer perceptron (MLP) baseline operating on the same features (0.624 vs. 0.596). Kaplan-Meier analysis showed significant prognostic group separation at all primary landmarks (log-rank p < 0.001; hazard ratios 3.46-3.93). A distilled student model retaining only the DeepInsight representation and five baseline clinical features achieved C-index 0.672 and tdAUC1yr 0.740 on an independent microarray cohort (GSE24080, n = 507) without retraining. Interpretability analysis identified prognostic associations consistent with established myeloma biology, including ubiquitin-proteasome pathway genes, endoplasmic reticulum stress markers, and Interferon Alpha Response pathway enrichment.

bioinformatics↗

bioRxiv2026

PARP16 protects against cardiac hypertrophic response by ADP-ribosylation-dependent inhibition of NFAT transcription factor

Mono-ADP-ribosylation is a post-translational modification that regulates diverse cellular processes. PARP16 is an endoplasmic reticulum-associated mono-ADP-ribosyltransferase implicated in stress-response signalling; however, its role in cardiac remodelling and dysfunction has not been fully defined. Our results suggest that PARP16 expression was reduced in human heart failure samples. Deletion of PARP16 in several mice models promoted ventricular dilatation, fibrosis, fetal gene reactivation, and systolic dysfunction, whereas cardiomyocyte-specific overexpression of PARP16 attenuated isoproterenol-induced remodelling in mice. Transcriptomic profiling and functional studies identified NFAT signalling as a major downstream pathway activated following PARP16 deficiency. Specifically, loss of PARP16 increased nuclear accumulation, promoter occupancy, and transcriptional activity of NFAT1. Mechanistically, PARP16 interacted with NFAT1 and suppressed NFAT-dependent transcription through a catalytic activity-dependent mechanism. Proteomic, structural, and functional analyses identified E398 and T533 residues of NFAT1 associated with PARP16-mediated regulation. Furthermore, pharmacological inhibition of NFAT improved cardiac function and remodelling in PARP16-deficient mice. These findings indicate that PARP16 acts as a negative regulator of NFAT signalling and contributes to protection against adverse cardiac remodelling.

cell biology↗

bioRxiv2026

Sex differences in osteoblast matrix maturation regulate osteoblast-endothelial interactions

BackgroundBone formation during development and repair is divergently modulated by osteoblast (OB)-derived vascular endothelial growth factor (VEGF) which drives the skeletal sexual dimorphism of the bone vasculature. While the extracellular matrix (ECM) provides both structural and instructive cues to developing vasculature, the contributions of the bone matrix to this skeletal vascular dimorphism in bone remains undefined at the cellular level. MethodsPrimary OBs were isolated from neonatal female and male C57BL/6 long bones and cultured under basal or osteogenic conditions. ECM composition was quantified by Raman spectroscopy. Primary murine bone marrow endothelial cells (BMECs) were seeded directly onto established OB layers and maintained in heterotypic cocultures to assess contact-mediated effects of OB ECM on BMEC survival and expansion. OB-conditioned media (CM) was used to evaluate soluble-factor contributions, with VEGF-A concentration quantified by ELISA. ResultsRaman spectroscopy, on individual OBs from monotypic cultures, revealed sexually dimorphic ECM signatures that were independent of cellular growth profiles. Female OB matrices were enriched with type I collagen-specific proline and hydroxyproline and octacalcium phosphate with enhanced collagen intra-strand stability consistent with a matrix-dominant signature. Male OB matrices exhibited relatively lower type I collagen content and higher carbonated apatite resulting in an elevated mineral-to-matrix ratio indicative of advanced mineral maturation. After 24-hours of heterotypic culture of BMECs with OBs, BMEC numbers were 1.39-fold higher when in contact with male OBs. CM treatment of BMECs did not recapitulate these effects despite higher VEGF-A release from male OBs. ConclusionsSex differences in OB ECM are linked to divergent, contact-dependent regulation of BMEC behaviour. These findings suggest that differences in matrix maturation stat contribute to the sex-specific regulation of the skeletal vascular niche. Elucidating the mechanisms that regulate sex-specific OB-ECM production may reveal new therapeutic targets for selectively modulating pathological skeletal angiogenesis in men and women. SummaryBone is a sexually dimorphic organ, with men and women differing in bone size, strength and risk of fracture. The skeletal vasculature is essential for bone growth and repair, with bone forming osteoblast (OB) cells influencing blood vessel development through the skeletal extracellular matrix (ECM). Although the interactions between OB and vascular cells are crucial for lifelong skeletal health, it is not yet known whether sex differences in bone structure between men and women arise from differences in OB activity, or whether this divergence is driven by sex differences in blood vessel growth. Here, we show that male and female mouse OBs deposit distinct ECMs that differentially influence vascular endothelial cell behaviour. Female OBs produce a collagen-rich matrix with low mineral content. In contrast, male OB matrices contain less collagen and more mineral while releasing elevated levels of blood vessel promoting VEGF-A than females. When placed directly onto these OBs, vascular cell growth was greater when in contact with male than female OBs. Notably, this sex-dependent effect requires direct contact between both cell types and was not reproduced by exposure to OB-derived substances alone. These findings identify a cellular mechanism by which sex differences in OB matrix composition influences vascular cell behaviour in bone. Understanding how OB-vascular interactions differ by sex may help explain variation in bone health, healing capacity and disease risk between men and women. Further, our approach may support the discovery of new therapeutic targets that support bone growth and repair while targeting abnormal blood vessel growth in a sex-specific manner. HighlightsO_LIPrimary OBs from male and female C57BL/6 mouse long bones synthesise compositionally distinct ECMs. C_LIO_LIFemale OB matrices are type I collagen-rich and enriched with octacalcium phosphate, whereas male OB matrices contain less type I collagen and higher levels of carbonated apatite. C_LIO_LIBone marrow-derived endothelial cell (BMEC) growth is enhanced in heterotypic cocultures with male, but not female, OBs after 24 hours. C_LIO_LIMale OBs release higher levels of the pro-angiogenic factor VEGF-A than female OBs. C_LIO_LIThe sex-specific effects of the OB ECM on BMECs is contact-dependent and are not reproduced by treatment with OB-derived conditioned media. C_LI

cell biology↗

bioRxiv2026

Inhibition of Gasdermin D by Disulfiram Attenuates Cardiac Inflammation and Fibrosis following Ischaemia Reperfusion Injury

IntroductionInadequately controlled inflammation is a key driver of adverse cardiac remodelling after acute myocardial infarction (AMI). Central to this process is activation of the NLRP3 inflammasome-gasdermin D (GSDMD) pathway, which promotes pyroptosis and the release of the pro-inflammatory cytokine interleukin-1{beta} (IL-1{beta}), a mediator strongly associated with infarct severity and poor clinical outcomes. This study investigates whether repurposing the FDA-approved therapeutic Disulfiram, recently shown to inhibit GSDMD pore formation, could reduce inflammation and thus improve cardiac injury after AMI. Methods and ResultsCardiac ischemia-reperfusion (I/R) injury was induced in C57BL/6 mice by 60-minute ligation of the left coronary artery followed by reperfusion. Disulfiram (25 or 50 mg/kg) was administered at reperfusion and daily thereafter. Cardiac function was assessed by echocardiography, while fibrosis and inflammation were evaluated by histology, RT-PCR, immunohistochemistry and immunoblotting. Leukocyte populations in blood, spleen, bone marrow and heart were analysed by flow cytometry. In vitro, mouse bone marrow-derived macrophages (BMDMs) and PMA-differentiated THP-1 cells were treated with Disulfiram. Cytokine secretion, inflammatory gene expression and changes in cell viability (propidium iodide (PI) staining and lactate dehydrogenase (LDH) release) were measured. Disulfiram (50 mg/kg) significantly improved cardiac function 7 days post-I/R. This was accompanied by a significant reduction in cardiac fibrosis and inflammation, as reflected by a lower abundance of inflammatory cells in circulation and cardiac tissue. In LPS- and ATP/Nigericin-stimulated BMDMs and THP-1 cells, Disulfiram dose-dependently (0.1-50 {micro}M) reduced IL-1{beta} and IL-6 secretion and attenuated membrane permeability and cell lysis. ConclusionsThis study demonstrates that Disulfiram improves cardiac function post-AMI by ameliorating inflammation and fibrosis, which was associated with reductions in cytokine release from inflammatory cells in vitro. Therefore, targeting GSDMD by "repurposing" the FDA-approved drug, Disulfiram, may represent a novel way to provide cardio-protection post-AMI. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=82 SRC="FIGDIR/small/710794v1_ufig1.gif" ALT="Figure 1"> View larger version (11K): org.highwire.dtl.DTLVardef@7fd82eorg.highwire.dtl.DTLVardef@149de52org.highwire.dtl.DTLVardef@a2fe0eorg.highwire.dtl.DTLVardef@d56b4f_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2026

SUMO mediates the coordinate regulation of meiotic chromosome length and crossover rate

Meiotic prophase-I chromosomes are organized into linear arrays of chromatin loops anchored to proteinaceous axes that define the interaction interfaces for the pairing and synapsis of homologous chromosomes. Chromatin loop size and axial chromosome length are inversely correlated and vary widely both between and within species, including between the sexes. The molecular basis of this variation remains unclear. Here, we provide evidence that the small ubiquitin-like modifier, SUMO, regulates loop-axis organization in mouse meiosis. Our analysis shows that the longer axes of oocyte chromosomes contain more SUMO per unit length than the shorter axes of spermatocyte chromosomes. In mouse models, the loss of SUMO1 results in shorter axes and longer chromatin loops. Conversely, increased SUMO1 conjugation, caused by mutation of the SENP1 isopeptidase, produces longer axes with shorter loops. Axis length positively correlates with meiotic recombination. Accordingly, Sumo1 and Senp1 mutations respectively decrease and increase crossover frequency. These findings identify SUMO as a key regulator of meiotic chromosome architecture and suggest a molecular basis for the physiological variation in chromosome length and recombination rates seen among species, sexes, individuals, and individual meiocytes. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=101 SRC="FIGDIR/small/710713v1_ufig1.gif" ALT="Figure 1"> View larger version (31K): org.highwire.dtl.DTLVardef@145c465org.highwire.dtl.DTLVardef@160c8aborg.highwire.dtl.DTLVardef@1165b76org.highwire.dtl.DTLVardef@ced5e0_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2026

Biological Evaluation of Novel 2-Benzimidazole Derivatives for Antibacterial Activity

Infectious diseases remain a persistent global health burden, with bacterial infections accounting for a substantial disease burden. The increasing prevalence of antimicrobial resistance has emphasised the need for the development of novel antibacterial drugs. In the present study, antibacterial activity of novel 2-substituted benzimidazole derivatives (NR-1 to NR-9) was evaluated against three bacteria, viz. M. smegmatis, B. subtilis and E. coli using estimation of Minimum Inhibitory Concentration (MIC) and Minimum Bactericidal Concentration (MBC). Two (NR-4 and NR-5) exhibited inhibitory activity against M. smegmatis, while two (NR-5 and NR-7) were active against B. subtilis, with MICs ranging from 62.5 to 250 g/mL. Notably, NR-5 demonstrated antibacterial activity against both M. smegmatis and B. subtilis, with more efficacy against M. smegmatis (MIC: 62.5 g/mL) and bactericidal activity with an MBC/MIC ratio of 1. Cytotoxicity assessment in Vero cells indicated low toxicity for NR-4 and NR-5, and SwissADME evaluation suggested favourable physicochemical properties and drug-likeness. The growth kinetics profiling and time kill kinetics of the NR-5 Benzimidazole derivative demonstrated concentration-dependent activity, with complete growth suppression at 2x MIC. Additionally, checkerboard assay evaluation revealed a synergistic interaction of NR-5 with Rifampicin (FICI: 0.48), highlighting the enhanced antimycobacterial activity in combination. Molecular docking and binding-pocket analysis identified thymidylate kinase (tmk) as a potential target of NR-5. Thus, we have identified and characterised NR-5 as a promising benzimidazole-based antibacterial candidate that shows potent, low-toxicity antimycobacterial activity and works synergistically with rifampicin, making it a potential lead for future anti-tuberculosis drug development.

microbiology↗

bioRxiv2026

A consensus genome sequence for the social amoeba Dictyostelium giganteum

The life cycle of the Dictyostelid amoebae is unusual in that it alternates between a free-living solitary phase and an aggregative social phase. We used six previously collected Dictyostelium giganteum strains from distinct ecological niches in the Mudumalai Nature Reserve, India. From them, we generated short Illumina reads and assembled a consensus genome, comprising nuclear and mitochondrial genomes, representative of all six strains. The nuclear assembly has an AT content of 75.76%, accounting for 38.52 Mb, and resolves into five chromosome-scale scaffolds that are consistent with the published karyotype. Its N50 is 3.01 Mb and L50 is 5. The BUSCO analysis shows 3.9% fragmentation and 92.1% completeness. Genome assembly and completeness are also validated using [~]5,500 genes from a publicly available transcriptome dataset (PRJNA48443) derived from the post-aggregation stage. 13,251 predicted proteins are encoded by the genome, including ABC transporters, polyketide synthases, Ras/Rho GTPases, and expanded families of protein kinases. Comparative analysis demonstrates extensive conservation of syntenic blocks related to the dictyostelids D. discoideum and D. firmibasis as well as lineage-specific rearrangements. About 18% of the nuclear genome is made up of repetitive DNA, mostly in the form of simple repeats. Major transposable element classes, including piggyBac-like fragments, were found by homology searches. Long poly-asparagine/glutamine tracts are less common than in D. discoideum, but low-complexity sequences are common due to strong AT-driven codon bias. Comparative proteome-level orthology analysis across Dictyostelium species and Entamoeba identified a conserved Amoebozoan core together with a substantial Dictyostelium-specific gene repertoire. Domain-level comparisons further revealed widespread conservation of intracellular signalling and cytoskeletal modules shared with animals, whereas canonical metazoan extracellular adhesion domains were absent, highlighting the deep evolutionary roots of regulatory complexity underlying aggregative multicellularity.

genomics↗

bioRxiv2026

Minimum inoculum of resistance assay for evaluating for anti-toxoplasmosis compounds that target phenyl alanine tRNA synthetase

Toxoplasma gondii is a globally important intracellular parasite, and treatment regimens are limited by the failure of drugs to target latent tissue cysts. Developing new candidates for treatment also needs to address the potential for resistance to arise. Here, we developed a Minimum Inoculum for Resistance (MIR) assay as a quantitative metric for evaluating inhibitors of T. gondii. The MIR assay, adapted from assays used in malaria drug discovery, measures the frequency for pre-existing resistance alleles by exposing different sized parasite populations to drug pressure. We profiled a series of bicyclic pyrrolidone analogs that inhibit phenylalanine tRNA synthetase (PheRS). We demonstrate that these inhibitors require higher inocula to lead to parasite resistance (up to > 108 parasites) in comparison with an inhibitor of DNA synthesis, and that MIR values vary across inhibitors with closely related chemical structures. Clonal analysis of resistant parasites emerging from MIR assays revealed both new and previously identified resistance conferring mutations in TgPheRS, and structural modeling revealed their potential impact the enzyme active site. The MIR assay provides a functional benchmark to compare new and existing inhibitors, allowing for rational prioritization of lead compounds with a high genetic barrier to resistance.

microbiology↗

bioRxiv2026

TNAP and PHOSPHO1 function synergistically to afford critical control over the mineralisation of the postnatal murine skeleton

Biomineralisation is essential for skeletal integrity, yet the synergistic roles of tissue non-specific alkaline phosphatase (TNAP) and PHOSPHO1 in postnatal bone mineralisation remain poorly defined. To decipher this, we generated a novel murine model in which Alpl was deleted in Prx1- expressing cells (AlplPrx1/Prx1) in mice with a global Phospho1-/- deficiency to overcome the perinatal lethality that arises upon dual global deletion. Using a multi-modal approach to spatially phenotype the limbs of these animals, we reveal mice lacking both TNAP and PHOSPHO1 exhibit a distinct lack of mineralisation and altered anatomical structure at postnatal day 1 (PN1) and 3-weeks of age. Although viable, these mice did not thrive due to their reduced size, thus further investigations were conducted on mice with a heterozygous deletion of TNAP (Alplwt/Prx1;Phospho1-/-). Although smaller than wild-types at PN1 and 3 weeks old, these mice did not display the gross limb deformations observed in the homozygous animals and the single, functioning Alpl allele rescued the loss of biomineralisation observed following dual phosphatase deletion. At 6-weeks of age, compromised epiphyses and metaphyses were only seen in AlplPrx1/Prx1 animals. Further, we found that tibial geometry and porosity was significantly altered by Phospho1 deletion (Phospho1-/-), which was compounded in the Alplwt/Prx1;Phospho1-/- mice and linked to alterations in collagen configuration, matrix mineralisation and growth plate deformities. Together, our findings establish the mechanistic framework for TNAP and PHOSPHO1 in permissive biomineralisation, providing critical insights into this fundamental process. Significance StatementBiomineralisation is essential for skeletal development and is critically dependent on phosphatases that release inorganic phosphate for hydroxyapatite formation. Our study investigates the dual role of PHOSPHO1 and TNAP in this process, using a novel murine knockout model. Deletion of both enzymes results in complete loss of bone mineralisation, demonstrating their critical synergistic function. Further, we show that PHOSPHO1 and TNAP exhibit distinct, spatially-restricted functions in the tibia and thus enhances our understanding of the fundamentals processes underpinning biomineralisation. These findings also have clinical relevance as they have the potential to inform on treatment strategies for hypo- and hyper-mineralised pathologies.

developmental biology↗

bioRxiv2026

In silico transcriptomic analysis reveals shared molecular signatures and immune-associated pathways between Hashimotos thyroiditis and type 2 diabetes with exploratory drug repurposing

The management of Hashimotos thyroiditis (HT), one of the most prevalent autoimmune disorders worldwide, becomes more complex when it coexists with type 2 diabetes (T2D) compared with the management of either disease alone. This complexity may arise from overlapping genetic, metabolic, and immune dysregulation, as well as potential therapeutic conflicts. Although HT and T2D are known to co-occur and share immune and metabolic features, the molecular characteristics underlying these overlaps have not been systematically explored. This study aimed to identify shared gene expression signatures and associated biological pathways between HT and T2D using an in silico, hypothesis-generating approach, and to explore candidate compounds that may be relevant to both conditions. Independent transcriptomic datasets (GSE138198 for control/HT and GSE29231 for control/T2D) were analyzed, leading to the identification of 59 genes that were differentially expressed in both HT and T2D compared with control samples. Protein-protein interaction (PPI) network analysis prioritized five shared key genes (sKGs): CDC42, CD74, FOS, RAC2, and YWHAB. Functional enrichment analysis of these sKGs revealed overlapping biological processes, molecular functions, cellular components, and immune-related signaling pathways, as well as shared regulatory networks involving transcription factors (FOXC1 and HNF4A) and microRNAs (hsa-miR-221-3p and hsa-miR-29a-3p). Immune infiltration analysis demonstrated broadly similar patterns of immune dysregulation in both diseases, providing additional biological context for the observed shared molecular signatures. Finally, an exploratory in silico drug repurposing pipeline incorporating molecular docking, ADMET profiling, drug-likeness assessment, and molecular dynamics simulations prioritized three candidate compounds: gliquidone, oleanolic acid, and glipizide for further investigation. Overall, this study provides a hypothesis-generating framework highlighting shared molecular features between HT and T2D, which may inform future experimental validation and clinical research. Author SummaryIn this work, we wanted to better understand why Hashimotos thyroiditis, an autoimmune condition that affects the thyroid gland, is often seen in people who also have type 2 diabetes. Treating patients who live with both conditions can be difficult, and we were interested in finding out whether they share common biological causes. To do this, we examined genetic data from individuals with each disease and looked for patterns that appeared in both groups. We discovered several genes that seem to act in similar ways in the two conditions, particularly genes linked to immune system activity and associated pathways. This finding suggests that shared molecular signatures and immune-associated pathways may play a role in the development of both diseases. We also explored how these shared genetic features influence larger biological processes and immune responses. The similarities we found support the idea that the two diseases may be connected through related biological pathways. In addition, we used computer-based screening methods to identify existing drugs that might influence these shared pathways. While these results need further testing, we hope our findings help open new directions for research and eventually contribute to better care for patients affected by both conditions.

bioinformatics↗

bioRxiv2026

Cell-Autonomous AR Dependence in Luminal Prostatic Epithelium Governs Survival and Lineage Plasticity

Prostate cancer resembles differentiated secretory luminal cells and shows cell-autonomous dependence on androgen receptor (AR) signaling, yet normal luminal cells are often considered dependent on paracrine stromal AR signaling. To resolve this, we conditionally deleted Ar in luminal acinar cells in vivo. Ar-deleted luminal cells persisted short-term, in contrast to the rapid regression observed after castration, but were impaired in regeneration and progressively lost. Their depletion was accompanied by replacement through basal-to-luminal differentiation of AR intact basal cells. Transcriptomic and chromatin profiling showed cell-autonomous suppression of the secretory program with induction of stemness, inflammatory, and epithelial-to-mesenchymal transition signatures after AR loss. Mechanistically, the MAP kinase pathway and downstream AP-1 transcription factors were activated and functionally validated, and MAP kinase inhibition selectively depleted AR-deleted luminal cells, indicating a compensatory survival pathway. These findings define intrinsic roles for luminal AR in maintaining differentiation, restraining plasticity, and sustaining regeneration and homeostatic turnover, providing a mechanistic basis for AR dependence in prostate cancer.

cell biology↗

bioRxiv2026

Xanthomonas imtechensis sp. nov. - a novel member of non-pathogenic Xanthomonas with bioprotection function from healthy rice seeds

Non-pathogenic Xanthomonas (NPX) from a diverse plant hosts are being reported on an increasing basis. There are also reports of multiple species forming communities on a single host plant, such as rice, and, given their role as core endophytes in protecting plants from pathogens, it is essential to isolate and characterization of more NPX species from diverse host plants. Using phylogenomic analysis of publicly available Xanthomonas genome sequences, we identified a novel clade comprising NPX strains from diverse hosts. One of the strains previously reported from our lab is from healthy rice seeds and was reported to be non-pathogenic, with bio-protection function against the bacterial leaf blight pathogen. Genomic investigation confirmed the lack of type III secretion system and its effectors, consistent with their non-pathogenic nature. These strains also harbour core and unique biosynthetic loci identified in other non-pathogenic Xanthomonas (NPX) strains. Further investigation using multiple genomic-based taxonomic indices indicates that these strains represent a potential new species. Hence, we propose Xanthomonas imtechensis sp. nov. as a new species of the genus Xanthomonas, with the type strain being PPL568 = MTCC 13186 = CFBP 9040 = ICMP 24395.

microbiology↗

bioRxiv2026

Integrated multi-omics profiling uncovers the epigenetic, transcriptional, and metabolic landscape of prostate cancer progression

A comprehensive understanding of the underlying molecular mechanisms of prostate cancer is essential for the development of precise diagnostic biomarkers. In this study, we applied unsupervised multi-omics factor analysis (MOFA) to integrate DNA methylation, gene expression, and metabolic profiles derived from the same individuals, aiming to characterize the biological landscape of normal, malignant, and aggressive prostate tissue. Our analysis identified distinct molecular pathways associated with aggressive disease, specifically those involved in zinc metabolism, cell cycle regulation, smooth muscle architecture, immune activation, and tissue morphology. Key metabolites within the TCA cycle, amino acid metabolism, and lipid pathways were central to these signatures. Furthermore, we observed a consistent co-enrichment of SP1 and CTCFL binding regions among factor-associated CpGs, suggesting a model of global epigenetic reprogramming. These findings indicate a novel interplay between Polycomb deregulation, CTCFL-mediated chromatin remodeling, and SP1-driven transcriptional activation in shaping the prostate cancer epigenome. Apart from immune activation, the identified molecular signatures were validated in the TCGA cohort and demonstrated significant predictive value for disease recurrence. Overall, these results underscore the power of multi-omics integration in providing a holistic understanding of prostate cancer biology and its potential for clinical translation into prognostic biomarkers.

cancer biology↗

bioRxiv2026

Regulation and function of trans-physeal growth plate bridges: evidence for a mechanical base isolation role to minimise epiphyseal shear stress

The cartilaginous growth plate (GP) is responsible for all bone elongation during post-natal growth yet must simultaneously contribute to mechanical epiphyseal stability for articulation. How the GP balances these dual functions across the bone-cartilage-bone epiphyseal interface during complex load-growth transitions is not defined. Herein, we examine regulation and mechanobiology of GP bridges - mineralised trans-physeal GP structures - to explore whether they serve these dual GP functions. We have determined the effects of age and sex, short- and long-term joint loading and several established and new osteotropic pharmacological agents on mouse tibial GP bridge number and areal density using micro-computed tomography. We also explored temporal formation and progression of GP bridges by serial in vivo scanning and we imaged epiphyseal load-transfer in young and mature mice in situ via synchrotron X-ray computed tomography (sCT) of intact joints under physiologically oriented load. Our utilisation of digital volume correlation revealed regional 3D load-induced strain inhomogeneities in the GP that are synchronised to bridge location and this was substantiated using finite element modelling. Furthermore, direct micro- and sCT examinations showed that bridges consistently contain a singular epiphyseal/metaphyseal discontinuity which appear to serve a novel mechanical base isolation role to minimise shear stress across the GP. Our data indicate that bridges are regulatable, dynamic structures that synchronise GP strains and exhibit sensitivity to local joint mechanics. We highlight that trans-physeal bridges may contribute to longitudinal bone growth cessation whilst simultaneously stabilising the epiphysis by absorbing compression and shear strains.

bioengineering↗

bioRxiv2026

In vitro evaluation of Escherichia coli and Staphylococcus aureus translocation in 3D printed material

Vascular graft infection is a rare but life threating condition, primarily occurring after 30 days post-surgery. Meta-analysis has shown that antimicrobial coatings on graft materials do not prevent these infections. Moreover, infection still occurs even though studies have also shown that there is no bacterial proliferation on or bacterial penetration of common vascular graft material. The time frame of infection, meta-analysis, and in situ studies suggest that bacteria present at the suture site are introduced into the surrounding tissue or that systemically circulating bacteria may be surviving, proliferating, diffusing slowly, and evading host immune defense in synthetic vascular grafts. De novo vascular graft materials, such as tissue-engineered vascular graft material and decellularized vasculature may provide an in situ platform for studying survival, proliferation, and diffusion in tissue and tissue-like materials. In this study, we use confocal microscopy to image penetration depth of bacteria over time as a proxy for diffusion of Staphylococcus aureus and Escherichia coli into alginate, GelMA, and decellularized porcine vascular tissue. We quantified viable bacteria breakthrough as a function of biomaterial type. We found penetration depth over time was similar in all three biomaterials, however E. coli broke through much less from tissue than from engineered materials, while S. aureus had higher breakthrough in the GelMa but otherwise equal rates. These results point to the possibility of interstitial growth control relative to surface coatings as a future target for engineering infection resistance in engineered vascular grafts. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=140 SRC="FIGDIR/small/703277v1_ufig1.gif" ALT="Figure 1"> View larger version (34K): org.highwire.dtl.DTLVardef@193760org.highwire.dtl.DTLVardef@1829d6corg.highwire.dtl.DTLVardef@2d4535org.highwire.dtl.DTLVardef@1ab869_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2026

Zero-shot ecological annotation of microbial genomes with myLLannotator accelerates scientific discovery

Large language models (LLMs) are promising scientific assistants, but many models remain inaccessible for resource-constrained scientists. To address this, we present myLLannotator, a python package for metadata annotation built on llama3.2-3B. myLLannotator labels 18,000+ genomes in ~2 hours on a laptop, reproducing a discovery involving substantial manual annotation. We use myLLannotator to discover that duplicated genes are depleted in endosymbiotic bacteria, demonstrating its power to accelerate hypothesis testing and discovery.

bioinformatics↗

bioRxiv2026

Geometry-Controlled Diffusion in Bicontinuous Cubic Lipid Networks

Bicontinuous cubic lipid phases exhibit complex internal aqueous networks that strongly influence molecular transport, yet a predictive framework linking internal geometry to effective diffusion remains lacking. In this study, we isolate and quantify the role of geometry alone in governing diffusive transport within bicontinuous cubic lipid networks by modeling diffusion in idealized triply periodic minimal surface geometries, namely the gyroid, diamond, and primitive phases. Monte Carlo random-walk simulations were performed with tracer particles confined to the aqueous domains and reflecting boundaries at the lipid interface, and effective diffusion coefficients were extracted from the long-time mean-squared displacement while tortuosity was independently quantified from geometric path-length statistics. The simulations reveal a clear hierarchy of transport efficiency across cubic phases, with the gyroid exhibiting the highest effective diffusion, followed by the diamond and primitive geometries. Despite identical volume fractions and microscopic diffusion parameters, substantial differences in macroscopic transport emerge solely from geometric connectivity and path elongation, and when normalized diffusion coefficients are plotted against tortuosity, data from all geometries collapse onto a common scaling relationship, identifying tortuosity as a unifying geometric descriptor of transport. These results establish geometry as the dominant control parameter governing diffusion in bicontinuous cubic lipid networks and provide a geometry-only predictive framework that offers a minimal baseline for interpreting experimental transport measurements in cubic lipid phases and supports the rational design of cubosome-based systems with tunable transport properties.

biophysics↗

bioRxiv2026

Conserved Roles of Sp1 in Zebrafish Development and Early Organogenesis

Transcription factors (TFs) function in combinatorial networks to orchestrate gene expression during development and disease. Yet, the mechanisms underlying their context-specific regulatory roles remain poorly understood. Here, we investigate Specificity Protein 1 (Sp1), the first sequence-specific transcription factor identified and a key regulator of TATA-less gene promoters as a model to elucidate conserved and lineage-specific functions in vertebrate development. While Sp1 is extensively studied in mammalian systems, particularly in cancer progression, its evolutionary acquisition and developmental roles in early vertebrates remain unexplored. Using zebrafish as a model, we characterized the spatiotemporal expression dynamics and functional significance of sp1 during embryogenesis. Loss-of-function analyses revealed profound morphological defects across multiple organ systems, including skeletal, neural, and gastrointestinal tissues. Complementary stage-specific transcriptomic profiling uncovered widespread dysregulation of lineage-defining genes and perturbations in core cellular pathways related to the cell cycle, DNA metabolism, and apoptosis. Together, our findings establish Sp1 as a pivotal transcriptional regulator in early vertebrate development and reveal mechanistic insights into how conserved TF networks coordinate developmental programs and context-dependent disease states. Summary statementThis study characterizes the expression profile and establishes the conserved role of SP1 in specific processes during zebrafish development, which were previously unreported.

developmental biology↗