Biology subjects

Sharma, A. K.

Publications and source records attributed to Sharma, A. K..

At least 19 recordsLinked to original sources

bioRxiv2026

Structural Insights into the Expanded Substrate Scope of a Cysteine-Dependent Hydrolase from Rhodococcus opacus for Polyethylene, Polypropylene, and Polystyrene Biodegradation

Microplastic pollution from homopolymers such as polypropylene (PP), polystyrene (PS), and polyethylene (PE) poses growing health and environmental concerns, highlighting the need for robust polymer-degrading biocatalysts. We previously identified a naturally occurring cysteine-dependent hydrolase (CsdH) from Rhodococcus opacus, featuring a unique Cys160-Lys127-Asp39 catalytic triad and providing a novel mechanism for polyethylene terephthalate (PET) degradation. In this study, we have determined crystal structures of CsdH in complex with PP, PS, PE, and styrene and demonstrated the potential of the enzyme to directly degrade these homopolymers into their respective low molecular weight degradation products using LC-MS. Structural analysis reveals that the enzyme retains a conserved principal access tunnel while undergoing subtle substrate-dependent changes to accommodate different substrates. The enzyme exhibited broad plastic degradation activity with the highest weight loss observed for PE, followed by PP and PS. SEM analysis reveals surface roughness, cracks and grooves, confirming polymer degradation. Further, these results corroborate through FTIR and TGA analysis. These findings establish a strong foundation for enzyme engineering and aim at developing efficient microplastic degradation.

biophysics↗

bioRxiv2026

Integrated miRNA-protein profiling of small extracellular vesicle cargo reveals dynamic cargo remodelling during tissue repair in UV-C-damaged C. elegans

Ultraviolet-C (UV-C) radiation is a potent environmental stressor that induces DNA damage, accumulation of reactive oxygen species (ROS), and cellular dysfunction. This also initiates coordinated molecular responses to regulate cellular adaptation and recovery. Small extracellular vesicles (sEVs) have emerged as key mediators of intercellular communication through the selective incorporation of microRNAs (miRNAs), proteins, and lipids. However, the temporal changes of sEV-associated cargo during the progression from UV-C-induced damage to recovery remain uncharacterized. We hypothesised that UV-C exposure induces stage-specific changes in sEV cargo (miRNA and proteins) that promote the transition of cells from damage to the response and recovery phases. To examine this, a time-resolved UV-C exposure model was established using Caenorhabditis elegans (C. elegans). In this paper, we studied 2.5 hours of UV-C exposure, including cellular damage, intracellular ROS levels, and DNA integrity, to define the damage and repair state. Based on these temporal variations, samples were collected: i) immediately after exposure, ii) 6 hours post-exposure, and iii) 16 hours post-exposure were designated as damage, response, and recovery conditions, respectively. sEVs isolated from whole-worm preparations were characterised using biophysical and molecular approaches, followed by miRNA sequencing and proteomic analyses. Integrative analysis further identified miRNA-protein associations and associated them with pathways involved in stress adaptation, metabolism, signal transduction, and cellular homeostasis. Collectively, these findings provide a temporal molecular framework of sEV cargo associated with UV-C-induced damage, response, and recovery in C. elegans. Overall, this study identified candidate molecular signatures and miRNA-protein associations that underlie the temporally selective packaging of sEV-associated cargo following UV-C-induced damage, providing a basis for future tissue-specific and mechanistic investigations.

molecular biology↗

bioRxiv2026

Spindle Assembly Checkpoint Competency Determines Sensitivity to KIF18A Inhibition in Small-Cell Lung Cancer

BackgroundSmall-cell lung cancer (SCLC) is characterized by pervasive chromosomal instability (CIN) and remains largely refractory to targeted therapies. KIF18A, a motor protein that regulates chromosome alignment during mitosis, has emerged as a selective dependency in CIN-high tumors. Whether this dependency extends to SCLC, a prototypical CIN-high cancer, has not been established, and biomarkers predicting response to KIF18A inhibition, currently in clinical trials, are lacking. MethodsWe integrated analyses of patient tumor datasets, neuroendocrine (NE) and non- NE SCLC cell lines, and functional perturbation models to define the determinants of response to KIF18A inhibition. Chromosomal instability metrics, transcriptional programs, mitotic dynamics, and spindle assembly checkpoint (SAC) function were assessed using genomic profiling, live-cell imaging, genetic perturbation, and pharmacologic inhibition. ResultsKIF18A expression was elevated in SCLC tumors and correlated with CIN-associated transcriptional programs, proliferative markers, and NE status; however, these features did not predict sensitivity to KIF18A inhibition. Instead, response was determined by the functional integrity of the SAC. SAC-proficient SCLC cells underwent sustained mitotic arrest followed by apoptotic cell death upon KIF18A inhibition, whereas SAC-defective cells failed to maintain checkpoint activation and survived. Mechanistically, resistant cells exhibited impaired kinetochore recruitment of core SAC components, including MAD1 and BUBR1. Importantly, transient induction of acute CIN through MPS1 inhibition partially restored sensitivity to KIF18A inhibition in resistant models. ConclusionsThis study provides the first mechanistic characterization of KIF18A dependency in SCLC, identifying SAC competency as the primary determinant of response. These findings establish a biologically informed framework for patient stratification and rational combination strategies. Translational RelevanceSmall-cell lung cancer (SCLC) is an aggressive malignancy with few effective targeted therapies and marked chromosomal instability. KIF18A has emerged as a potential therapeutic target in genomically unstable cancers, but biomarkers predicting response to KIF18A inhibition are lacking. We demonstrate that sensitivity to KIF18A inhibition in SCLC is determined not by KIF18A expression, neuroendocrine subtype, or baseline chromosomal instability, but by the functional integrity of the spindle assembly checkpoint (SAC). SCLC cells with intact SAC signaling undergo sustained mitotic arrest and apoptosis upon KIF18A inhibition, whereas SAC-defective cells bypass checkpoint activation and survive aberrant mitosis. Notably, transient induction of acute chromosomal instability through MPS1 inhibition partially restores sensitivity in resistant models. Together, these findings identify mitotic checkpoint competency as a mechanistic determinant and candidate predictive biomarker for KIF18A-targeted therapies, providing a biologically informed framework for patient stratification and rational combination strategies relevant to ongoing KIF18A inhibitor clinical trials.

cancer biology↗

bioRxiv2026

Tumor-hepatocyte crosstalk drives a hepatic lactate-TGF-β axis of CD8⁺ T cell exhaustion and immunotherapy resistance in small-cell lung cancer liver metastases

PurposeLiver metastases confer poor outcomes and attenuate the benefit of immunotherapy across solid tumors. This study investigated how the hepatic metastatic niche promotes CD8 T cell dysfunction and immunotherapy resistance in small-cell lung cancer (SCLC). Experimental DesignClinical outcomes and tumor gene expression were integrated with multi-region single-cell RNA sequencing of T cells from rapid-autopsy SCLC metastases, together with spatial transcriptomics. SCLC-hepatocyte conditioned-media models were combined with stable-isotope tracing, mass spectrometry, functional and metabolic assays, and ChIP-qPCR to define mechanisms of CD8 T cell suppression. ResultsLiver metastases were associated with inferior survival and reduced benefit from immune checkpoint blockade. Multi-region single-cell analysis showed that CD8 T cells from liver metastases exhibited an exhaustion-associated state enriched for hypoxia, lactate, and TGF-{beta} programs. SCLC-hepatocyte crosstalk generated a lactate- and TGF-{beta}-rich microenvironment that reduced CD8 T cell effector function, proximal T cell receptor signaling, glycolytic fitness, viability, and proliferation. Stable-isotope tracing demonstrated transfer and accumulation of co-culture-derived lactate in recipient CD8 T cells, with limited entry into downstream pyruvate-linked pathways. Lactate accumulation was accompanied by increased H3K18 lactylation at the PDCD1, LAG3, and TGFB1 regulatory loci. In parallel, SCLC-hepatocyte crosstalk increased paracrine TGF-{beta} and activated canonical SMAD2 signaling in CD8 T cells. TGF-{beta} receptor inhibition restored CD8 T cell proliferation. In the phase III IMpower133 cohort, a combined lactate-TGF-{beta} transcriptional program was associated with inferior survival, most strongly in patients with liver metastases. ConclusionsTumor-hepatocyte crosstalk generates convergent lactate and TGF-{beta} signals that drive CD8 T cell dysfunction in liver metastases. This hepatic immune-metabolic circuit provides a potential mechanism for immunotherapy resistance and supports therapeutic strategies targeting TGF-{beta} signaling in liver-metastatic SCLC. Translational RelevancePatients with SCLC liver metastases have poor outcomes and derive limited benefit from immune checkpoint blockade, but actionable mechanisms of hepatic immune resistance remain undefined. We identify an immune-metabolic circuit in which SCLC-hepatocyte crosstalk generate lactate and TGF-{beta} signals that converge on CD8 T cells. Stable-isotope tracing demonstrates the transfer and accumulation of tumor-hepatocyte-derived lactate in recipient T cells, which causes H3K18 lactylation at exhaustion- and TGFB1-associated loci. In parallel, paracrine TGF-{beta} activates canonical SMAD signaling and reinforces proliferative dysfunction. TGF-{beta} receptor inhibition restores CD8 T cell proliferation. In the phase III IMpower133 cohort, a combined lactate-TGF-{beta} program is associated with inferior survival, particularly among patients with liver metastases. These findings provide a mechanistic and biomarker framework for testing TGF-{beta}-directed strategies in liver-metastatic SCLC, a population with substantial unmet clinical need.

cancer biology↗

bioRxiv2026

YAP/TAZ Signaling in Endothelial Cells Mediates the Pathogenesis of Abdominal Aortic Aneurysm Formation

BackgroundAbdominal aortic aneurysms (AAA) are characterized by dilation of the aorta that can lead to aortic rupture and death. The transcriptional co-activators Yes-Associated Protein (YAP) and WW-domain-containing transcriptional co-activator with PDZ-binding motif (TAZ) are mechanosensitive effectors of the highly conserved Hippo signaling pathway. It is hypothesized that cell-specific YAP/TAZ signaling in endothelial cells (EC) plays a pivotal role in mediating AAA formation and rupture. MethodsSingle-cell RNA-sequencing in human AAAs was performed and differentially expressed genes (DEGs) were identified in the endothelial cell cluster. YAP/TAZ mRNA and protein expression were also assessed in human AAA and control aortic tissue. Two established murine AAA models were used with male C57BL/6 and EC-CreERT2-YAPfl/fl/TAZfl/fl mice with/without Verteporfin (VPF, YAP/TAZ inhibitor) and XMU-MP-1 (YAP/TAZ activator) treatments. On postoperative days 14 and 28, aortic diameter, histology, cytokine, and MMP2 expressions were evaluated. ResultsA significant alteration in EC-specific differentially expressed YAP/TAZ-related genes was observed in which 242 genes were upregulated and 71 genes were downregulated in AAA compared to controls. Human AAA tissue showed a significant increase in YAP and TAZ protein expressions compared to controls. Elastase-treated EC-YAP/TAZ-/- mice showed a significant decrease in AAA diameter compared to littermate controls. Histological quantification revealed preservation of -smooth muscle actin, reduced elastin fiber breaks, and decreased macrophage infiltration in EC-YAP/TAZ-/- mice compared to littermate controls. Importantly, pharmacological inhibition of YAP/TAZ using VPF significantly attenuated AAAs in two experimental murine models. In vitro data demonstrates that VPF inhibits endothelial cell YAP expression, downregulating pathways associated with pathogenic angiogenesis and vascular inflammation. ConclusionsThese data suggest that EC-specific YAP/TAZ signaling mediates AAA formation. Pharmacological inhibition of the Hippo pathway can significantly mitigate aortic inflammation and vascular remodeling to decrease the progression of AAAs and prevent aortic rupture. HighlightsO_LIExpression of YAP/TAZ in endothelial cells is dysregulated in human AAAs. C_LIO_LIExperimental murine models demonstrate that: a) endothelial-cell specific deletion of YAP/TAZ protects against AAA formation, and pharmacologic alteration with b) verteporfin attenuates AAA formation, and c) XMU-MP-1 significantly exacerbates aortic inflammation, vascular remodeling, and rupture. C_LIO_LIVerteporfin inhibits endothelial YAP/TAZ activation by modulating ECM remodeling, pathogenic angiogenesis, pro-inflammatory cytokine and chemokine expression. C_LI

immunology↗

bioRxiv2026

Hepatobiliary Progenitor-like Reprogramming in Liver Metastases

Metastatic progression requires cancer cells to adapt to the unique constraints of distant organ microenvironments, yet the mechanisms that drive organ-specific adaptations remain poorly understood. Here, we show that the liver actively rewrites metastatic cancer cell identity, driving tumor cells toward a hepatobiliary progenitor-like state. Through integrated transcriptomic, proteomic, metabolomic, and epigenomic analyses of patient-derived rapid-autopsy samples and experimental models, we identify this state as selectively enriched in liver metastases. It is characterized by co-activation of hepatic and biliary/progenitor regulators HNF4A and SOX9 and is observed across multiple epithelial cancers, indicating a conserved response to the hepatic niche. Mechanistically, hepatocyte-derived TGF-{beta} and hypoxia converge to activate a HIF-1-ACLY axis, increasing nuclear acetyl-coenzyme A availability and histone acetylation at hepatic lineage regulatory elements to drive hepatobiliary reprogramming. This coordinated niche-response program can be captured transcriptionally and is associated with inferior overall survival. Disruption of this pathway suppresses hepatic reprogramming and impairs liver metastatic fitness. These findings identify the liver as an active determinant of metastatic cell fate, linking microenvironmental signaling to metabolic and chromatin remodeling programs that enable lineage plasticity. More broadly, they reveal organ-specific reprogramming as a fundamental principle of metastasis and a therapeutic vulnerability in liver metastases.

cancer biology↗

bioRxiv2026

Proprotein convertase subtilisin kexin type 9 (PCSK9) inhibition attenuates abdominal aortic aneurysm formation via enhanced macrophage-dependent efferocytosis

Abdominal aortic aneurysms (AAAs) occur predominantly in the elderly population and currently there is no effective pharmacological therapy for mitigating AAA growth and preventing impending rupture. Proprotein subtilisin kexin type 9 (PCSK9) gene has been identified as a specific risk-locus for AAA development. However, the mechanistic and clinical role of PCSK9-mediated signaling in AAAs has not been delineated. We demonstrate that treatment with PCSK9 inhibitors, such as Evolocumab, mitigates vascular inflammation and remodeling, resulting in attenuated aneurysm growth in clinical datasets as well as experimental models of AAA and aortic rupture. Mechanistically, Evolocumab immunomodulates macrophage reprogramming to enhance clearance of apoptotic smooth muscle cells via MerTK-dependent efferocytosis that ameliorates aortic inflammation and vascular remodeling. Furthermore, Evolocumab increases the expression of oxidized phosphatidylserine species and decreases expression of lysophospholipids, succinate, and glycolytic intermediates within the aortic wall compared to untreated controls, further enhancing the pro-resolving functions of macrophages. Collectively, our data demonstrates the ability of PCSK9 inhibition to regulate macrophage-specific efferocytosis that limits AAA progression and prevents aortic rupture.

immunology↗

bioRxiv2026

Vitamin D3 Deficiency Exacerbates Abdominal Aortic Aneurysm Progression Via Complement C3a Activation

Abdominal aortic aneurysm (AAA) is a chronic inflammatory vascular disease characterized by progressive extracellular matrix degradation, vascular smooth muscle cell (VSMC) loss, and immune cell infiltration, ultimately leading to aortic dilation and rupture. Although vitamin 25(OH)D3 deficiency has been associated with cardiovascular inflammation, its mechanistic role in AAA pathogenesis remains poorly defined. Here, we investigated the role of vitamin D{square} mediated signaling to regulate complement pathway activation, particularly the C3a axis, to modulate aneurysm development. Single cell-RNA sequencing analysis of human tissue demonstrated significant differences in Vitamin D and complement pathway-related genes in VSMCs in AAAs compared to control aortic tissue. Using a murine elastase-induced AAA model, we observed that vitamin D3-deficient diet significantly enhances aortic dilation, leukocyte infiltration, proinflammatory cytokine expression and elastin fragmentation, as well as decreases SMC -actin expression compared with vitamin D3-sufficient conditions. Furthermore, vitamin D3 deficiency was accompanied by increased aortic expression of complement component C3a that correlated with vascular inflammation and remodeling during AAA progression. Pharmacological blockade with a C3a receptor antagonist (C3aRA) markedly attenuated AAA formation in two established murine AAA models with concomitant reductions in proinflammatory cytokines and preservation of aortic wall structure. In vitro studies demonstrated that stimulation of VSMCs significantly increased C3a production, which was suppressed by calcitriol (active form of Vitamin D) treatment. These studies suggest that the vitamin D-C3a axis is a critical regulator of vascular inflammation and AAA progression, and postulate that restoring vitamin D{square} sufficiency or targeting C3a signaling may represent a novel therapeutic strategy to limit AAA growth and rupture. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=162 SRC="FIGDIR/small/730431v1_ufig1.gif" ALT="Figure 1"> View larger version (36K): org.highwire.dtl.DTLVardef@1e6a56dorg.highwire.dtl.DTLVardef@176b1b9org.highwire.dtl.DTLVardef@18e1fcdorg.highwire.dtl.DTLVardef@1c9eb4d_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2026

SuFEx and macrocyclic chelation define orthogonal reactivity domains enabling isotopically versatile radiopharmaceuticals from a single peptide precursor

The design of radiotheranostic agents has been constrained by a fundamental chemical incompatibility: existing strategies for fluorine-18 incorporation -- nucleophilic substitution, silicon-fluoride exchange, aluminum fluoride chelation, and prosthetic conjugation -- either require conditions incompatible with macrocyclic metal coordination, consume the chelator site needed for radiometal labeling, or introduce non-native structural appendages that alter pharmacokinetic behavior. Here we show that sulfur(VI) fluoride exchange (SuFEx) chemistry and macrocyclic metal coordination define non-overlapping reactivity domains co-embeddable within a single peptide precursor. An aryl fluorosulfate on tyrosine accepts {superscript 1}F under mildly basic conditions; a spatially distinct macrocyclic chelator, DOTA, NOTA, NODAGA, or any compatible macrocycle, independently coordinates diagnostic (68Ga, 64Cu) or therapeutic (177Lu) radiometals under mildly acidic conditions. The labeling pathways proceed independently under mutually compatible conditions, and both preserve receptor-binding affinity. Validated across PD-L1- and CD38-targeting scaffolds, this platform delivers nanomolar target affinity, high radiochemical yields, and matched pharmacokinetics, establishing isotopic orthogonality as a designable, intrinsic property of synthetic molecular radiopharmaceuticals.

bioengineering↗

bioRxiv2026

Delivery of defective interfering RNA antivirals to the lungs using hyperbranched poly(beta-amino ester) nanoparticles

Hyperbranched poly(beta-amino ester) (hPBAE) nanoparticles represent a promising platform for nucleic acid delivery, particularly to the lungs. In this study, we evaluate the potential of hPBAE nanoparticles to deliver defective interfering RNA (diRNA) antivirals targeting betacoronaviruses under a range of formulations and storage conditions. hPBAE-diRNA nanoparticles demonstrated efficient cellular uptake of functional diRNA across diverse cell types, conferred protection against nuclease-mediated degradation, and exhibited low in vitro cytotoxicity. In vivo, these nanoparticles enabled effective delivery of functional diRNA to the lungs of golden hamsters without inducing adverse physiological effects. Collectively, these findings support hPBAE nanoparticles as a safe and effective platform for diRNA delivery for the treatment of respiratory viral infections. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=66 SRC="FIGDIR/small/721911v1_ufig1.gif" ALT="Figure 1"> View larger version (19K): org.highwire.dtl.DTLVardef@2fc386org.highwire.dtl.DTLVardef@1cda4f9org.highwire.dtl.DTLVardef@9f61borg.highwire.dtl.DTLVardef@1fc8461_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical Abstract.C_FLOATNO Defective interfering RNA was mixed with hyperbranched poly(beta-amino ester) nanoparticles and delivered to cells in vitro and to golden hamsters in vivo, to measure toxicity and the replication potential of the RNA. C_FIG

microbiology↗

bioRxiv2026

Calmodulin requires calcium to be a constitutive component of the spindle pole bodies in fission yeast

Although calmodulin is best known as a calcium sensor, it also possesses Ca2+-independent functions, exemplified by the surprising finding that the budding yeast cells remain viable using a calmodulin mutant that cant bind Ca2+ (Geiser et al., 1991). It remains unclear why Ca2+-calmodulin is required in other yeasts or vertebrates. Here, we determined whether such holo-calmodulin is an essential cytoskeletal protein in fission yeast. The S. pombe calmodulin Cam1 was an integral part of both the spindle pole body (SPB) and many actin structures at the equatorial division plane. Two mutants Cam1-2V and -3V, which bound Ca2+ poorly, reduced their localization at the SPBs by 90%. However, their presence in the actin structures remained unchanged. Replacing the endogenous cam1 with cam1-2V cut the number of the Cam1-interacting protein Pcp1 in the SPB by [~]70% and delayed mitosis. In contrast, the assembly and constriction of the cytokinetic ring, which depends on the Cam1-interacting myosins Myo1, Myo51 and Myo52, accelerated. The temperature-sensitive cam1-2V mutant was rescued by either over-expression of pcp1 or deletion of myo1. Thus, Cam1 depends on Ca2+ to promote the SPB assembly and to modulate the actomyosin ring constriction, suggesting holo-calmodulin as an essential cytoskeletal protein.

cell biology↗

bioRxiv2026

Tryptophan degradation by intestinal Bacteroides induces anti-tumor immunity and limits melanoma growth

Defining mechanisms used by gut microbiota to control anti-tumor immunity may offer novel therapeutic modalities. Here, we demonstrate that Bacteroides rodentium and closely related Bacteroides uniformis species induce anti-tumor immunity and limit melanoma development when colonized in either germ-free (GF) mice, mice with a complex microbiome, or WT mice. Enhanced CD8+ T cell infiltration seen in tumors of mice harboring B. rodentium coincided with increased expression of immune-stimulating pathways and activation of bone marrow-derived dendritic cells that were co-cultured with the B. rodentium secretome. Metabolomic analyses of cecal samples from GF mice colonized with Altered Shedlar Flora (ASF) plus B. rodentium revealed lower tryptophan levels than in ASF-colonized controls, and WT mice fed a tryptophan-deficient diet exhibited inhibition of melanoma development. In silico genomic reconstruction of metabolic pathways revealed that both B. rodentium and B. uniformis harbor tryptophanase A (TnaA) and aromatic amino transferase (ArAT) genes, both of which function in tryptophan degradation. Administration of a B. uniformis harboring TnaA mutant failed to inhibit melanoma growth in gnotobiotic mice. Notably, administration of indoles, but not kynurenines, also effectively inhibited melanoma development, increasing immune cell infiltration into the tumors. Correspondingly, levels of bacterially encoded tryptophan-degrading enzymes were higher in cohorts of melanoma patients responding to immune checkpoint blockade. These findings highlight a novel mechanism of anti-tumor immunity and tumor growth inhibition dependent on the tryptophan degradation products, indoles, produced by intestinal Bacteroides species.

cancer biology↗

bioRxiv2026

Structural basis of substrate recognition and conformational gating in the bacteriophage M15 metalloendopeptidase LysPH

The rapid emergence of antimicrobial resistance has led to a surge in multidrug-resistant strains, jeopardising the efficacy of frontline and last-resort antibiotics and thereby aggravating the antimicrobial resistance crisis. Bacteriophage-derived endolysins represent a promising class of next-generation antimicrobials. Here, we report the isolation of a novel bacteriophage, PA_Ganga_001, targeting multidrug-resistant Pseudomonas aeruginosa. Genomic sequencing of this phage identified a previously uncharacterised endolysin LysPH, a zinc-dependent globular endolysin that exhibits antibacterial activity against multiple multidrug-resistant Gram-negative pathogens, including Pseudomonas aeruginosa, Acinetobacter baumannii, and Klebsiella pneumoniae. Site-directed mutagenesis of the endolysin LysPH suggests that His77, Asp84, His159, Arg41, and Asp156 are essential for catalysis and substrate accommodation. To understand the structural basis of substrate binding and catalysis, we determined the crystal structures of the apo-enzyme (1.8 [A]) and the catalytically attenuated D156A mutant in complex with a synthetic pentapeptide stem (PGX) of peptidoglycan (2.0 [A]). The pentapeptide-bound complex revealed a defined substrate-binding groove, and a pronounced displacement of the Thr42-Ser75 loop was observed. This led to an approximately six-fold volumetric expansion of the catalytic cleft, indicative of a substrate-induced transition to an open, catalytically competent conformation. Notably, a distinctive C-terminal helical element, which diverges sequentially from characterised M15 homologues, is predicted to interact with the NAG-NAM scaffold and may contribute to the positioning of the stem pentapeptide for Zn2+ dependent catalysis. These distinct structural features establish the molecular basis for L-Ala-D-Glu hydrolysis by M15 bacteriophage endolysins and provide a foundational framework for the rational design and engineering of the next generation of antimicrobial enzymes.

biochemistry↗

bioRxiv2026

Targeting the DNA damage repair protein RAD51 alters fibroblast metabolism and enhances apoptosis in pulmonary fibrosis

BackgroundIdiopathic pulmonary fibrosis (IPF) is a progressive and fatal lung disease characterized by aberrantly activated, apoptosis-resistant profibrotic lung (myo)fibroblasts. Prior research has demonstrated that lung fibroblasts from patients with IPF exhibit resistance to DNA damage, suggesting that this behavior contributes to their persistent survival and continuous proliferation. We propose that elevated levels of the DNA damage repair protein RAD51 regulate myofibroblast activation and apoptosis and provide a potential therapeutic target to impede fibrosis progression. MethodsHuman lung fibroblasts were transfected with siRNA against RAD51 or treated with RAD51-specific inhibitor B02 and markers of fibrosis, DNA damage, apoptosis, metabolic reprogramming, and mitochondrial dynamics were assessed. The preclinical efficacy of B02 was evaluated in human precision cut lung slices (PCLS) and in a mouse model of pulmonary fibrosis. FindingsRAD51 expression was significantly upregulated in the lungs and lung fibroblasts of IPF patients. Knockdown or inhibition of RAD51 in fibroblasts reduced profibrotic marker expression, suppressed mTORC1 signaling and mitochondrial function, and increased apoptosis susceptibility. Pharmacological inhibition of RAD51 shifted the profibrotic phenotype towards a fibrosis-resolving state in human and mouse PCLS, and in a bleomycin-induced mouse model of lung fibrosis. InterpretationThe inhibition of RAD51 exerts therapeutic benefits in lung fibrosis by promoting apoptosis. Our findings identify that inhibiting RAD51 with B02 in fibroblasts impairs DNA repair and induces metabolic reprogramming, making it a potential therapeutic target. Research in contextO_ST_ABSEvidence before this studyC_ST_ABSPulmonary fibrosis (PF) is characterized by excessive fibroblast activation and subsequent deposition of extracellular matrix (ECM) proteins, which ultimately disrupt normal lung architecture. A significant contributing factor to the pathogenesis of pulmonary fibrosis is the presence of fibroblasts that are resistant to apoptosis, preventing normal wound healing. Recent studies highlight the DNA repair protein RAD51 as effective in protecting fibroblasts from death induced by chemotherapy and ionizing radiation. These finding suggested that RAD51 could have a role in fibroblast activation and apoptosis resistance in pulmonary fibrosis. Added value of this studyWe demonstrated that RAD51 is important for maintaining apoptosis-resistant fibrotic fibroblasts and their metabolic abnormalities. Our findings indicated that TGF{beta}-mediated upregulation of RAD51 reduces DNA damage, activates multiple pathways related to fibroblast activation and proliferation, and induces metabolic reprogramming, ultimately regulating apoptosis. Mechanistically, RAD51 inhibition enhanced p53 acetylation at lysine 120 and upregulated the expression proapoptotic proteins PUMA/BAK in mitochondria, promoting apoptosis. Pharmacological inhibition of RAD51 using the specific inhibitor B02 during the fibrotic phase of experimental lung disease effectively ameliorated pulmonary fibrosis. Implications of all the available evidenceOur findings establish that RAD51 plays an important role in the survival of apoptosis-resistant fibrotic fibroblasts. We propose that reducing RAD51 expression leads to the metabolic reprogramming of activated fibroblasts, resulting in decreased mitochondrial respiration, reduced ATP levels, and diminished glycolysis or glutaminolysis. These observations suggest that targeting energy metabolism through RAD51 inhibition could be a viable strategy to enhance apoptosis, thereby creating a therapeutically targetable pathway in fibrotic cells. These findings highlight the potential of RAD51 as a therapeutic target for the treatment of IPF.

cell biology↗

bioRxiv2025

Chemical Dice Integrator (CDI): A Scalable Framework for Multimodal Molecular Representation Learning

The machine learning landscape for molecular property prediction is fragmented, with numerous Featurizers each capturing a narrow, specialized view of chemical structure. This heterogeneity forces a suboptimal choice of representation a priori, limiting model generalizability. We introduce the Chemical Dice Integrator (CDI), a hierarchical framework that unifies six orthogonal molecular representations, physicochemical (Mordred), topological (GROVER), visual (ImageMol), biological (Signaturizer), quantum-mechanical (MOPAC), and linguistic (ChemBERTa), into a single, coherent embedding. The framework consists of CDI-Basic, a two-tiered autoencoder that fuses these modalities, and CDI-Generalised, a Mamba State-Space Model (SSM) that learns a direct, efficient map from SMILES strings to the unified embedding space. Extensive benchmarking across 23 classification (171 tasks) and 10 regression datasets demonstrates that CDI embeddings consistently achieve superior predictive performance compared to individual Featurizers and standard feature aggregation methods. The CDI-Generalised model achieves this performance with exceptional computational efficiency, outperforming deep learning Featurizers in terms of speed and resource overhead. Furthermore, we demonstrate that the CDI embedding is chemically intuitive, allowing for the sensitive distinction of nuanced structural variants, such as chiral enantiomers and kekulized SMILES forms. By bridging multimodal chemical intelligence with scalable, sequence-based inference, CDI offers a strong foundation for molecular machine learning.

bioinformatics↗

bioRxiv2025

Protectin D1/GPR37 signaling enhances macrophage-dependent efferocytosis to attenuate experimental abdominal aortic aneurysm formation

Abdominal aortic aneurysms (AAAs) are chronic inflammatory vascular disorders characterized by progressive aortic dilation and destruction of the vascular wall, often culminating in rupture. Current management is limited to surgical repair, with no approved targeted pharmacologic therapies. In this study, we investigated the immunomodulatory role of Protectin D1 (PD1), a specialized pro-resolving lipid mediator, through G-protein-coupled receptor 37 (GPR37) signaling on macrophages in mitigating AAA progression and preventing aortic rupture. Single cell-RNA sequencing analysis of human tissue demonstrated significant differences in PD1/GPR37 axis-related genes in macrophages in AAAs compared to control aortic tissue. Using an established murine AAA model, PD1 administration significantly attenuated aortic diameter, pro-inflammatory cytokine and matrix metalloproteinase (MMP2) expression, as well as maintained aortic morphology in a GPR37-dependent manner. Importantly, PD1 treatment prevented preformed AAA progression to aortic rupture in another preclinical elastase+BAPN model of aortic rupture, by attenuating aortic diameter, tissue inflammation as well as decreasing macrophage infiltration, preserving elastin integrity, and restoring smooth muscle -actin expression in the aortic wall. Mechanistically, PD1 enhanced macrophage efferocytosis of apoptotic vascular smooth muscle cells in the murine aortic tissue as well as in isolated macrophages via GPR37-dependent manner and attenuated the inflammatory paracrine secretion of macrophage-specific paracrine release of TNF- and IL-{beta}. These findings suggest that PD1/GPR37 signaling on macrophages promotes inflammation-resolution by enhancing efferocytosis of apoptotic SMCs conferring protection against aortic inflammation and remodeling to mitigate AAA formation and rupture. Significance StatementThis study elucidates the protective role of specialized proresolving lipid mediator, Protectin D1, by activating macrophages via GPR37 receptors, to enhance the clearance of apoptotic smooth muscle cells to mitigate aortic inflammation and vascular remodeling during abdominal aortic aneurysm formation. We observed that several key inflammation related genes were associated with PD1/GPR37-dependent signaling in macrophages of human AAAs. Detailed analysis in experimental models delineated the signaling pathway where upregulating macrophage-dependent efferocytosis via immunomodulation by Protectin D1 attenuated aortic inflammation and remodeling, indicating a potential mechanism for therapeutic intervention in the pathobiology of AAAs to prevent aortic rupture.

immunology↗

bioRxiv2025

Exogenous BMP9 therapy ameliorates primary graft dysfunction post lung transplantation

Primary graft dysfunction (PGD) is a leading cause of early mortality after lung transplantation and is driven by ischemia-reperfusion injury (IRI), which destabilizes the pulmonary endothelium. Bone morphogenetic protein 9 (BMP9), a vascular quiescence factor of the TGF superfamily, maintains endothelial homeostasis through ALK-1/BMPR2-mediated signaling. Herein, this work identified a previously unrecognized suppression of BMP9 signaling during early reperfusion in a murine orthotopic lung transplant model. Allograft transcriptomic profiling revealed rapid downregulation of BMP9 pathway components, including Bmpr2, Acvrl1, Smad5, and Eng. Recombinant BMP9 administered at reperfusion enhanced Id1 expression in pulmonary endothelium, reduced neutrophil infiltration, preserved vascular barrier function, and improved oxygenation. In vitro, BMP9 attenuated proinflammatory cytokine release following simulated cold ischemia-reperfusion injury in human lung endothelial cells. Plasma from lung transplant recipients, regardless of PGD status, had impaired BMP9-induced ID1 expression in endothelial cells, with the most profound suppression observed in patients with interstitial lung disease. These findings implicate transient loss of BMP9 signaling as a key feature of transplant-induced vascular injury and support the therapeutic potential of BMP9 supplementation to restore endothelial homeostasis and improve early graft outcomes.

immunology↗

bioRxiv2025

CerS2 is a druggable target in triple-negative breast cancer

Triple-negative breast cancer (TNBC) remains a significant clinical challenge due to its aggressive nature and lack of effective targeted therapies. The enzyme ceramide synthase 2 (CerS2), which synthesizes pro-apoptotic very long-chain ceramides (VLCCs), represents a promising therapeutic target. Here, we identify and characterize DH20931, a novel, first-in-class small-molecule agonist of CerS2. We demonstrate that DH20931 directly activates CerS2 with nanomolar potency, leading to significant VLCC accumulation in breast cancer cells. This lipotoxic event induces endoplasmic reticulum (ER) stress and triggers apoptosis via the canonical ATF4/CHOP/PUMA signaling pathway. Mechanistically, we uncover a novel interaction between CerS2 and the ER calcium channel, Inositol 1,4,5-trisphosphate receptor 1 (IP3R1). We demonstrate that DH20931 promotes this interaction, enhancing ER-mitochondria proximity and facilitating a CerS2-dependent flux of calcium (Ca{superscript 2}) from the ER into mitochondria. This subsequent mitochondrial Ca{superscript 2} overload serves as a critical trigger for apoptosis. In preclinical evaluations, DH20931 potently inhibited the growth of TNBC cells in 2D and 3D cultures and significantly suppressed tumor progression in orthotopic and patient-derived xenograft (PDX) models, all while exhibiting a favorable safety profile. Our findings validate CerS2 as a druggable target in TNBC and establish a novel therapeutic strategy that leverages a coordinated attack on cancer cells through ER stress and calcium-mediated mitochondrial dysfunction. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=100 SRC="FIGDIR/small/670525v1_ufig1.gif" ALT="Figure 1"> View larger version (33K): org.highwire.dtl.DTLVardef@2db377org.highwire.dtl.DTLVardef@6175d4org.highwire.dtl.DTLVardef@7edb8corg.highwire.dtl.DTLVardef@80042e_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIDH20931 is a first-in-class, potent agonist of Ceramide Synthase 2 (CerS2). C_LIO_LICerS2 activation induces ER stress and engages the ATF4/CHOP/PUMA apoptotic pathway. C_LIO_LIDH20931 promotes a novel CerS2-IP3R1 interaction, causing lethal mitochondrial calcium overload. C_LIO_LITargeting CerS2 shows significant preclinical efficacy against triple-negative breast cancer. C_LI

cancer biology↗