Biology subjects

Qian, J.

Publications and source records attributed to Qian, J..

At least 37 records · Page 2Linked to original sources

bioRxiv2025

ATHENA: A deep learning-based AI for functional prediction of genomic mutations and synergistic vulnerabilities in prostate cancer

Identifying functional mutations that drive therapy resistance remains a major challenge in prostate cancer. Large-scale sequencing often produces extensive lists of mutations but provides limited insight into which alterations are functionally relevant. To overcome this gap, we developed ATHENA (Attention-based Therapeutic Network Analyzer), a deep learning-based AI framework that predicts the functional impact of genomic mutations and reveals their synergistic vulnerabilities. Integrated with our RNA/DNA-informed variant discovery pipeline OncoVar, ATHENA models nonlinear dependencies among mutations to distinguish driver events from passenger variants. Trained on large multi-cohort datasets and interpreted using SHAP analysis, ATHENA not only stratifies patients by clinical outcomes but also predicts which specific mutations alter tumor behavior and therapy response, enabling direct validation through base editing experiments. Applied to prostate cancer progression models, the OncoVar-ATHENA framework identified stage-specific driver signatures across castration-resistant, AR-variant-driven, and metastatic disease, and uncovered cooperative interactions such as SYVN1-STC2 that promote tumor proliferation. By moving beyond simple mutation identification, ATHENA enables functional prediction of genomic interactions. This approach accelerates the discovery of actionable targets and provides a foundation for rational design of next-generation combination therapies in advanced prostate cancer.

cancer biology↗

bioRxiv2025

Pro4S: prediction of protein solubility by fusing sequence, structure, and surface

Protein solubility is a critical physicochemical property influencing protein stability, therapeutic efficacy, and overall developability in drug discovery. However, traditional experimental methods for assessing solubility are often resource-intensive and time-consuming. To address these limitations, computational approaches leveraging artificial intelligence have emerged, yet current models generally treat qualitative classification and quantitative regression as separate tasks and rely predominantly on sequence-based information, neglecting crucial structural and surface characteristics. Here, we introduce Pro4S, a novel multimodal predictive model that integrates protein language models, structural data, and surface descriptors using advanced contrastive learning techniques. Our unified framework achieves significant improvements in prediction accuracy, robustness, and generalizability for both qualitative and quantitative solubility assessments. Benchmark comparisons demonstrate that Pro4S consistently outperforms existing state-of-the-art predictors across diverse datasets. Furthermore, by applying Pro4S to the emerging area of de novo protein design, we validated a strong correlation between predicted solubility and experimental expression levels, reducing the proportion of non-expressed proteins by 52.7% while retaining 96.7% of highly expressed proteins. This highlights Pro4Ss potential to serve as a reliable upfront screening tool for increasing expression success rates and accelerating rational protein engineering.

bioinformatics↗

bioRxiv2025

In-situ Observation of Fast Chloroplast Dynamics in Intact Leaves

Chloroplast relocation is a hallmark of plant photoprotection, yet has long been regarded as a slow, minute-scale process. Here we overturn this view by directly visualizing chloroplast motility in intact leaves with the second near-infrared (NIR-II, 900-1880 nm) fluorescence confocal microscopy, an optical strategy uniquely suited for deep, in situ imaging. By harnessing the intrinsic long-wavelength fluorescence tail of chloroplasts, this method minimizes scattering, extends imaging depth, and enables simultaneous stimulation-imaging with subcellular resolution--capabilities not attainable with conventional visible fluorescence or multiphoton fluorescence microscopy. Using this approach, we discover that submerged leaves of amphibious plants exhibit remarkably rapid avoidance responses to red light, whereas aerial leaves show negligible relocation. Control experiments exclude influence of the physical structure of leaves, confirming that these contrasting responses reflect distinct physiological adaptations to environmental light regimes. Beyond revealing unexpected speed and flexibility in chloroplast dynamics, our findings establish the second near-infrared fluorescence confocal microscopy as an important tool for direct observation of fast subcellular processes in deep photosynthetic tissues and advancing plant photobiology.

plant biology↗

bioRxiv2025

Integrated single-cell whole genome sequencing and spatial transcriptomics reveal latent intra-tumoral heterogeneity in ovarian cancer

The mortality rate of ovarian cancer remains disproportionately high compared to its incidence. This is partly due to a high level of intra-tumoral heterogeneity that promotes disease recurrence and treatment failure. In this study, we describe degrees of heterogeneity revealed by single-cell whole genome sequencing and spatial transcriptomics of five epithelial ovarian carcinomas. At the cellular level, we describe pseudo-diploid cells that match the malignant cell population in both somatic variant and copy number patterns. At the clonal and subclonal levels, we describe diversification associated with copy number gains and whole genome doubling. In multi-clonal samples, we infer evolutionary relationships from single cell copy number, loss of heterozygosity analysis, and somatic variant detection, and correlate these with tissue histology and gene expression programs. In one sample, we identify functionally consequential copy number alterations that contribute to molecular diversity, cell proliferation, and inflammation in a minor clone that persisted without major expansion alongside a more complex major clone. In another, we describe a complex evolutionary history including a spontaneous reversion of a driver mutation in a secondary clone, which correlated with a switch in oncogenic expression programs.

cancer biology↗

bioRxiv2025

Binding of inhibitory checkpoints to CD18 in cis hinders anti-cancer immune responses

SIRP is an inhibitory receptor on macrophages that limits phagocytosis and anti-tumor activity of macrophages by "trans" interacting with CD47 on tumor cells. Herein, we found that a large component of SIRPs inhibitory function occurred independently of CD47-binding and phosphatase signaling. This function resulted from a direct interaction between SIRP and CD18 ({beta}2 integrin) in "cis" at the surface of macrophages, involving SIRP amino acids distinct from those implicated in the SIRP-CD47 interaction. The cis interaction prevented activation of CD18, which is necessary for phagocytosis. Combined blockade of SIRP-CD18 and SIRP-CD47 was essential for maximizing phagocytosis and suppression of tumor growth in vivo. Similar cis interactions between CD18 and other inhibitory checkpoints, including PD-1, were also observed. Thus, in addition to mediating effects when engaged by ligands in trans, inhibitory checkpoints suppress immune cell activation through a mechanism targeting CD18 in cis. This dual mode of action should be considered when developing blockers of inhibitory checkpoints for immunotherapy. One-Sentence SummaryIn addition to being engaged in "trans" by ligands on tumor cells, inhibitory receptors, such as SIRP and PD-1, hinder anti-cancer immune responses by "cis" interacting with {beta}2 integrin CD18.

immunology↗

bioRxiv2025

Comparative single-cell multiomic analysis reveals evolutionarily conserved and species-specific cellular mechanisms mediating natural retinal aging.

Biological age is a major risk factor in the development of common degenerative retinal diseases such as age-related macular degeneration and glaucoma. To systematically characterize molecular mechanisms underlying retinal aging, we performed integrated single- cell RNA- and ATAC-Seq analyses of the retina and retinal pigment epithelium (RPE) across the natural lifespan in zebrafish, mice, and humans. By profiling gene expression and chromatin accessibility, we identified extensive cell type- and species-specific aging-dependent changes, with a much smaller number of broadly expressed and conserved genes that include regulators of inflammation and autophagy. We constructed predictive aging clocks for retinal cell types and observed dynamic, reversible shifts in cellular age following acute injury. Spatial transcriptomic analysis revealed region-specific aging signatures and proximity effects, with Muller glia exhibiting pro-rejuvenating influences on neighboring neurons. Targeted Muller glia-specific induction of Yamanaka factors reduced molecular age in rod photoreceptors and bipolar cells without altering glial age. Our findings define conserved and divergent regulatory and signaling pathways mediating retinal aging, highlighting Muller glia as potential therapeutic targets for combating age-associated retinal dystrophies.

neuroscience↗

bioRxiv2025

The Eukaryotic homology search complex distorts donor DNA structure to probe for homology

Homologous recombination (HR) is a DNA double-strand break repair pathway that facilitates genetic exchange and protects damaged replication forks during DNA synthesis. As a template-based repair process, the successful repair of a double-strand break depends on locating suitable homology from a donor DNA sequence elsewhere in the genome. In eukaryotes, Rad51 catalyzes the homology search in coordination with the ATP-dependent motor protein Rad54. The mechanism by which these two proteins regulate forces on dsDNA substrates during homology search remains unknown. Here, we have utilized single-molecule magnetic tweezers and optical trapping methods to monitor remodeling of the DNA template during the homology search. We find that the activity of Rad51 and Rad54 remodels the donor DNA substrate to control the association and dissociation of Rad51-ssDNA filaments in the absence of DNA homology. This mechanism occurs through the application of both linear (tension) and rotational (torsion) forces on the donor DNA. Finally, failure of Rad54 to act processively disrupts target selection in vivo. This study provides a basic understanding of how motorized homology search manipulates the donor DNA during the search for a suitable repair template. Significance StatementHomologous recombination (HR) is a double-strand DNA break repair pathway that utilizes a template-based target search process to locate a suitable homologous DNA sequence in the genome, thereby initiating DNA repair. Called the homology search, in eukaryotes, this process is carried out by the RecA family member Rad51. During the homology search, Rad51 collaborates with the motor protein Rad54 to identify and interrogate homologous DNA sequences within the genome. In this study, we have measured the forces applied by the combination of Rad51 and Rad54 to the donor DNA duplex. These measurements reveal a coordinated effort by these motor proteins to remodel donor DNA to probe for homology, shedding new light on how template-based homology searches interrogate the DNA strands.

biochemistry↗

bioRxiv2025

Single-Cell Characterization of Anterior Segment Development: Cell Types, Pathways, and Signals Driving Formation of the Trabecular Meshwork and Schlemm's Canal

Morphogenesis of the anterior segment (AS) is crucial for healthy ocular physiology and vision but is only partially understood. The Schlemms canal (SC) and trabecular meshwork (TM) are essential drainage tissues within the AS, and their proper development and function are critical for maintaining normal intraocular pressure; abnormalities in either tissue can result in elevated pressure and glaucoma. Here, we use single-cell transcriptomic profiling to provide high-resolution molecular detail of AS development with a particular focus on SC and TM. We report transcriptomes for [~]130,000 single cells at key developmental stages from postnatal day 2 (P2) to P60. We provide the first annotation of cell types across these developmental stages and crucial information about dynamic changes in pathways/gene expression. Further, we trace developmental trajectories for TM cell and SC endothelial cell (SEC) subtypes and determine genes and signaling networks driving their specific cell fates. We demonstrate dynamic changes in signaling interactions between SC and the TM cells during their synchronized development. Collectively, our data lay a deep molecular foundation for AS development that will direct understanding of normal ocular physiology, glaucoma, and other AS conditions.

developmental biology↗

bioRxiv2025

The ribosome-associated complex regulates cytosolic translation upon mitoprotein-induced stress

The biogenesis of mitochondria relies on the import of newly synthesized precursor proteins from the cytosol. Tom70 is a mitochondrial surface receptor which recognizes precursors and serves as an interface between mitochondrial protein import and the cytosolic proteostasis network. Mitochondrial import defects trigger a complex stress response, in which compromised protein synthesis rates are a characteristic element. The molecular interplay that connects mitochondrial (dys)function to cytosolic translation rates in yeast cells is however poorly understood. Here, we show that the deletion of the two Tom70 paralogs of yeast (TOM70 and TOM71) leads to defects in mitochondrial biogenesis and slow cell growth. Surprisingly, upon heat stress, the deletion of ZUO1, a chaperone of the ribosome-associated complex (RAC), largely prevented the slow growth and the reduced translation rates in the tom70{Delta}/tom71{Delta} double deletion mutant. In contrast, the mitochondrial defects were not cured but even enhanced by ZUO1 deletion. Our study shows that Zuo1 is a critical component in the signaling pathway that mutes protein synthesis upon mitochondrial dysfunction. We propose a novel paradigm according to which RAC serves as a stress-controlled regulatory element of the cytosolic translation machinery.

biochemistry↗

bioRxiv2025

Accelerating protein design by scaling experimental characterization

Recent advances in de novo protein design have greatly outpaced standard protein biochemistry workflows, and experimental testing has been a bottleneck in the validation of new designs and methodologies. Here, we describe experimental and computational workflows to address the issues of scale, speed and reproducibility of common in vitro protein testing methods, enabling at least an order of magnitude increase in throughput while reducing wetlab time. Semi-Automated Protein Production (SAPP) is a rapid, modular, scalable and cost-effective protocol, enabling up to milligram-scale protein production, and standardized characterization including yield, dispersity, and oligomeric state of hundreds of designs per day, at the cost-equivalent of a few DNA oligos per construct. End-to-end protocol execution takes 48 hours, with about 6 hours spent benchside using mostly standard laboratory equipment. This protocol has become the standard at our institute, providing critical experimental validation for dozens of projects spanning tens of thousands of designs. We showcase the power of the platform by using it to rapidly characterize de novo designed inhibitors of respiratory syncytial virus. Since at least 80% of SAPPs total cost comes from synthetic DNA, we also developed a scalable demultiplexing protocol (DMX) to leverage oligo pools as input DNA, providing a further 5-fold reduction in costs, enabling >1000 designs to be purified and characterized in arrayed, clonal format at a cost of $5 per construct. By reframing standard molecular biology practices and orchestrating wetlab workflows with partial automation instead of complex end-to-end robotics, these protocols should be widely adoptable, accelerating protein design.

biochemistry↗

bioRxiv2025

Netrin-1 promotes pancreatic tumorigenesis and innervation through NEO1.

Nerves have been shown to regulate cancer progression. However, a clear demonstration of a role for axon guidance molecules in pancreatic tumorigenesis, innervation, and metastasis has been lacking. Using murine KrasG12D-mutant pancreatic organoids, we screened axon guidance molecules by qRT-PCR, identified Ntn1 upregulation, and then verified its in vivo upregulation during pancreatic tumorigenesis in humans and mice. NTN1 and its receptor NEO1 were upregulated in epithelial cells by the Kras mutation and {beta}-adrenergic signaling, in part, through the MAPK pathway. Ex-vivo culture of celiac ganglia showed that NTN1 promoted the axonogenesis of sympathetic neurons through the nerve NEO1 receptor. In the Pdx1-Cre;LSL-KrasG12D/+ model, Ntn1 knockout decreased sympathetic innervation and the development of pancreatic intraepithelial neoplasia. Treatment of pancreatic tumor organoids with recombinant NTN1 enhanced cell growth, epithelial-mesenchymal transition (EMT), and cancer stemness with the upregulation of ZEB1 and SOX9 through NEO1-mediated activation of focal adhesion kinase (FAK). In Pdx1-Cre;LSL-KrasG12D/+;LSL-Trp53R172H/+mice, Ntn1 knockout reduced innervation, FAK phosphorylation, and the features of EMT and stemness to extend mouse survival. In a liver metastasis model of PDAC (pancreatic ductal adenocarcinoma), treatment with a NTN1-neutralizing antibody or tumoral knockdown of Neo1 reduced ZEB1 and SOX9 and decreased tumor progression. In contrast, Ntn1 overexpression promoted innervation and the progression of PDAC liver metastasis. These data suggest that the NTN1/NEO1 axis is a key regulator of PDAC progression, directly influencing cancer cell stemness and EMT, while indirectly promoting tumor growth through nerves. Inhibiting the NTN1/NEO1 axis could represent a potential therapeutic approach for PDAC. Statement of SignificanceNTN1 promotes pancreatic tumorigenesis and metastasis directly and indirectly through nerves, highlighting the importance of tumor cell-nerve crosstalk in cancer. NTN1 blockade could represent a promising strategy for treating PDAC liver metastasis. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=88 SRC="FIGDIR/small/666009v1_ufig1.gif" ALT="Figure 1"> View larger version (19K): org.highwire.dtl.DTLVardef@ca611corg.highwire.dtl.DTLVardef@ad9264org.highwire.dtl.DTLVardef@1661c00org.highwire.dtl.DTLVardef@b86798_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2025

De novo design of protein-binding aptamers through deep reinforcement learning assembly of nucleic acid fragments

Nucleic acid aptamers targeting proteins are becoming increasingly important in biopharmaceuticals and molecular diagnostics. Traditionally, aptamers are discovered through labor-intensive screening of nucleic acid libraries using the SELEX method. However, de novo design approaches without experimental screening remain a significant challenge. Here, we employed deep reinforcement learning to develop an artificial intelligence (AI) agent capable of de novo aptamer design, termed AiDTA (AI-driven Docking-Then-Assembling). First, nucleic acid fragments were docked to the target protein to identify target-binding fragments. Then, AiDTA automatically assembled these fragments into aptamers using the Monte Carlo tree search algorithm and a policy-value neural network to guide the agent in generating aptamers with secondary structures similar to the original constituent fragments. Experimental validation demonstrated that the AiDTA-designed DNA aptamers targeting disease-related proteins exhibited high binding affinities in the nanomolar range, achieving the de novo design of protein-binding aptamers for the first time. Our study establishes a new approach to obtaining protein-binding aptamers for potential applications in biopharmaceuticals and diagnostics.

bioinformatics↗

bioRxiv2025

Resources for molecular studies of unculturable obligate biotrophic fungal plant pathogens using their saprotrophic relatives

Obligate biotrophic plant pathogens like the powdery mildew fungi commit to a closely dependent relationship with their plant hosts and have lost the ability to grow and reproduce independently. Thus, at present, these organisms are not amenable to in vitro cultivation, which is a prerequisite for effective genetic modification and functional molecular studies. Saprotrophic fungi of the family Arachnopezizaceae are the closest known extant relatives of the powdery mildew fungi and may hold great potential for studying genetic components of their obligate biotrophic lifestyle. Here, we established telomere-to-telomere genome assemblies for two representatives of this family, Arachnopeziza aurata and A. aurelia. Both species harbor haploid genomes that are composed of 16 chromosomes at a genome size of 43.1 and 46.3 million base-pairs, respectively, which, in contrast to most powdery mildew genomes that are transposon-enriched, show a repeat content below 5% and signs of repeat-induced point mutation (RIP). Both species could be grown in liquid culture and on solid standard media and were sensitive to common fungicides such as hygromycin and fenhexamid. We successfully expressed a red fluorescent protein and hygromycin resistance in A. aurata following polyethylene glycol-mediated protoplast transformation, demonstrating that Arachnopeziza species are amenable to genetic alterations that may include gene replacement, gene modification, and gene complementation. With this work, we established a potential model system that promises to sidestep the need for genetic modification of powdery mildew fungi by using Arachnopeziza species as a proxy to uncover the molecular functions of powdery mildew proteins.

genomics↗

bioRxiv2025

Heterochronic transcription factor expression drives cone-dominant retina development in 13-lined ground squirrels.

Evolutionary adaptation to diurnal vision in ground squirrels has led to the development of a cone-dominant retina, in stark contrast to the rod-dominant retinas of most mammals. The molecular mechanisms driving this shift remain largely unexplored. Here, we perform single-cell RNA sequencing (scRNA-Seq) and chromatin accessibility profiling (scATAC-Seq) across developmental retinal neurogenesis in the 13-lined ground squirrel (13LGS) to uncover the regulatory basis of this adaptation. We find that 13LGS cone photoreceptors arise not only from early-stage neurogenic progenitors, as seen in rod-dominant species like mice, but also from late-stage neurogenic progenitors. This extended period of cone generation is driven by a heterochronic shift in transcription factor expression, with cone-promoting factors such as Onecut2, Pou2f1, and Zic3 remaining active in late-stage progenitors, and factors that promote cone differentiation such as Thrb, Rxrg, and Mef2c expressed precociously in late-stage neurogenic progenitors. Functional analyses reveal that Zic3 and Mef2c are sufficient to promote cone and repress rod photoreceptor-specific gene expression, and act through species-specific regulatory elements that drive their expression in late-stage progenitors. These results demonstrate that modifications to gene regulatory networks underlie the development of cone-dominant retinas, and provide insight into mechanisms of sensory adaptation and potential strategies for cone photoreceptor regeneration in vision disorders.

neuroscience↗

bioRxiv2025

Tff2 marks gastric corpus progenitors that give rise to pyloric metaplasia/SPEM following injury

In BriefTu et al. show that Tff2+ corpus isthmus cells are TA progenitors, and they, not chief cells, are the primary source of SPEM following injury. Upon Kras mutation, these progenitors directly progress to dysplasia, bypassing metaplasia, highlighting them as a potential origin of gastric cancer. HighlightsO_LITff2+ corpus cells are TA progenitors that give rise to secretory cells. C_LIO_LITff2+ progenitors, not chief cells, are the primary source of SPEM after injury. C_LIO_LIKras-mutant Tff2+ progenitors progress directly to dysplasia, bypassing metaplasia. C_LIO_LIMulti-omics analysis reveals distinct trajectories for SPEM and gastric cancer. C_LI O_FIG O_LINKSMALLFIG WIDTH=191 HEIGHT=200 SRC="FIGDIR/small/647847v1_ufig1.gif" ALT="Figure 1"> View larger version (46K): org.highwire.dtl.DTLVardef@48a2d1org.highwire.dtl.DTLVardef@b96642org.highwire.dtl.DTLVardef@1e89a4dorg.highwire.dtl.DTLVardef@1ea6a86_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical abstractC_FLOATNO C_FIG Pyloric metaplasia, also known as spasmolytic polypeptide-expressing metaplasia (SPEM), arises in the corpus in response to oxyntic atrophy, but its origin and role in gastric cancer remain poorly understood. Using Tff2-CreERT knockin mice, we identified highly proliferative Tff2+ progenitors in the corpus isthmus that give rise to multiple secretory lineages, including chief cells. While lacking long-term self-renewal ability, Tff2+ corpus progenitors rapidly expand to form short-term SPEM following acute injury or loss of chief cells. Genetic ablation of Tff2+ progenitors abrogated SPEM formation, while genetic ablation of GIF+ chief cells enhanced SPEM formation from Tff2+ progenitors. In response to H. pylori infection, Tff2+ progenitors progressed first to metaplasia and then later to dysplasia. Interestingly, induction of KrasG12D mutations in Tff2+ progenitors facilitated direct progression to dysplasia in part through the acquisition of stem cell-like properties. In contrast, Kras-mutated SPEM and chief cells were not able to progress to dysplasia. Tff2 mRNA was downregulated in isthmus cells during progression to dysplasia. Single-cell RNA sequencing and spatial transcriptomics of human tissues revealed distinct differentiation trajectories for SPEM and gastric cancer. These findings challenge the conventional interpretation of the stepwise progression through metaplasia and instead identify Tff2+ progenitor cells as potential cells of origin for SPEM and possibly for gastric cancer.

cell biology↗

bioRxiv2025

Lignature: A Comprehensive Database of Ligand Signatures to Predict Cell-Cell Communication

Ligand-receptor interactions mediate intercellular communication, inducing transcriptional changes that regulate physiological and pathological processes. Ligand-induced transcriptomic signatures can be used to predict active ligands; however, the absence of a comprehensive set of ligand-response signatures has limited their practical application in predicting ligand-receptor interactions. To bridge this gap, we developed Lignature, a curated database encompassing intracellular transcriptomic signatures for 362 human ligands, significantly expanding the repertoire of ligands with available intracellular response signatures. Lignature compiles signatures from published transcriptomic datasets and established resources such as CytoSig and ImmuneDictionary, generating both gene- and pathway-based signatures for each ligand. We applied Lignature to predict active ligands driving transcriptomic changes in controlled in vitro experiments and real-world single-cell sequencing datasets. Lignature outperformed existing methods such as NicheNet, achieving higher accuracy in identifying active ligands at both the gene and pathway levels. These results establish Lignature as a robust platform for ligand signaling inference, providing a powerful tool to explore ligand-receptor interactions across diverse experimental and physiological contexts.

bioinformatics↗

bioRxiv2025

Macrophage ferroptosis inhibits Aspergillus conidial killing in lung transplantation

Immune suppression heightens the risk for fungal infections, but the mechanisms that result in clinical disease are poorly understood. Here we demonstrate that macrophage ferroptosis, an iron-dependent form of regulated cell death, inhibits Aspergillus fumigatus (Af) killing. In a mouse tracheal transplant model of Af infection, we observed an increase in macrophage lipid peroxidation, a decreased expression of negative ferroptosis regulators Gpx4 and Slc7a11, and an increase in positive regulators Ptgs2 and Nox2, relative to syntransplants. Depletion of macrophages in transplant recipients decreased Af invasion. In vitro, iron overload reduced macrophage viability and decreased their capability to kill Af spores, through a decrease in lysosomal acidification and lysosomal loss. Treatment with ferrostatin-1, a ferroptosis inhibitor, and deferasirox (an iron chelator) restored Af killing. Ferroptotic alveolar macrophages isolated from lung transplant patients also showed a decreased ability to kill Af spores and the patients bronchoalveolar lavage was characterized by higher iron levels and markers of ferroptotic stress compared to non-lung transplants. These characteristics were strongly correlated with a clinical history of fungal infections, independent of immune suppressive medications. Our findings indicate that macrophage ferroptosis augments the risk of invasive aspergillosis, representing a novel mechanism for host immune dysfunction. Graphical AbstractSchematic of proposed mechanism underlying ferroptosis induced immune dysregulation and increased Af invasion in lung transplantation. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=150 SRC="FIGDIR/small/643092v1_ufig1.gif" ALT="Figure 1"> View larger version (104K): org.highwire.dtl.DTLVardef@1112102org.highwire.dtl.DTLVardef@18e2ec1org.highwire.dtl.DTLVardef@19f9c5forg.highwire.dtl.DTLVardef@1d325e8_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2025

SUMO2 Promotes Histone Pre-mRNA Processing by Stabilizing Histone Locus Body Interactions and Facilitating U7 snRNP Assembly

Histone mRNAs are the only non-polyadenylated mRNAs in eukaryotic cells and require specialized processing in the histone locus body (HLB), a nuclear body where essential processing factors, including the U7 snRNP, are concentrated. Recent studies have revealed that misregulation of histone pre-mRNA processing can lead to polyadenylation of histone mRNAs and disruption of histone protein homeostasis. Despite links to human disease, the factors contributing to polyadenylation of histone mRNAs and the mechanisms underlying HLB assembly and U7 snRNP biogenesis remain unclear. Here, we report novel functions of the small ubiquitin-related modifier 2 (SUMO2) in promoting histone pre-mRNA processing. Using a SUMO2 knockout osteosarcoma cell line, we identified a defect in 3 end cleavage and a global increase in histone mRNA polyadenylation. Subsequent analysis of HLBs revealed increased dynamics and reduced levels of the U7 snRNP complex. By over-expressing U7 snRNP-specific components, Lsm11 and U7 snRNA, we rescued U7 snRNP levels and processing defects in SUMO2 knockout cells. Through analysis of Lsm11, we identified a SUMO-interacting motif in its N-terminus required for efficient formation of U7 snRNP. Collectively, we demonstrate that SUMO2 promotes histone pre-mRNA 3 end processing by stabilizing HLB interactions and facilitating U7 snRNP assembly.

molecular biology↗