Biology subjects

Zhou, B.

Publications and source records attributed to Zhou, B..

At least 37 records · Page 2Linked to original sources

bioRxiv2026

MolClaw: An Autonomous Agent with Hierarchical Skills for Drug Molecule Evaluation, Screening, and Optimization

Computational drug discovery, particularly the complex workflows of drug molecule screening and optimization, requires orchestrating dozens of specialized tools in multi-step workflows, yet current AI agents struggle to maintain robust performance and consistently underperform in these high-complexity scenarios. Here we present MolClaw, an autonomous agent that leads drug molecule evaluation, screening, and optimization. It unifies over 30 specialized domain resources through a three-tier hierarchical skill architecture (70 skills in total) that facilitates agent long-term interaction at runtime: tool-level skills standardize atomic operations, workflow-level skills compose them into validated pipelines with quality check and reflection, and a discipline-level skill supplies scientific principles governing planning and verification across all scenarios in the field. Additionally, we introduce MolBench, a benchmark comprising molecular screening, optimization, and end-to-end discovery challenges spanning 8 to 50+ sequential tool calls. MolClaw achieves state-of-the-art performance across all metrics, and ablation studies confirm that gains concentrate on tasks that demand structured workflows while vanishing on those solvable with ad hoc scripting, establishing workflow orchestration competence as the primary capability bottleneck for AI-driven drug discovery.

bioinformatics↗

bioRxiv2026

Abnormal ventricular wall patterning precedes and drives MYBPC3 hypertrophic cardiomyopathy

BACKGROUNDExcessive trabeculations and myocardial crypts are recurrent features across cardiomyopathies, yet their developmental origins and clinical significance remain poorly defined. To reveal the link between cardiac morphogenesis and disease, we generated humanized mouse models carrying patient-derived MYBPC3 frameshift mutations associated with overlapping hypertrophic cardiomyopathy (HCM) and left ventricular non-compaction (LVNC). METHODSWe applied CRISPR-Cas9 to introduce distinct MYBPC3 frameshift alleles into the mouse genome and performed comprehensive phenotypic and transcriptomic profiling from fetal life through adulthood. RESULTSAdult homozygous Mybpc3 frameshift mutant mice like humans displayed hallmark HCM; however, without LVNC. Fetal and neonatal mutant hearts exhibited markedly enlarged ventricular trabeculae and crypts that progressed postnatally into the observed adult hypertrophy. Transcriptomic analysis revealed stage-specific dysregulation of oxidative metabolism, nonsense-mediated decay (NMD), and cell cycle pathways, peaking at postnatal days 1 and 7, indicating that these stages represent critical time points in disease onset. The persistent NMD signature, also observed in phenotype-negative heterozygotes, suggests a compensatory stress response. Enlarged trabeculae exhibited 2-fold increased trabecular cardiomyocyte proliferation, reversing the normal compact-trabecular proliferative gradient and leading to impaired ventricular compaction in neonates. Hey2CreERT2 lineage tracing demonstrated invasion of Hey2+ compact cardiomyocytes into the trabeculae and ectopic trabecular expression of the Prdm16 transcription factor, indicating defective ventricular wall patterning and maturation. Postnatally, Hey2+-derived cardiomyocytes became restricted to the outer/compact myocardium in mutants, while the inner/trabecular myocardium underwent accelerated hypertrophy concurrent with Prdm16 downregulation. Mice with a Mybpc3 missense variant also exhibited Hey2+ myocardial lineage expansion into trabeculae but no increased proliferation, implicating additional mechanisms beyond Hey2 regulation. Postnatal Prdm16 restoration, via transgenic expression in Mybpc3-null mice effectively attenuated hypertrophy, establishing a causal link between Mybpc3 loss, Prdm16 decline, and pathological remodeling. CONCLUSIONSMybpc3 governs ventricular wall maturation by regulating cardiomyocyte proliferation, patterning, and maturation, partly via Prdm16. Disruption of these developmental programs precedes and drives adult HCM, highlighting a developmental role for sarcomeric proteins, and revealing postnatal Prdm16 modulation as an antihypertrophic therapeutic strategy.

developmental biology↗

bioRxiv2026

Wnt/β-catenin signaling restrains developmental beiging and imprints long-term energy expenditure

Beige adipocytes that emerge during the peri-weaning period support sympathetic nervous system (SNS)-independent thermogenesis, yet the mechanisms governing this spontaneous beiging remain unclear. Here, by integrating transcriptomic profiling with adipocyte-targeted Ctnnb1 deletion in mice, we identify the canonical Wnt signaling as an endogenous brake on developmental beige thermogenesis. Peri-weaning inguinal fat from adipocyte Ctnnb1 knockout mice exhibits enhanced beige adipocyte biogenesis, with increased thermogenesis-related gene expression and mitochondrial oxidative capacity, which programs durable activation of adaptive thermogenesis and augmented whole-body energy expenditure into adulthood. Mechanistically, suppression of Wnt/{beta}-catenin signaling induces a non-canonical Wnt5a-Ca2-AMPK axis that promotes triglyceride lipolysis and subsequent PPAR-driven fatty acid oxidation, thereby fueling mitochondrial respiration. Genetic or pharmacological disruption of this axis blunts thermogenic responses induced by {beta}-catenin inhibition in both murine and human subcutaneous adipocytes, indicating that Wnt5a-Ca2-AMPK axis is required for the cell-autonomous activation of beige fat. These results reveal Wnt/{beta}-catenin signaling as a developmental constraint on beige adipocyte formation and suggest an SNS-independent route to sustainably raise energy expenditure and improve metabolic health.

physiology↗

bioRxiv2026

A synonymous mutation in MSMEG_4729 occurs at a high frequency in spontaneous D29-resistant mutants of Mycobacterium smegmatis

Compassionate use of mycobacteriophage therapy highlights the promising potential of phage therapy as an alternative treatment option for antibiotic-resistant infections when conventional treatments fail. However, realizing the full potential of phage therapy requires addressing key challenges, including host immune responses, the limited arsenal of therapeutically-useful mycobacteriophages, and the emergence of phage resistance. Dissecting the mechanisms of phage resistance is critical for ensuring the effectiveness and sustainability of phage therapy. In this study, we demonstrate that exposure to the lytic mycobacteriophage D29 triggers diverse genetic changes in Mycobacterium smegmatis. A synonymous mutation in MSMEG_4729 arises frequently but is insufficient to confer D29 resistance on its own. Instead, we identified possible Lsr2-independent activation of the lipooligosaccharide (LOS) biosynthesis cluster in a D29-resistant mutant harboring this mutation. We have also detected the possible activity of MSMEG_3213, a type II methyltransferase associated with m6A modifications in M. smegmatis. Finally, we isolated defense escape mutants (DEMs) of D29 capable of overcoming resistance in a strain with the MSMEG_4729 synonymous mutation. This profiling of M. smegmatiss likely defensive arsenal against the therapeutically-useful mycobacteriophage D29 provides a roadmap for further investigations and rational engineering of next-generation mycobacteriophages to combat drug-resistant mycobacterial infections. Impact statementInterest in phage therapy has been gaining traction recently, which is largely due to the serious threat of antimicrobial resistance. However, the efficacy and sustainability of phage therapy is threatened by certain challenges, which includes the ever existent threat of phage resistance. In this study, we identified several likely factors involved in D29 interaction with the model mycobacterium M. smegmatis. These findings set a roadmap for future investigations that would guide rational phage engineering to expand the currently limited arsenal of therapeutically useful mycobacteriophages as well as improve the efficiency of existing ones.

microbiology↗

bioRxiv2026

ChiMER: Integrating chromatin architecture into splicing graphs for chimeric enhancer RNAs detection

MotivationEnhancer-derived RNAs (eRNAs) and their fusion with protein-coding genes represent a crucial yet understudied layer of transcriptional regulation. eRNAs are typically expressed at low levels, which makes fusion events difficult to detect with conventional fusion detection tools. In addition, these tools are not designed to capture fusion transcripts arising from spatial proximity between distal regulatory elements and gene loci. Reads spanning such regions are also frequently filtered as mapping artifacts. As a result, computational approaches for systematically identifying spatially mediated enhancer-exon fusion transcripts remain lacking. MethodsWe developed ChiMER, a graph-based framework for detecting ChiMeric Enhancer RNAs from short-read RNA-seq data. ChiMER constructs splice graphs with chromatin contact information to introduce enhancer-exon edges and uses graph alignment to search for potential transcriptional paths. A ranking-based scoring module then prioritizes high-confidence events. Evaluations on simulated and real RNA-seq datasets show that ChiMER achieves higher sensitivity than conventional linear fusion detection methods while maintaining low false-positive rates. ResultsApplied to cancer cell line RNA-seq datasets, ChiMER identified multiple enhancer-exon chimeric transcripts, several associated with super-enhancer regions. Multi-omics analysis further shows that fusion transcripts occur in transcriptionally active regulatory environments and frequently coincide with strong R-loop signals, suggesting a potential role of RNA-DNA hybrid structures in facilitating long-range transcriptional joining events. Availabilityhttps://github.com/Candlelight-XYJ/ChiMER Contactyujia.xiang@outlook.com, xielinhai@ncpsb.org.cn

bioinformatics↗

bioRxiv2026

MATR3 is essential for oocyte growth and maturation quality through a dual molecular mechanism

The molecular mechanisms governing mRNA accumulation during oocyte growth, essential for developmental competence, remain poorly understood. This study investigates the role of Matrin-3 (MATR3), a highly expressed RNA-binding protein in growing oocytes (GOs), using oocyte-specific knockout mouse models and human oocyte maturation arrest (OMA) samples. The results showed that MATR3 was more abundant in GOs than fully-grown oocytes (FGOs), highly expressed in the nucleus of non-surrounded nucleolus (NSN) oocytes, and exited the nucleus during the NSN-to-surrounded nucleolus (SN) transition. In OMA patients, MATR3 nuclear localization was missed, with smaller oocytes than FGOs. Further, Matr3 deletion in mouse GOs caused restricted oocyte growth, global transcription disorders, follicle development failure, blocked GO-granulosa cell communication (via reduced Gdf9 and Radixin expression), and infertility. Mechanistically, MATR3 regulated transcription by recruiting H3K9me2-demethylating lysine-specific demethylase 3B or binding target gene promoters, like Radixin. These findings reveal a critical role of MATR3 in orchestrating transcription and paracrine signaling during oogenesis and suggest its potential as a diagnostic and therapeutic target for OMA.

physiology↗

bioRxiv2026

Natural variation in the atypical resistance gene Pita2 confers broad-spectrum neck blast resistance in rice

Neck blast (NB), caused by Magnaporthe oryzae, damages rice panicles and reduces yield. Knowledge of NB resistance remains limited due to the lack of reliable resistance evaluation methods. Here, we applied a newly established neck injection method and performed a GWAS on 335 diverse accessions from the 3K Rice Genomes Project to identify loci associated with NB resistance. We detected a significant association on chromosome 12, explaining 15-18% of the symptom variations caused by a highly virulent Philippine blast isolate (M64-1-3-9-1). Linkage disequilibrium analysis refined this region to a 42.3-kb interval containing Pita2, a known leaf blast resistance gene. We found that two Pita2 allelic variants, Pita2a and Pita2c, both harboring the variant A/G (Lys879) in the last exon (Chr12:10,833,400), are associated with NB resistance. IR64 and a CO39 near-isogenic line (NIL) IRBLta2-Pi[CO] harboring Pita2a were resistant, whereas CRISPR-Cas9 knock-out of Pita2a in IR64 caused susceptibility to M64-1-3-9-1 and IK81-25. These results indicate that Pita2a is required for NB resistance. Furthermore, the CO39 NIL, IRBLta2-Pi[CO], and Lijiangxintuanheigu monogenic line (IRBLta2-Pi) harboring the Pita2a allele exhibited broad-spectrum resistance to 75% and 80% of Philippine differential blast isolates, respectively. The superior haplotype of Pita2 contains two major SNPs (A/G and A/C at Chr12:10,833,400 and Chr12:10,845,095) occurs in 83% of IRRI elite breeding lines and can be used to select NB-resistant genotypes with an accuracy of 86%. Our findings identify Pita2a as a major gene for NB resistance and provide a valuable genetic resource for developing blast-resistant rice. PLAIN LANGUAGE SUMMARYRice blast, caused by the fungus Magnaporthe oryzae, is a major threat to global rice production. Neck blast (NB) is the most severe type of blast, however, the genetic basis of NB resistance remains poorly understood. In this study, we analyzed 335 rice accessions to identify genes underlying the resistance against a Philippine blast isolate. We found that allelic variants Pita2a and Pita2c are strongly-associated with NB resistance. Knock-out of Pita2a allele made resistant rice plants susceptible while introgression into susceptible rice lines enhanced resistance to multiple blast isolates, confirming its role in NB resistance. Importantly, the superior alleles of Pita2 are already present in 83% of elite breeding lines and can be used to select NB-resistant genotypes with an accuracy of 86%. Our findings clarify the genetic control of NB resistance and offer new tools for protecting rice yields in blast-endemic regions.

pathology↗

bioRxiv2026

Isthmin-1 is a Key Regulator of Induced Pluripotent Stem Cell-Derived Cardiomyocytes Maturation through Activation of p53 Signaling

AimsHuman induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs) exhibit an immature structural and metabolic phenotype that limits their utility for cardiac disease modeling and regenerative therapy. Although multiple extrinsic strategies have been proposed to enhance iPSC-CM maturation, intrinsic molecular regulators governing this process remain incompletely defined. This study aimed to identify and characterize a novel molecular factor that promotes cardiomyocyte maturation. Methods and ResultsCross-species transcriptomic analyses comparing adult versus fetal hearts and hypertrophic cardiomyopathy versus healthy myocardium identified Isthmin-1 (ISM1) as a conserved maturation-associated gene. In human iPSC-CMs, ISM1 overexpression enhanced sarcomere organization, mitochondrial oxidative phosphorylation, ATP production, and calcium-handling properties, whereas ISM1 knockdown impaired these maturation features. RNA sequencing revealed global transcriptional reprogramming toward an adult-like state, characterized by suppression of cell-cycle-related gene programs and activation of oxidative metabolic pathways. KEGG pathway enrichment, GSVA, and GSEA consistently identified p53 signaling as the most significantly activated pathway in ISM1-overexpressing iPSC-CMs. Mechanistically, ISM1 directly interacted with p53, enhanced its protein stability, promoted nuclear localization, and increased transcription of p53 downstream targets involved in metabolic remodeling and cell-cycle exit. Pharmacological inhibition of p53 abolished ISM1-induced structural and metabolic maturation, demonstrating that ISM1 promotes cardiomyocyte maturation in a p53-dependent manner. ConclusionsISM1 is a previously unrecognized molecular driver of cardiomyocyte maturation that promotes structural, metabolic, and functional maturation of iPSC-CMs through activation of p53-dependent transcriptional programs. These findings provide new mechanistic insight into cardiomyocyte maturation and identify ISM1 as a promising target for improving the maturity of stem cell-derived cardiomyocytes. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=142 SRC="FIGDIR/small/698535v1_ufig1.gif" ALT="Figure 1"> View larger version (43K): org.highwire.dtl.DTLVardef@15daca3org.highwire.dtl.DTLVardef@f1396dorg.highwire.dtl.DTLVardef@f13400org.highwire.dtl.DTLVardef@18d0b41_HPS_FORMAT_FIGEXP M_FIG C_FIG

developmental biology↗

bioRxiv2025

Adeno-associated viruses (AAVs) induce dose-dependent neonatal ventriculomegaly following intracerebroventricular administration

Cell-type-specific expression of synthetic/endogenous proteins or genetic sequences has significantly advanced our understanding of the central nervous system (CNS). Adeno-associated virus (AAV)-delivery to cerebrospinal fluid (CSF) mediates transfection of target cells to enable sustained delivery of secretory proteins into the CSF, offering promising avenues for both CNS therapy and mechanistic studies. However, despite the advantages afforded by AAV tropism-based cellular selectivity and transgene delivery, both preclinical studies and clinical trials report short- and long-term adverse effects, particularly immune activation. Especially relevant for CSF biology, CNS immune insults raise the risk of CSF dysregulation, including hydrocephalus. These risks may be exacerbated in pediatric populations, where ongoing CNS development, including immature meninges, choroid plexus (ChP), and skull structures, may further impair any ability to compensate for CSF dysregulation. To systematically address these risks and provide guidelines for minimizing CNS immune insults by AAVs, we test the dose-dependent effects of intracerebroventricular (ICV) injections of 3 AAV serotypes (AAV2/5, AAV2/4, and AAV.PHP.eB) to neonatal (P0.5) CD1 mouse pups. Histological analysis verified AAV2/5 tropism limited to ChP epithelial cells (CPECs), whereas AAV.PHP.eB transfected both CPECs and ependymal regions. By contrast, AAV2/4 shows limited transfection in the brain. Further, we find that ICV injections of all 3 AAV serotypes at the high dose (4x109 genome copy GC/pup) induced ventriculomegaly by P7.5, while the low dose (1x109 GC/pup) was well tolerated. Additionally, high-dose AAV2/5 tropism became more permissive, transfecting the ChP and also ependymal cells and some neurons. Longitudinal MRI of P0.5 pups with high-dose AAV2/5 ICV injections highlighted quick progression of ventriculomegaly. CSF ELISA analysis detected elevated pro-inflammatory cytokine CCL2 in AAV2/5 and AAV2/4 high-dose groups, indicating CNS inflammation. Moreover, decreased CSF TTR concentrations in high-dose groups suggest ChP dysfunction. We further revealed that earlier in utero high-dose ICV AAV2/5 injections at E13.5 induced even more severe ventriculomegaly and that adult animals were also susceptible to ventriculomegaly after high-dose AAV ICV delivery. Taken together, our data emphasize critical safety considerations of CSF-based AAV delivery, particularly during brain development. Further, these results call for an optimized dosage for perinatal ICV AAV applications. HighlightsO_LICSF-administration of AAVs results in unique cellular tropism in neonatal brains. C_LIO_LIIntracerebroventricular AAV delivery induces dose-dependent neonatal ventriculomegaly. C_LIO_LINeonatal ventriculomegaly by AAV overdose develops quickly and progressively. C_LIO_LIAAV overdose ventriculomegaly correlates with ChP/CSF dyshomeostasis and inflammation. C_LIO_LIAdult and embryonic brains are also susceptible to dose-dependent AAV-induced ventriculomegaly. C_LI

neuroscience↗

bioRxiv2025

Tirzepatide Synergizes with Leptin on Weight Loss and Restoring Metabolic Homeostasis in Diet-induced Obesity Model

Leptin resistance limits anti-obesity efficacy. We identified a leptin-sensitizing mechanism through tirzepatide (TZP), a glucagon-like peptide-1 receptor (GLP-1R) and glucose-dependent insulinotropic polypeptide receptor (GIPR) dual-agonist. Our tirzepatide clinical trial revealed that circulating leptin levels at baseline correlated with weight loss efficacy in patients with obesity, suggesting leptin and tirzepatide could interact to achieve stronger effects on weight loss. Next, we utilized the diet-induced obesity (DIO) mice and demonstrated the synergistic effects of tirzepatide and leptin combination (TZP+Lep) on weight loss. TZP+Lep treatment further improved hepatic insulin sensitivity and upregulated thermogenetic gene expression in brown adipose tissue. Metabolic profiling under thermoneutrality revealed TZP+Lep treatment further reduced food intake and increased energy expenditure. Tirzepatide sensitized leptin signaling in hypothalamic pro-opiomelanocortin (POMC) and GLP-1R expressing neurons. TZP+Lep synergistically increased POMC neuronal firing by decreasing the inhibitory postsynaptic input. Together, our work showed combining tirzepatide and leptin as a potential way for better maintenance of metabolic homeostasis in obesity management. HighlightsO_LITirzepatide and leptin synergistically promote weight loss through reduced food intake and increased energy expenditure. C_LIO_LITirzepatide and leptin synergistically improve insulin sensitivity and metabolic homeostasis with altered hepatic and adipose gene expression. C_LIO_LITirzepatide sensitizes leptin signaling in hypothalamic GLP-1R and POMC neurons. C_LIO_LITirzepatide and leptin synergistically increase POMC neuronal firing by decreasing inhibitory postsynaptic input. C_LI

neuroscience↗

bioRxiv2025

Closing the Sim-to-Real Gap: An End-to-End Robotic Ultrasound System Leveraging In Vivo Reinforcement Learning and 3D-Prior Guided Hybrid Control

Abdominal ultrasound is a crucial first-line diagnostic tool, yet its efficacy is inherently constrained by a strong dependency on operator skill, leading to significant inter-operator variability and limiting its widespread adoption. While robotic ultrasound systems with artificial intelligence have emerged to mitigate this, current approaches face critical limitations: they often rely on simulated or phantom data for training, which hampers generalizability, and employ control strategies that lack the flexibility to adapt to complex human anatomy. To address these challenges, this paper introduces a novel, end-to-end robotic system for autonomous abdominal scanning. Our methodology is systematic: it begins with coarse scan planning via RGB and 3D point cloud-based localization of key anatomical landmarks (e.g., xiphoid process). The core of our approach involves training a reinforcement learning scanning policy directly on live human volunteers, enabling the development of a strategy that is robust to anatomical diversity. This high-level policy is executed by a sophisticated hybrid force-position controller, enhanced with real-time normal vector calibration and 3D point cloud-based respiratory phase detection to dynamically adjust contact force, particularly during inspiration. This innovation proves critical for improving scan quality in subjects with higher Body Mass Index (BMI). Extensive validation against expert sonographers demonstrates that our system achieves high precision in standard plane recognition and superior scanning efficiency. Furthermore, to holistically assess performance where standard planes are difficult to acquire, we introduce a 3D reconstruction-based coverage metric. Results confirm that our system delivers strong adaptability and significantly improved consistency, marking a substantial step toward clinically viable, operator-independent ultrasound robotics.

bioengineering↗

bioRxiv2025

Metabolic dysfunction related to specific genetic variant sites of methylmalonic acidemia

Methylmalonic acidemia (MMA) is a genetic metabolic disease, with mut (mut-MMA, caused by MMUT gene variation) and cblC (cblC-MMA, caused by MMACHC gene variation) being the predominant subtypes. MMA patients carrying c.729_730insTT and c.609G>A exhibit severe clinical manifestations and have poorer outcomes. Little information is known on the potential mechanism. The metabotypes of MMA patients carrying c.729_730insTT and c.609G>A were profiled. The potential effect of genetic variation sites on the metabolism were explored. Leveraging the gene variation spectrum and the targeted metabolomics, propionic acid, indolelactic acid, myristoleic acid, tetradecenoic acid, tridecanoic acid, and oxoadipic acid showed strong enrichment in c.729_730insTT carrying mut-MMA patients. Whereas mutation c.609G>A caused adipic acid, pimelic acid, fructose, AMP, hexanylcarnitine, and methionine significnatly altered in cblC-MMA patients. Furthermore, the metabolomic profiles were obviously different in c.729_730insTT and non-c.729_730insTT carrying mut-MMA patients after treatment. Different metabolic alterations in cblC-MMA patients carrying c.609G > A and non-c.609G > A under treatment were also observed. Our findings provide unique insights into the metabolic basis of MMA specific subtypes and its implications across different variants.

molecular biology↗

bioRxiv2025

Sexual life cycle establishes the unicellular red algae Cyanidiophyceae as a genetically tractable model lineage for eukaryotic evolution

The thermo-acidophilic unicellular algal class Cyanidiophyceae is the earliest-branching lineage in red algae, which diverged from Viridiplantae lineage (green algae and land plants) soon after chloroplast establishment in the common ancestor of Archaeplastida. Cyanidiophyceae possess extremely simple genomes (8.7-17.8 Mb; approximately 4,800- 7,800 genes), and the cell-wall-less, genetically tractable strain Cyanidioschyzon merolae 10D has served as a model organism. However, its unknown sexual life cycle has limited its utility in studies of evolution and genetics. Inspired by the recent discovery of sexual reproduction in the cyanidiophycean genus Galdieria, we identified similar life cycles in the other cyanidiophycean genera Cyanidioschyzon, Cyanidiococcus, and Cyanidium. In these genera, the cell-walled diploid form, exclusively observed in nature, produces a cell-wall-less haploid form when the culture pH is lowered, and both proliferate asexually. In addition, the cell-wall-less Cyanidioschyzon merolae 10D strain has been shown to be a haploid clone that forms a cell-walled diploid through mating with other haploid clones. Building on these findings, we generated high-quality genomic resources with phase-specific transcriptomes and developed genetic manipulation systems using the cell-wall-less haploids of these genera. We further uncovered phase-specific distribution of histone H3 lysine 27 trimethylation linked to haploid- and diploid-specific gene expression, including transcription factors involved in differentiation associated with sexual reproduction in plants. Additionally, biparental inheritance of organelle DNA occurs following isogamous mating of haploid cells but resolves into uniparental inheritance during diploid proliferation. These advances position Cyanidiophyceae as a powerful model lineage for studying early Archaeplastida evolution, the shared mechanisms of photosynthetic eukaryotes, and their environmental adaptation.

plant biology↗

bioRxiv2025

Loss of tight junction protein claudin 18 uncovers alveolar epithelial stem cell plasticity and emergence of non-fibrogenic transitional progenitors

Persistence of senescent alveolar transitional progenitors following lung injury is implicated in the pathogenesis of fibrosis. We identified transitional cells in uninjured Cldn18 knockout (KO) mouse lungs distinct from previously reported damage-associated transitional progenitors (DATPs) with a less fibrogenic transcriptomic profile. Cldn18 KO mice are protected from bleomycin-induced fibrosis, with early restoration of cellular homeostasis. Lineage tracing implicates accelerated differentiation as a mechanism for protection from fibrosis, leading us to name these cells regeneration-associated transitional progenitors (RATPs). Multiome confirms that RATPs and DATPs are epigenetically distinct, with RATPs comprised of RATP2s and RATP1s based on epigenomic proximity to AT2s and AT1s, respectively, and suggests dynamic regulatory remodeling during AT2-to-AT1 differentiation, with NKX2.1 and AP-1 active in early transitions and TEAD factors in later stages. These results reveal an unexpected role for Cldn18 in regulation of AEC plasticity, while identification of RATPs challenges the notion that persistence of transitional alveolar cells is invariably pathologic.

cell biology↗

bioRxiv2025

No more than three PlpE non-overlapping epitopes trigger significant antibody production in individuals vaccinated with the Pasteurella multocida epitope-chimeric proteins

Current vaccine research still confronts multiple challenges, and epitope-focused vaccine design serves as an effective technical approach to address these issues. Antigens harbor multiple epitopes; however, the number of epitopes capable of triggering significant antibody responses in vaccinated individuals remains undefined. This study aimed to determine the number of non-overlapping epitopes--designated "effective epitopes" hereafter--that trigger significant antibody production in vaccinated individuals when presented in distinct PlpE epitope-chimeric proteins. Herein, chimeric proteins incorporating varying numbers of PlpE non-overlapping B-cell epitopes were generated. By analyzing serum antibody responses in vaccinated individuals, the number characteristic of PlpE effective epitopes was elucidated. The total number of PlpE effective epitopes in vaccinated individuals was 2.6 (95%CI: 1.909-3.201) for full-length PlpE, and 1.2 (95%CI: 0.5426-1.857), 0.9 (95%CI: 0-1.820), and 0.2 (95%CI: 0-0.5016) for the PlpE chimeric proteins (PlpE-VP60P, PlpE-BcfA, PlpE-PtfA), respectively. With an increase in the number of PlpE non-overlapping epitopes incorporated into the chimeric proteins, the number of PlpE effective epitopes exhibited a trend of initial increase followed by a decrease. Ultimately, the average total number of effective epitopes across all PlpE chimeric proteins did not exceed 3, with the highest number 2.1 (95%CI: 1.572-2.628). In conclusion, the number of PlpE non-overlapping epitopes on an antigen, that trigger significant antibody responses in each vaccinated individual, is very limited. IMPORTANCEEpitopes underpin the antigenicity of protein antigens. Although the concept of antigenic epitopes has been proposed over 50 years, our understanding on epitopes remains incomplete. Multiple antigenic epitopes can be identified on a single antigen, while the number of these epitopes that function in vaccinated individuals remains unclear--a gap hindering the rational design of vaccines. In previous studies, we identified 6 non-overlapping epitopes of Pasteurella multocida PlpE. Herein, we found that the total number of non-overlapping epitopes--capable of significantly triggering antibody production--that are present in PlpE chimeric proteins does not exceed 3 per vaccinated individual. This finding offers important insights for rational vaccine design: given the highly limited number of non-overlapping epitopes that function in vaccinated individuals, only a limited number of epitopes can be grafted onto scaffold proteins. Epitope-focused vaccine design must therefore account for competitive interactions between epitopes on the new antigen.

immunology↗

bioRxiv2025

Cerebellum metastasis model of HER2-positive breast cancer unveils key role of IL34-induced Arg1+ macrophages.

Brain metastases occur in up to 40% of Stage IV breast cancer patients. The cerebellum is a frequent location for metastases in HER2-positive breast cancer patients, but the mechanisms for this are unknown. Here, we developed a syngeneic, immunocompetent mouse model for breast cancer brain metastases by stereotactically injecting mouse HER2-overexpressing breast cancer organoids into the cerebellum. Growth of these cerebellar metastases was monitored by MRI and trastuzumab optical imaging using a near-infrared fluorophore conjugated to trastuzumab. Spatial transcriptomics identified interleukin-34 production by breast cancer cells inducing ARG1+ macrophages at the invading edge of the metastasis. Treatment with a blocking antibody to interleukin-34s receptor, CSF1R, produced tumor shrinkage. These findings have immediate translation potential as a CSF1R-blocking antibody is FDA-approved. Further, it demonstrates that cancer-associated inflammation bordering the brain metastasis promotes metastatic growth and offers a molecularly targeted strategy to treat inflammation in brain metastasis. Graphical summary O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/660224v1_ufig1.gif" ALT="Figure 1"> View larger version (38K): org.highwire.dtl.DTLVardef@9f1a50org.highwire.dtl.DTLVardef@178acc5org.highwire.dtl.DTLVardef@196d803org.highwire.dtl.DTLVardef@3fe631_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2025

Joint Modeling of Longitudinal Biomarker and Survival Outcomes with the Presence of Competing Risk in Nested Case-Control Studies with Application to the TEDDY Microbiome Dataset

MotivationLarge-scale prospective cohort studies collect longitudinal biospecimens alongside time-to-event outcomes to investigate biomarker dynamics in relation to disease risk. The nested case-control (NCC) design provides a cost-effective alternative to full cohort biomarker studies while preserving statistical efficiency. Despite advances in joint modeling for longitudinal and time-to-event outcomes, few approaches address the unique challenges posed by NCC sampling, non-normally distributed biomarkers, and competing survival outcomes. ResultsMotivated by the TEDDY study, we propose "JM-NCC", a joint modeling framework designed for NCC studies with competing events. It integrates a generalized linear mixed-effects model for potentially non-normally distributed biomarkers with a cause-specific hazard model for competing risks. Two estimation methods are developed. fJM-NCC leverages NCC sub-cohort longitudinal biomarker data and full cohort survival and clinical metadata, while wJM-NCC uses only NCC sub-cohort data. Both simulation studies and an application to TEDDY microbiome dataset demonstrate the robustness and efficiency of the proposed methods.

bioinformatics↗

bioRxiv2025

Xcr1+ type 1 conventional dendritic cells are essential mediators for atherosclerosis progression

BackgroundAtherosclerosis is characterized by lipid accumulation within plaques, leading to foam cell formation and an inflammatory response within the aortic lesions. Lipid disorders have been extensively investigated, however the cellular and molecular mechanisms that trigger the inflammatory response in atherosclerotic plaques remain far from being fully understood. Xcr1+ cDC1 cells are newly identified antigen-presenting cells in activating immune cells. However, the role of cDC1 cells in the development of atherosclerosis remains highly controversial. ResultsWe first confirmed the presence of cDC1 within human atherosclerotic plaques and discovered a significant association between the increasing cDC1 numbers and atherosclerosis progression in mice. Subsequently, we established Xcr1Cre-Gfp Rosa26LSL-DTA ApoE-/- mice, a novel and complex genetic model, in which cDC1 was constitutively depleted in vivo during atherosclerosis development. Intriguingly, we observed a notable reduction in atherosclerotic lesions in hyperlipidemic mice, alongside suppressed T cell activation of both CD4+ and CD8+ subsets in the aortic plaques. Notably, aortic macrophages and serum lipid levels were not significantly changed in the cDC1-depleted mice. Single-cell RNA sequencing revealed heterogeneity of Xcr1+ cDC1 cells across the aorta and lymphoid organs under hyperlipidemic conditions. As Xcr1 is the sole receptor for Xcl1, we next explored to target Xcr1+ cDC1 cells via Xcl1 by establishing Xcl1 and ApoE deficient mice. Xcl1 knockout mice exhibited decreased atherosclerotic plaque formation and reduced aortic cDC1 accumulation, indicating that Xcl1 contributes to cDC1-mediated atherosclerotic lesion development. ConclusionsOur results reveal crucial roles of cDC1 in atherosclerosis progression and provide insights into the development of immunotherapies by targeting cDC1 through Xcl1.

immunology↗