Biology subjects

Li, Y.

Publications and source records attributed to Li, Y..

At least 325 records · Page 18Linked to original sources

bioRxiv2026

Engineering autologous ossicles for the personalized modeling of acute myeloid leukemia

Acute Myeloid Leukemia (AML) is the most lethal hematological malignancy in adults and is characterized by significant genetic and cytogenetic heterogeneity. This diversity drives substantial patient-to-patient variability in disease progression and therapeutic response. Increasing evidence indicates that bone marrow mesenchymal stem/stromal cells (MSCs) play a critical role in AML emergence, evolution and treatment resistance. However, progress in the field is challenged by the lack of experimental models supporting sustained AML survival while faithfully recapitulating the human bone marrow niche. Humanized ossicles (hOss) have recently emerged as ectopic human bone/bone marrow microenvironments composed of MSCs and hematopoietic elements, enabling improved AML engraftment in vivo. Nonetheless, those models typically exploit healthy MSCs largely because primary patient-derived cells exhibit diminished ossification potential. Here, we introduce OssiGel, a novel engineered human cartilage extracellular matrix produced by a mesenchymal cell line. We hypothesized that combining OssiGel with primary MSCs would enable the robust formation of hOss in healthy and malignant settings. We report that OssiGel supports fast and reproducible formation of hOss through endochondral ossification using MSCs isolated from both healthy and AML bone marrow samples. Within hOss, AML-MSCs were shown to persist long-term and to generate a human stromal microenvironment supporting the establishment of autologous AML hematopoietic cells, enabling the generation of autologous (autologOss). Single-cell RNA sequencing (scRNA-seq) revealed that autologOss recapitulate the majority of the AML blood populations observed in the corresponding patient bone marrow samples. Moreover, proof-of-concept sequencing of AML-MSCs from autologOss allowed predictive interrogation of interactions with leukemic populations and revealed the acquisition of an inflammatory-like phenotype, characteristic of AML. Taken together, our study establishes OssiGel as a novel platform for the robust engineering of autologous ossicles from AML patient samples. This provides a relevant tool to decipher patient-specific cellular interactions and drug responses, with potential translational value to broad hematological malignancies.

bioengineering↗

bioRxiv2026

Latent Effector Capacity Governs Reversible T Cell Exhaustion: A Mathematical Model for Mechanistically Predictive AI in PD-1 Blockade

T cell exhaustion is commonly viewed as a terminal differentiation state marked by irreversible loss of effector function during chronic infection and cancer. However, the rapid restoration of cytotoxic activity following PD-1 checkpoint blockade challenges this view, revealing a central paradox: T cells that appear functionally inert can regain effector function on timescales incompatible with de novo differentiation or extensive epigenetic reprogramming. To resolve this contradiction, we present a mathematical framework that explicitly decouples latent effector capacity from active effector output. We define latent effector capacity as a slow, history-dependent state variable representing preserved epigenetic accessibility and regulatory readiness at effector loci, distinct from instantaneous transcriptional activity. Within this framework, PD-1 signaling functions as a reversible, graded masking mechanism that suppresses effector realization without erasing latent capacity, thereby explaining the coexistence of preserved chromatin accessibility, rapid functional rebound, and heterogeneous responses to checkpoint blockade. Incorporating nonlinear self-maintenance of epigenetic programs together with checkpoint-dependent erosion of latent capacity reveals a bistable regime and a history-dependent point of no return, beyond which exhaustion becomes irreversible. Critically, the model demonstrates that PD-1 checkpoint blockade unmasks pre-existing effector potential but cannot recreate lost capacity, because therapeutic reversibility is governed by the prior dynamical stability of a latent epigenetic state rather than by instantaneous transcriptional output. This framework establishes a mathematical foundation for mechanistically predictive AI in PD-1 blockade therapy by identifying latent, history-dependent variables that can be inferred from epigenetic and transcriptional data to predict therapeutic responsiveness and irreversibility.

immunology↗

bioRxiv2026

Expanding the genetic code with diverse backbone structures across diverse sequence contexts

Expanding the genetic code to enable the selective and specific incorporation of non-canonical monomers (ncMs), beyond -L amino acids with variant sidechains, is a key outstanding challenge. Here we discover orthogonal aminoacyl-tRNA synthetases that selectively and specifically acylate their cognate orthogonal tRNA in vivo with eleven new ncMs spanning five different chemical classes: ,-disubstituted-amino acids, malonic acids, carboxylic acids, {beta}2-amino acids and N-cyclic amino acids. We demonstrate that co-translational incorporation of ,-disubstituted-amino acids, {beta}2-amino acids, {beta}3-amino acids and N-cyclic amino acids is strongly dependent on the codons either side of the codon used to direct ncM incorporation, with several ncMs incorporated at less than 1% of sequence contexts. We evolve orthogonal tRNAs that enable the incorporation of previously unincorporated ncMs, enable the incorporation of ncMs at >95% of sequence contexts and, increase the incorporation efficiency at challenging sequence contexts up to 40-fold. We demonstrate the encoded cellular synthesis of proteins and macrocycles containing ncMs and, explicitly demonstrate that our evolved tRNAs provide direct access to a wider range of genetically encoded macrocyclic sequences containing ncMs. Our results provide a foundation for composing, discovering and manufacturing proteins and peptides with functions augmented by ncMs.

synthetic biology↗

bioRxiv2026

Decoding Single-Cell Omics of Perturbation Responses Using DeSCOPE

Deciphering cellular responses to genetic perturbations is fundamental to modeling gene regulatory networks and understanding mechanisms that change cellular phenotypes. However, current computational approaches often fail to outperform simple baseline models, highlighting a critical bottleneck in their generalizability and robustness. Here, we present DeSCOPE, a lightweight conditional variational autoencoder framework for predicting genetic perturbation responses spanning transcriptomic, epigenomic, and broader multi-modal landscapes. We systematically benchmarked DeSCOPE across diverse datasets under two challenging out-of-distribution settings: unseen genes and unseen cell types. DeSCOPE uniquely surpasses simple baselines in the unseen gene scenario, and achieves substantially improved performance for unseen cell types while requiring fine-tuning with far fewer perturbed genes. Finally, DeSCOPE demonstrates superior performance in predicting combinatorial multi-gene perturbations. Overall, DeSCOPE serves as a versatile multi-modal virtual cell model that can effectively guide the design of therapeutic targets that change cellular phenotypes. DeSCOPE is available at https://github.com/wanglabtongji/DeSCOPE.

bioinformatics↗

bioRxiv2026

A correlational study of ABCA3 and SCN4B as exercise-related biomarkers of patients with Stanford type A aortic dissection

BackgroundAccumulating evidence indicates that moderate exercise may reduce the incidence of Stanford type A aortic dissection (TAAD), but the specific mechanisms remain unclear. This study aims to identify exercise-related biomarkers in TAAD patients and to investigate their underlying mechanisms. MethodsTranscriptome data related to TAAD and exercise-related genes were obtained from publicly available databases. Candidate biomarkers for TAAD were identified through an integrative approach incorporating differential expression analysis, machine learning, and expression level assessment, leading to the construction of a diagnostic model. Subsequently, functional enrichment, immune infiltration, regulatory network analysis, and computational drug prediction were conducted to systematically investigate the pathological mechanisms and translational potential of the indentified biomarkers. ResultsABCA3 and SCN4B were identified as exercise-related biomarkers in TAAD progression. A nomogram incorporating these two biomarkers exhibited strong diagnostic performance for identifying the disease. Functional enrichment analysis revealed potential involvement of these biomarkers in disease progression through pathways including circadian rhythm regulation and ribosome biosynthesis. Additionally, immune cells like M1 macrophages and naive B cells, as well as regulatory factors including hsa-miR-1343-3p and XIST, were found to be involved in this process. Finally, zonisamide and MRS1097 were identified through computation prediction as potential therapeutic drugs. ConclusionABCA3 and SCN4B were identified as exercise-related biomarkers associatied with TAAD and represent potential valuable targets for both diagnosis and treatment strategies.

bioinformatics↗

bioRxiv2026

Invisible shield: Sprayable supramolecular antimicrobial microscale films for preventing wound and medical device infections

Wound and device-associated infections remain difficult to eradicate because biofilms block host immunity and antibiotics, accelerating chronicity and resistance. Here, we present a portable, low-cost dual-syringe spray that deposits an ultra-thin, self-assembling antimicrobial film directly on wounds and implant surfaces. The device co-delivers oppositely charged hyaluronic acid (HA) and a cationic antimicrobial peptide (polyarginine, PAR30), which rapidly form a conformal nanometric polyelectrolyte complex at the tissue-material interface. Molecular dynamics simulation revealed pronounced positional heterogeneity within the PAR30/HA complex and identified an N-terminal arginine as a dominant interaction hotspot. The resulting coating adheres to diverse substrates, kills bacteria on contact, prevents biofilm formation, and sustains antimicrobial efficacy. Across vitro assays and murine wound infection models, treatment produced 4 to 5 log reductions in bacterial burden against methicillin-resistant Staphylococcus aureus and Gram-negative pathogens, including Pseudomonas aeruginosa and Escherichia coli. The formulation is biocompatible, did not increase cutaneous inflammation or IL-6 levels in vivo, and reduced post-surgical pain and motor deficits in a mouse incision model. To our knowledge, this is the first antimicrobial treatment system applicable to both tissues and medical devices. Developed under a safe-and-sustainable-by-design approach, this technology combines biocompatible components, nanometric coating for minimal material use, and a simple syringe-based delivery device, offering a scalable, antibiotic-free strategy for wound care and medical device infection prevention. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=173 HEIGHT=200 SRC="FIGDIR/small/717441v1_ufig1.gif" ALT="Figure 1"> View larger version (68K): org.highwire.dtl.DTLVardef@49381aorg.highwire.dtl.DTLVardef@1023e64org.highwire.dtl.DTLVardef@4e282aorg.highwire.dtl.DTLVardef@12eeae4_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

bioRxiv2026

Chemogenetic Pericyte Activation Reveals Broad Contractile Ability and Limbic Vulnerability to Capillary Flow Deficits

Capillary pericytes contact most of the brains microvasculature. Yet, their influence on blood flow remains incompletely understood both locally in capillary networks and across brain regions. Here, we sparsely expressed the chemogenetic actuator Gq-DREADD in mouse brain pericytes to stochastically probe their contractility and influence on tissue perfusion and oxygenation. Chemogenetic stimulation induced robust contraction of pericytes over minutes, including those with thin processes on capillary segments proximal to venules, indicating control of vascular tone across the entire capillary bed. Pericyte contraction combined circumferential compression with longitudinal tension applied through thin processes, resulting in vasoconstriction and hypoperfusion. Histology revealed hypoxic microdomains induced by sparse pericyte contraction across the brain, and enriched hypoxia in limbic structures including the amygdala and hippocampus. These microscale perfusion deficits were undetectable by arterial spin labeling MRI. Our findings reveal the in vivo mechanics of pericyte contraction and identify limbic system vulnerability to capillary flow impairment.

neuroscience↗

bioRxiv2026

Mechanical interaction enables a collective mode of protocell proliferation

The proliferation of primitive life-forms (known as protocells) without sophisticated cell-division molecular machineries has been an intriguing question in evolutionary biology, synthetic biology, and living matter physics. While various modes of protocell proliferation at the individual level have been proposed, the growth dynamics of protocell colonies (i.e., protocolonies) received less attention. Here we chose to study this question in protocolonies consisting of densely packed protocells derived from wall-deficient L-form bacteria. We discovered that protocolonies proliferated robustly under spatial confinement, while isolated protocells failed to divide and eventually experienced membrane rupture due to imbalance of surface and volume growth. Combining results from quantitative imaging and computational modeling, we attributed this unexpected finding to mechanical shearing between densely packed protocells driven by their growth activities; such mechanical shearing enhances cell deformation, thereby enabling cell division and sustaining population growth in a protocolony. Our study reveals a unique role of self-generated mechanical stresses in the lifestyle of primitive life-forms. The findings may help to understand and control the collective growth dynamics of synthetic protocells or active droplets.

biophysics↗

bioRxiv2026

ENPP1 buffers extracellular cGAMP in brown adipose tissue to limit insulin resistance

The ectonucleotide pyrophosphatase/phosphodiesterase 1 (ENPP1) has long been linked with metabolic diseases, with the common ENPP1 K173Q (historically K121Q) variant conferring increased risk for type 2 diabetes (T2D). However, the mechanistic basis of this association has remained unclear. Here, we demonstrate that the K173Q variant has decreased cGAMP hydrolysis activity, suggesting that this loss of enzymatic function could contribute to its pathogenesis. Using a cGAMP-hydrolysis-deficient knock-in mouse (Enpp1H362A), we show that selective loss of this activity leads to a primary defect in energy expenditure and exacerbates high-fat diet (HFD)-induced weight gain and insulin resistance. An unbiased in vivo glucose-uptake screen reveals brown adipose tissue (BAT) as a focal site of metabolic impairment, characterized by profound extracellular cGAMP accumulation and a selective failure of insulin-stimulated glucose uptake. Mechanistically, we demonstrate that nutrient excess drives mitochondrial DNA leakage in brown adipocytes, triggering cGAMP production and export. Excess cGAMP directly propagates STING-dependent suppression of glucose uptake and lipogenesis in brown adipocytes. Additionally, when ENPP1-mediated clearance is compromised, extracellular cGAMP acts as a paracrine immunotransmitter that remodels the BAT microenvironment by recruiting and polarizing macrophages toward an M1-like phenotype. Together, our findings nominate the impaired ENPP1-dependent buffering of extracellular cGAMP as one mechanism by which ENPP1 variants influence metabolic homeostasis.

immunology↗

bioRxiv2026

Long-lived yeast-derived lipids promote longevity via regional and systemic metabolic remodeling

Aging is marked by a progressive breakdown of intestinal integrity and metabolic homeostasis, which together drives systemic decline in physiology and reduces lifespan. Here, we found that dietary lipids extracted from a genetically engineered long-lived yeast strain robustly extend lifespan in Drosophila and further uncovered the mechanisms using deuterium oxide-probed stimulated Raman scattering microscopy to image metabolic dynamics and single nucleus RNA sequencing (scRNA-seq) to unveil the underlying pathways. These yeast lipids are enriched in shorter, more saturated fatty acids and phospholipids as revealed by Raman spectroscopy and lipidomics, contributing to increased membrane order and reduced lipid storage. Functionally, targeted dietary supplementation with these lipid components synergistically prolongs fly lifespan. We show that these lipids reverse age-related declines in gut lipid droplet abundance, enhance membrane lipid incorporation, and increase de novo lipid synthesis, thereby improving epithelial structural integrity and barrier function. snRNA-seq identifies transcriptional remodeling in metabolically active enterocytes, including upregulation of autophagy and protein turnover genes, alongside reduction of unsaturated fatty acid biosynthesis. In the brain, dietary lipids orchestrate a dual metabolic strategy--promoting energy conservation and enhanced signaling across most neuronal and glial populations, while selectively boosting mitochondrial function in memory-critical Kenyon cells. All these leads to the enhancement of gut-to-glia communication, particularly through EGFR and FGFR pathways. Finally, analysis of our data with the Fly Metabolic Analysis Pipeline (FLY-MAP) reveals that yeast lipids restructure gut metabolic modules to coordinate energy production, redox balance, and nutrient flexibility. Our study uncovers a cross-kingdom mechanism of metabolic longevity regulation, paving the way for leveraging yeast-derived nutritional components to support tissue homeostasis and promote healthy aging.

molecular biology↗

bioRxiv2026

Structure-based similarity network accelerates the discovery of lysins as oral microbiome modulators targeting periodontal pathogens

Microorganisms significantly influence human health, and dysbiosis of the oral microbiome plays a critical role in the development and progression of both oral and systemic diseases. This highlights the urgent need for novel therapeutics targeting specific pathogens. Here, we presented a structure-based pipeline to efficiently identify potential phage-derived periodontal lysins (LysPds) from nearly one million proteins. We predicted the structures of candidate lysins using AlphaFold2 and developed an innovative structure-based similarity network to classify them into distinct clusters, each with unique functional properties. A systematic characterization of 16 representative LysPds from 11 superfamilies revealed that over 90% demonstrated potent antibacterial activity against key periodontal pathogens. Among these, LysPd078 was identified as a promising preclinical drug candidate, effectively reconfiguring microbiome communities while demonstrating significant efficacy and safety in mouse models of periodontitis and calvarial infection. Our findings highlight the effectiveness of structure-based similarity networks in exploring vast protein spaces and underscore the potential of LysPd078 as a targeted modulating agent for the oral microbiome.

microbiology↗

bioRxiv2026

Mechanism of GPR84 allosteric modulation at a helix 8-proximate site

Allosteric modulators offer opportunities for pathway-selective GPCR signalling, but the structural mechanisms enabling biased allosteric modulation remain unclear. Here we identify a helix 8-proximate allosteric site in the immune-metabolic receptor GPR84 and define how it achieves Gi -biased signalling. Cryo-EM structures of the GPR84-Gi complexes bound to the orthosteric agonist OX04539 alone or in combination with the positive allosteric modulator (PAM) PSB-16671 reveal that PSB-16671 binds at the interface of TM1, TM7, and helix 8, a location distinct from previously characterized GPCR allosteric pockets. Molecular dynamics simulations and mutagenesis uncover a polar interaction network linking orthosteric and allosteric sites through conserved residues including Asp662.50, Asn1043.36, and Asn3627.45. Unexpectedly, disrupting this network enhances allosteric cooperativity, indicating that conformational flexibility within the network is essential for allosteric communication. PSB-16671 stabilizes a receptor conformation with pronounced TM6 displacement that favours Gi coupling while disfavouring {beta}-arrestin recruitment. This Gi-biased profile sustains macrophage phagocytosis of cancer cells without the desensitization induced by balanced agonists. Sequence analysis suggests that helix 8-proximate allosteric sites may be broadly targetable across class A GPCRs, while receptor-specific contacts enable selective modulation. These findings establish structural and mechanistic principles for biased allosteric modulation applicable beyond GPR84.

biochemistry↗

bioRxiv2026

TCMCard: A High-Confidence Digital Infrastructure for Traditional Chinese Medicine Quantified by Multi-Dimensional Evidence Integration

Network pharmacology has become a widely used approach for deciphering multi-component, multi-target mechanisms of traditional Chinese medicine (TCM). Here we introduce TCMCard, a high-confidence digital infrastructure built on a Multi-Dimensional Evidence Integration (MDEI) framework. The framework integrates experimental activity data from authoritative chemical databases, literature-derived evidence, and structure-based similarity inference. Preprocessing steps include chemical structure normalization, species-specific filtering, and target quality scoring. Applied to conventional interaction datasets, this pipeline leads to the removal of over 60% of low-confidence noise. TCMCard supports network pharmacology exploration through an interactive visualization platform, and module analysis identifies functionally relevant communities that offer insights into the synergistic actions of TCM formulas. Overall, TCMCard may help move the field beyond simple data aggregation toward evidence-informed curation and quality-driven analysis. As an interactive and publicly accessible platform, it reveals an organized backbone within complex interaction networks, offering a more reliable basis for understanding multi-component synergy in TCM.

bioinformatics↗

bioRxiv2026

A PTM Regulatory Enzyme Co expression Code Defines Microglial Functional Heterogeneity in Cerebral Ischemia Reperfusion Injury

BackgroundCerebral ischemia-reperfusion injury (CIRI) is a major determinant of poor outcome after recanalization therapy in acute ischemic stroke. Microglial functional heterogeneity underpins neuroinflammation, yet the molecular mechanisms governing microglial phenotypic transitions remain incompletely understood. Metabolite-driven post-translational modifications (PTMs) have emerged as key regulators of microglial metabolism and inflammation, but whether PTM regulatory enzymes form co-expression modules that define microglial states is unknown. MethodsWe analyzed single-cell RNA-seq datasets from five GEO studies (GSE174574, GSE227651, GSE245386, GSE267240, GSE319237) covering tMCAO reperfusion and permanent ischemia models. Microglia were purified using double filtration (P2ry12/Tmem119/Cx3cr1+, Cd68/Adgre1/Ly6c-). PTM enzyme co-expression modules were identified by non-negative matrix factorization (NMF). Spatiotemporal dynamics were assessed by module projection across timepoints (Sham, 1d, 3d, 7d) and pseudotime analysis. Independent validation was performed in an additional tMCAO dataset (GSE245386). Sex differences were explored in a mixed-sex permanent ischemia dataset (GSE267240). ResultsThree robust PTM enzyme co-expression modules were identified: Metabolic stress-associated (M1), Pro-inflammatory-associated (M2), and Reparative-associated (M3). M1 was enriched in TCA cycle enzymes, M2 in inflammatory pathways (leukocyte activation, chemotaxis), and M3 in vascular development and translation. Module proportions and scores showed dynamic transitions: M1 decreased after reperfusion, M2 peaked at day 1-3, and M3 slightly increased at day 7. Independent validation in GSE245386 yielded high module conservation (cosine similarity = 0.874). Sex-specific differences in module distribution were observed in permanent ischemia ({chi}2 = 14.98, p = 0.00056). ConclusionsPTM enzyme co-expression modules delineate metabolic, pro-inflammatory, and reparative microglial states in CIRI with distinct spatiotemporal dynamics. This transcriptional framework supports the "PTM enzyme code" hypothesis and provides stage-specific targets for stroke therapy.

neuroscience↗

bioRxiv2026

The HPV E7 oncoprotein promotes LIM and SH3 Domain Protein 1 (LASP1) transcription via the Rb/E2F1 signalling pathway in HPV-positive cervical cancer cells

Since its discovery in a metastatic lymph node in breast cancer patients, LIM and SH3 Domain Protein (LASP1) has been shown to be over-expressed in and promote the progression of various cancers. We recently demonstrated that LASP1 is highly expressed in human Papillomavirus positive (HPV+) cervical cancers where it promotes cell proliferation and invasion. Importantly, we showed that the HPV E7 oncoprotein increased LASP1 expression by downregulating the microRNA miR-203, which directly targets the LASP1 mRNA 3UTR. However, whether LASP1 is regulated by other mechanisms in HPV+ cervical cancers is unclear. Here, we demonstrate an additional mechanism by which HPV E7 regulates LASP1 transcription. Our data demonstrates an important the role for Rb/E2F1 signalling in promoting LASP1 expression in HPV+ cervical cancer cells. Mechanistically, E7-mediated Rb binding and degradation is required for E7-driven LASP1 promoter activity. Overexpression of Rb decreased LASP1 promoter activity, LASP1 mRNA expression and LASP1 protein levels, whereas E2F1 expression promoted LASP1 expression. Importantly, E2F1 directly bound to the LASP1 promoter region and the E2F1 binding sites are essential for LASP1 expression in HPV+ cervical cancer cells. Finally, we demonstrate that LASP1 can partially rescue the growth defects observed in E2F1 knockdown cervical cancer cells. Taken together, our data show that HPV E7 regulates LASP1 expression via the Rb/E2F1 signalling pathway. In combination with our previous work, our studies demonstrate that HPV E7 employs multiple mechanisms to drive LASP1 expression, reinforcing the importance of LASP1 in HPV+ cervical cancer.

cancer biology↗

bioRxiv2026

Transcription Factor Subtype Governs Response and Resistance to DLL3-Directed T-Cell Engagement in Small Cell Lung Cancer

Although small cell lung cancer (SCLC) comprises transcription factor (TF)-defined molecular subtypes (ASCL1, NEUROD1, POU2F3), the extent to which these subtypes predict response to clinically effective therapy in patients--and whether therapy can select for subtype switching--remains unknown. The recent approval of the DLL3xCD3 bispecific T-cell engager tarlatamab represents one of the first meaningful advances in relapsed small cell lung cancer (SCLC) in decades, yet responses remain heterogeneous and resistance is inevitable. Here, we inferred SCLC gene expression from circulating chromatin in prospectively collected patient plasma (46 patients; 167 samples), enabling interrogation of response and acquired resistance to tarlatamab. Parallel development of the first immunocompetent syngeneic mouse model to study tarlatamab response and resistance enabled functional validation. Across species, findings converged on a central principle: TF subtype governs both initial response and acquired resistance. Therapeutic response was significantly associated with ASCL1-subtype tumors, whereas NEUROD1-subtype tumors exhibited inferior responses and POU2F3-subtype tumors were uniformly resistant, consistent with DLL3 being a direct ASCL1 transcriptional target and most highly expressed in ASCL1-positive tumors. Strikingly, one mode of acquired resistance revealed therapeutic selection for a NEUROD1-high state with concomitant DLL3 downregulation. Other resistant tumors exhibited enrichment of regulatory and exhausted T-cell programs, highlighting tarlatamabs dual-targeting mechanism of action. Together, these results reveal that tarlatamab exerts selective pressure against ASCL1-driven lineages, facilitating resistance through loss of an antigen intrinsically linked to that state. These findings underscore the clinical relevance of TF-defined molecular subtypes in human SCLC. More broadly, they highlight the power of integrating longitudinal in vivo plasma transcriptional profiling from patient plasma with functional mouse modeling to uncover clinical and biological mechanisms of response and resistance to cell-surface-targeted therapies.

cancer biology↗

bioRxiv2026

Blockade of Tim-3 pathway in a mouse model of Toxoplasmosis: impact on brain leukocyte infiltration, parasite burden, and neuroinflammation

Cell-mediated immune responses are crucial for protecting the host against Toxoplasma gondii infection. However, impaired immunity, such as T-cell exhaustion, is a common phenomenon during chronic infection. This may represent a strategy employed by T. gondii to evade host defenses. T-cell immunoglobulin and mucin-domain containing 3 (Tim-3) is an important regulatory molecule involved in cell-mediated immunity. This study examined the expression of Tim-3 and the effects of its blockade in a mouse model of toxoplasmosis. In mice with chronic T. gondii infection, we found that Tim-3 is highly expressed in both cyst-bearing and non-cyst-bearing tissues, and its expression correlates with the parasite burden. Blocking the Tim-3 pathway with an anti-Tim-3 antibody enhances the immune response, resulting in elevated levels of cytokines (IFN-{gamma}, IL-12p70, IL-2, IL-9) and the chemokine CXCL1 in the serum, increased leukocyte infiltration (CD3+, CD14+ cells) in the brain, and downregulation of Tim-3 expression in microglial cells. As a result, the anti-Tim-3 treatment resulted in a 62% reduction in the number of tissue cysts and a trend towards an increase in the homeostatic signature, P2RY12, in microglia. Our study provides proof of concept for an anti-Tim-3 approach in treating chronic T. gondii infection and potentially other brain-residing pathogens.

microbiology↗

bioRxiv2026

Breast cancer interactions with osteoclasts generate osteoclast tumor hybrid like cells through dynamic non-canonical cell fusion and cell-in-cell processes

Macrophages/osteoclasts are highly fusogenic cells that interact closely with bone-metastatic breast cancer cells. These cancer cells adapt to bone microenvironments by undergoing osteomimicry, acquiring bone-like phenotypes. Exploration using human breast cancer-bone metastases dataset revealed that a small population of epithelial breast cancer cells express osteoclast-like and osteomimicry genes at the single-cell level. Cell fusion and cell-in-cell (CIC) processes are two uncommon yet prognostically significant mechanisms in cancer. We showed that co-culture between murine breast cancer cells and osteoclasts yielded a unique osteoclast phenotype through dynamic cell-in-cell (CIC) interactions and fusion-like behaviours between pre-osteoclasts/mature osteoclasts and breast tumor cells, resulting in osteoclast-tumor hybrid-like cells. These tumor cell interactions characterized by membrane retention and nuclear adjacency to host nuclei were consistently observed throughout osteoclast differentiation. Single-cell sequencing analysis and interpretative assays on hybrid-like cells revealed altered extracellular matrix (ECM) modification processes, immunoregulatory, and cancer-associated pathways compared to unfused osteoclasts. Tumor cells co-cultured with osteoclasts expressed hematopoietic and osteoclast-lineage factors more strongly than tumor cells cultured alone with their effects amplified under direct cell-cell contact. The presence of these hybrid-like cells was validated in human breast cancer-bone metastases. We propose that disseminated bone-tropic breast cancer cells were stimulated by osteoclasts to undergo a non-canonical, dynamic osteoclast differentiation and CIC formation to form hybrid-like cells that may facilitate bone metastatic lesions.

cancer biology↗