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Biology subjects

Tian, Y.

Publications and source records attributed to Tian, Y..

At least 19 recordsLinked to original sources

Brain state locks silent memories in a trained fly connectome

Complete connectomes now exist for insect nervous systems, but whether a fixed wiring diagram can learn, and what its memories consist of, is unknown. Here, we trained a spiking model of the whole male Drosophila central nervous system, 167,106 neurons with fixed wiring, to plan moves and to remember a visual cue. Spikes write the cue into neuronal adaptation, which holds it silently until the next input reads it out. Cells that hold the trace are enriched for transcripts of a calcium-activated potassium channel in fly cell atlases. The learned readout recalls the trace only in the brain state of learning: the same trace evokes a different response at another delay, and a disease-like loss of potassium current rewrites the trace and changes how it is read. Learning in the new state is spared. Memory failure can arise from a change of state rather than a loss of storage.

neuroscience↗

Susceptibility and cellular responses of COPD airway epithelium to cigarette smoke in stem cell-derived ALI models

Despite cigarette smoke being the chief driver of chronic obstructive pulmonary disease (COPD), numerous patients maintain their smoking habits by opting for low-yield or slim cigarettes under the misconception of diminished health risks. Differential effects of high-tar conventional versus low-tar slim cigarettes on COPD airway epithelium remain poorly defined. We established an air-liquid interface (ALI) model using patient-derived COPD airway epithelial stem cells and exposed cultures to high-tar conventional smoke (TC), low-tar slim smoke (SC), or filtered air (NC). Both regimens induced IL-1{beta} inflammation, ciliary structural changes, and oxidative stress, with TC eliciting stronger responses. Single-cell RNA sequencing resolved six epithelial populations. In ciliated cells, hdWGCNA showed NC modules associated with cilium organization and assembly, SC adaptive defense responses, and TC more extensive reprogramming of ciliary functional networks. Basal cells displayed stress-pathway activation, squamous metaplasia signatures, and developmental regression toward a stem-like state, with TC producing approximately 1.7-fold stronger regression than SC. Secretory cells exhibited identity erosion, antimicrobial program downregulation, and a shift toward keratinization and squamous-oriented programs, again more pronounced under TC. These findings indicate that high-tar conventional smoke exerts greater influence than low-tar slim smoke on COPD airway epithelium across inflammatory, structural, and lineage-specific molecular dimensions, providing high-resolution insight into cell-type-specific responses to continued smoke exposure.

cell biology↗

Pulmonary colonization of Candida albicans drives breast cancer lung metastasis via candidalysin

The intratumoral mycobiome is emerging as a key modulator of cancer progression, with specific fungal taxa as potential biomarkers. However, whether and how mycobiomes colonizing distant organs contribute to tumor evolution remains largely unexplored. Here, we identify selective enrichment of Candida albicans in breast cancer lung metastases. Mechanistically, the fungal virulence factor candidalysin activates pulmonary mast cells, which release chemotactic mediators that expand immunosuppressive populations and suppress cytotoxic lymphocyte activity, remodeling the lung into a metastasis-permissive microenvironment. Analysis of clinical isolates and isogenic mutants further demonstrates that candidalysin secretion levels dictate metastasis-promoting potential. Informed by these findings, we developed a combination regimen that concurrently eliminates fungal colonization, stabilizes mast cells, and reverses the immunosuppressive microenvironment, thereby significantly curtailing metastatic progression. Collectively, our study establishes pulmonary C. albicans colonization as a driver of breast cancer lung metastasis and provides a mechanistic framework for targeting mycobiome-host interactions in metastatic disease.

cancer biology↗

Affinity Maturation Enables Dual Targeting of Cancer-Associated MUC1-Tn/STn and Drives Potent Tumor Control

A major challenge in solid tumor immunotherapy is identifying tumor-restricted antigens while overcoming intratumoral antigen heterogeneity. The truncated O-glycans Tn (GalNAc-O-Ser/Thr) and STn (Neu5Ac2-6GalNAc-O-Ser/Thr) are aberrantly displayed on the transmembrane glycoprotein MUC1 across a broad spectrum of epithelial malignancies, making MUC1-Tn/STn an attractive shared tumor-associated antigen class. However, heterogeneous intratumoral Tn/STn expression renders single-glycoform-specific antibodies vulnerable to antigen-driven escape. To address this challenge, we used structure-guided directed evolution and yeast surface display to affinity-mature the anti-MUC1-Tn antibody 5E5, generating variants with high-affinity dual recognition of MUC1-Tn and MUC1-STn. Co-crystal structures revealed that heavy-chain CDR loops cooperatively engage the GalNAc moiety primarily through hydrogen-bonding networks, in which HCDR3 residue 98 fine-tunes glycoform preference: Tyr98 favors MUC1-Tn recognition, whereas His98 enhances MUC1-STn engagement, while both support high-affinity recognition of both glycoforms. When reformatted as bispecific T-cell engagers, the affinity-matured variants mediated potent and durable cytolytic activity against cancer cells with heterogeneous glycan profiles, suppressed mixed Tn/STn tumors in vivo where the parental antibody failed, and showed enhanced activity in patient-derived tumor-like clusters. Together, these findings establish functional glycoform coverage as a design principle for antibody engineering, whereby a single paratope is optimized to recognize a defined spectrum of tumor-associated glycoforms while preserving antigen specificity, providing a strategy to overcome glycan heterogeneity in solid tumor immunotherapy.

cancer biology↗

Dual blockade of IL-18 and IL-4Rα by a bispecific antibody for improved treatment of atopic dermatitis

Background: Atopic dermatitis (AD) is a chronic inflammatory dermatosis primarily driven by type 2 immunity, with additional type 1 and type 3 components that may limit the benifit of ILRalpha blockade alone. Interleukin18 (IL18), an epithelial alarmin genetically associated with AD and correlated with disease severity, has been implicated as an upstream amplifier of this mixed inflammatory response. Objective: To assess whether concurrent IL18 neutralization and IL4Ralpha; blockade with a bispecific antibody provides broader and more balanced suppression of AD relevant type 1, type 2, and type 3 pathways than single target inhibition. Methods: We generated FJ0125, a bispecific antibody comprising human IL18 binding protein fused to a novel humanized anti IL4Ralpha antibody, and characterized its binding, signaling, and functional activity in vitro and in vivo. The activity was evaluated in human group 2 innate lymphoid cell and primed Th2 cell assays, a keratinocyte & dendritic cell & T cell coculture system, and an MC903/Staphylococcus aureus induced dermatitis model in human IL4/IL4Ralpha; knock in mice. Results: FJ0125 bound to IL18 and IL4Ralpha; with high affinity, engaged both targets, inhibited IL4/IL13 signaling with dupilumab comparable potency, and neutralized human and mouse IL18. In vitro, FJ0125 more effectively suppressed IL18 driven lymphocyte activation and type 1, type 2, and type 3 cytokine production than IL18BPFc or IL4Ralpha; monotherapy. In vivo, FJ0125 reduced multitype cytokines, improved dermatitis, lowered serum IgE, and abrogated the paradoxical IL22 increase observed with selective IL4Ralpha; blockade. Conclusion: Dual IL18/IL4Ralpha; blockade with FJ0125 achieves coordinated suppression of multitype inflammation and represents a mechanistically substantiated therapeutic strategy for AD.

immunology↗

Distinct Strategies for Engineering Bioenergy Traits in Sorghum Drive Divergent Functional Shifts in the Rhizosphere Microbiome

Engineering bioenergy crops for enhanced biomass digestibility and high-value co-products is a promising approach to sustainable biofuel production. However, the impact of these engineered crops on the belowground microbiome remains poorly understood. In this study, we characterized the composition and functional responses of the belowground microbiome associated with transgenic sorghum lines: one with reduced cell wall crosslinking (AT10) and another with elevated protocatechuic acid (PCA) production (Qsub). The lines were grown under field conditions with four irrigation levels, and samples were collected twice during the growing season. We found that the two transgenic types drove a subtle but significant divergence in bacterial communities, both compositionally and functionally. Community-wide functional profiling showed that AT10 rhizospheres were consistently depleted in genes associated with mobile genetic elements, while Qsub rhizospheres were enriched in TonB-dependent transport and vanillate monooxygenase, an enzyme that funnels lignin-derived monomers toward PCA degradation, alongside reduced pectin- and cellulose-degradation genes. Genome-resolved analysis linked these community-level shifts to specific taxa: in Qsub, the enriched MAGs were taxonomically diverse, ranging from genome-reduced Patescibacteria with an episymbiotic lifestyle to taxa enriched in lignin-associated auxiliary activity enzymes. In AT10, the depleted Azospirillaceae MAGs carried unusually high mobile genetic element content, consistent with the community-wide pattern. Collectively, these findings offer new insights into how genetic modifications aimed at improving bioenergy traits shapes the composition and function of the rhizosphere microbiome, with potential downstream consequences for soil carbon cycling.

plant biology↗

An accumbal cholinergic ISR-HCN2 axis sustains maladaptive cue motivation

Environmental cues associated with rewarding outcomes can exert persistent control over behavior long after the reward is absent, yet the cellular adaptations that stabilize such maladaptive motivation remain unclear. Here we identify nucleus accumbens cholinergic interneurons (CINs) as causal regulators of persistent cue-driven seeking. Self-administration of addictive drugs or high-fat reward, but not sucrose, selectively increased CIN pacemaker firing. Cocaine-paired cues evoked rapid acetylcholine release in the nucleus accumbens core, and bidirectional manipulation of CINs suppressed or enhanced cue-induced cocaine seeking. Mechanistically, cocaine experience engaged the integrated stress response (ISR) in CINs, increased HCN2 expression and Ih, and stabilized a hyperexcitable state. CIN-specific ISR suppression or HCN2 knockdown reduced cocaine seeking, whereas HCN2 overexpression enhanced it. Local HCN blockade and systemic treatment with the clinically approved HCN blocker ivabradine reduced cue-driven seeking across addictive-drug and high-fat-reward paradigms while sparing sucrose seeking. These findings identify an ISR-HCN2-dependent cholinergic mechanism that stabilizes maladaptive cue-driven motivation and nominate HCN-dependent excitability as a tractable target for therapeutic intervention.

neuroscience↗

Nitrite reductase NirB mediates an unconventional nitrogen assimilation strategy to enhance adaptations of extremophile

Microbial metabolism in extreme environments has long been shrouded in profound mystery. Distinct from the direct assimilation of exogenous organic carbon, microorganisms predominantly exploit inorganic nitrogen substrates as their primary nitrogen sources. As a critical nitrogen assimilation pathway, assimilatory nitrite reduction plays a vital role in microbial nitrogen acquisition, especially in extreme environments with poor nutrient availability. In this study, we identified the coexistence of two isoforms of NADH-dependent nitrite reductase in single genomes. NIR- and NIR-{beta}, named based on their phylogenetic relationships, exhibit significant differences in protein sequence, genomic context and evolutionary relationship, a phenomenon that has rarely been reported before. They also show distinct expression patterns, which may allow bacteria to achieve efficient nitrogen conversion in nutrient-poor environments. This finding calls for a revision of the conventional model of nitrogen cycling gene combinations inferred from common model microorganisms and holds numerous implications for how we understand and study the environmental adaptation mechanisms of extremophiles.

microbiology↗

Transcription factors read a second regulatory code in chromatin

Transcription factors (TFs) decode gene regulatory information written in DNA, yet how this vocabulary is interpreted within chromatin remains largely unexplored. Here, using an upgraded NCAP-SELEX platform, we systematically map the nucleosomal DNA recognition landscapes of 269 human TFs. We uncover a widespread, chromatin-dependent mode of sequence recognition: many TFs recognize motifs on nucleosomal DNA that are distinct from their canonical naked-DNA binding sites, revealing that nucleosome architecture encodes a second gene regulatory code in chromatin. Cryo-electron microscopy structures of TF-nucleosome complexes demonstrate that this second code is read through a combination of nucleosome-induced DNA deformation and direct protein-histone contacts. Functional analyses show that these chromatin-encoded motifs actively promote chromatin accessibility and drive cell-type-specific cis-regulatory activity in vivo. Strikingly, a single TF can deploy its canonical and nucleosome-derived motif repertoires to partition and govern entirely distinct physiological programs. Together, our findings establish that TFs interpret two complementary layers of genomic information: the primary DNA sequence and a second code written into the nucleosome architecture. This chromatin-encoded layer of regulatory information fundamentally expands our understanding of how TF specificity is achieved and how gene regulatory networks are wired in multicellular organisms.

systems biology↗

AI-like parallelogram geometry of word relations in the human neocortex

The same semantic relation (e.g., queen-king and woman-man) is encoded as a shared vector direction in language AI, forming parallelogram geometry, whereas its presence in the human brain remains unknown. Our fMRI analysis revealed similar geometry in the neocortex, particularly in higher-order language regions. Our findings link the brain and AI through a common geometry, advancing understanding of how abstract relational knowledge is organized and used in human language processing.

neuroscience↗

Rethinking Platelet Identity from an Extracellular Vesicle-Centric View: A Proof-of-Concept Study

The long-standing ambiguity surrounding whether platelets are cells or particles has hindered a unified understanding of their biology. In this study, we characterized the morphology of platelet-like particles (PLPs) using nanoparticle tracking analysis, transmission electron microscopy, and immunofluorescence. Notably, we observed that platelets can be endocytosed by living cells. We also indicate that platelets express the canonical extracellular vesicles (EVs) markers CD9, CD63, CD81, and TSG101. Our results demonstrate that platelets share six key similarities with EVs--in size, morphology, surface markers, function, biogenesis, and mode of action--leading us to propose a novel classification. Our findings suggest that platelets fulfill the current minimal criteria for EVs, raising the possibility that they could be conceptually viewed as a specialized EVs subset rather than conventional blood cells. Adopting this EVs-centric perspective could broaden the current conceptual framework for EVs and offer an alternative lens for interpreting platelet functions, which may in turn help guide future translational research and clinical exploration.

cell biology↗

A T2T Benchmark Reveals How Reference Choice Shapes Human Genome Interpretation

The completion of telomere-to-telomere (T2T) human genomes has expanded the accessible landscape of human genetic variation, yet benchmark resources remain limited to conventional high-confidence regions defined by existing reference frameworks. Here, we generated a near-perfect diploid T2T genome (T2T-LIN) from a Chinese individual and established assembly-based truth sets by comparison with T2T-YAO, an ancestry-matched near-perfect T2T reference genome. The benchmark showed a heterozygous/homozygous SNV ratio of ~2, consistent with expectations under Hardy-Weinberg equilibrium, and enabled genome-wide evaluation of reference-dependent biases. We found that reference choice substantially influences genome interpretation: ancestry-matched linear T2T references provided the most faithful representation of individual genomic variation and enabled more accurate genome reconstruction than unmatched linear, diploid and graph-based references. Benchmarking previously inaccessible repetitive and structurally complex regions revealed substantial limitations of current variant callers that were masked by conventional metrics. The T2T-LIN and YAO-LIN benchmarks establish a T2T-era framework for evaluating reference-dependent genome interpretation and variant discovery across nearly the complete human genome.

genomics↗

Targeting Macrophage Connexin 43 Hemichannels Suppresses Synovial Inflammation and Osteoarthritis

Osteoarthritis (OA) is the most common chronic joint disease and a leading cause of disability worldwide, yet no disease-modifying therapies are available. Although OA has traditionally been viewed as a cartilage-centered degenerative disease, growing evidence suggests that synovial inflammation is a critical driver of disease progression. However, the upstream mechanisms and actionable targets that govern this inflammatory response remain poorly defined. Connexin 43 (Cx43), a key regulator of musculoskeletal homeostasis that forms both gap junctions and hemichannels (HCs), is upregulated in osteoarthritic cartilage and synovium, but the specific contribution of Cx43 channels remains unclear. Here, we show that selective inhibition of Cx43 HCs attenuates OA progression in a murine post-traumatic OA model. Using adeno-associated virus (AAV)-mediated gene deletion, we found that Cx43 knockdown in joint tissues reduced cartilage erosion, synovial hyperplasia, subchondral bone sclerosis, and OA-associated pain. To dissect HC-specific functions, we developed a monoclonal antibody, Cx43(M1), that blocks Cx43 HCs without affecting junctional communication. Cx43(M1) preserved cartilage integrity, suppressed synovial inflammation, and alleviated pain behaviors, even when treatment was initiated after established cartilage damage. Mechanistically, the antibody preferentially localized to synovial macrophages, where it inhibited HC activity, reduced ATP and PGE2 release, and suppressed pro-inflammatory gene expression. Macrophage-specific Cx43 deletion recapitulated these protective effects, and Cx43 HC blockade in primary human OA synovial macrophages similarly inhibited inflammatory and catabolic responses. These findings identify synovial macrophage Cx43 HCs as upstream drivers of OA and support a paradigm shift from a predominantly chondrocyte-centered view toward synovial macrophage directed intervention.

immunology↗

SPC-Clean: A napari Plugin for Reducing Speckle and Isolated Pixel Noise in Fluorescence Microscopy Images

Speckle artifacts and isolated foreground pixels are common in fluorescence microscopy and can interfere with segmentation and subsequent quantitative image analysis. Conventional denoising methods often modify image intensities through filtering or smoothing, potentially altering biologically relevant fluorescence signals. We introduce Sparse Pixel Cluster Cleaning (SPC-Clean), a topology-aware method that removes poorly supported foreground pixels through iterative neighborhood analysis of a thresholded mask. SPC-Clean is deterministic, training-free, preserves original fluorescence intensities for practical microscopy workflows.

bioinformatics↗

Microbial Metabolites Potentiate MAIT Cell Anti-Tumor Immunity Against Solid Tumors

Mucosal-associated invariant T (MAIT) cells sense riboflavin metabolites through the monomorphic antigen-presenting molecule MR1, providing a unique opportunity to therapeutically mobilize a broadly shared T cell population without genetic engineering. Here, we show that the highly potent microbial metabolites, 5-OP-RU and 5-OE-RU, can be exploited as pharmacologic precision immune activators to drive human MAIT cell responses against solid tumors. Ligand stimulation in human co-culture systems elicited robust MAIT cell cytotoxicity, inflammatory cytokine secretion, and transcriptional states transformation. In vivo administration of riboflavin ligands 5-OP-RU significantly suppressed tumor growth in xenograft liver cancer models. Metabolite-driven MAIT activation also reprogrammed the local immune landscape, enhancing effector function and overcoming features of the immunosuppressive niche by markedly eliminating tumor-associated macrophages (TAMs) and myeloid-derived suppressor cells (MDSCs) within the tumor microenvironment (TME). These findings reveal that microbial riboflavin metabolites can power and redirect MAIT cells to solid tumors, establishing MR1-metabolite signaling as a tractable therapeutic axis for liver cancer and other solid malignancies.

cancer biology↗

Termination dynamics set RNAPII elongation rate and gate the response to CDK12 inactivation

The transcriptional fidelity of RNA polymerase II (RNAPII) is governed by a tight equilibrium between elongation and termination activities, a balance frequently disrupted in human diseases such as cancer. The transcriptional cyclin-dependent kinase 12 (CDK12) maintains RNAPII elongation rate and processivity throughout the gene body. Inactivation of CDK12 disrupts this homeostatic balance and causes elongation stress, slowing RNAPII and triggering premature termination at intronic polyadenylation sites (IPAs). Despite this, the precise executors of intronic premature termination under CDK12-inactivation-induced elongation stress remain poorly understood. Using genome-wide CRISPR screening combined with chemical-genetic approach, we identified a pro-termination mechanism at intronic checkpoints; upon CDK12 inactivation, SCAF4 recruits the cleavage and polyadenylation (CPA) complex through its catalytic endonuclease CPSF3 to execute premature cleavage at IPAs. Disruption of SCAF4-CPA axis prevents early termination, restores full length transcription and confers resistance to CDK12/cyclin K inhibition. Genetic loss of SCAF4 restores the RNAPII elongation rate under CDK12 inhibition, revealing that termination dynamics actively shape the rate of transcription. Supporting this model, we uncovered an anti-termination mechanism driven by KHDRBS1/SAM68, whose depletion promotes proximal termination and sensitises cells to CDK12 targeting. Our findings mechanistically couple elongation and termination activities at intronic checkpoints as joint contributors to both the processivity and elongation rate of RNAPII. This establishes termination dynamics as an active and tractable axis of the cellular response to elongation stress.

molecular biology↗

Rational and computation-assisted engineering of a compact and efficient StaCas9 genome editor

Type II-A CRISPR-Cas9 nucleases are widely used for genome editing, yet their functional diversity and therapeutic potential remain incompletely explored. In this study, we systematically analyzed natural variation in PAM recognition among SaCas9 orthologs and identified StaCas9 as a compact and efficient nuclease recognizing an NNG PAM. Structural and sequence analyses revealed that S983 within the PAM-interacting domain contributes to the PAM preference of StaCas9. StaCas9 enabled efficient genome editing across multiple endogenous loci in human cells and achieved high-efficiency disruption of the therapeutically relevant PCSK9 gene, supporting its potential for gene therapy. Furthermore, guided by structural insights, we significantly enhanced the editing activity of StaCas9. Together, these results expand our understanding of PAM recognition in type II-A Cas9 nucleases and establish StaCas9 as a high-performance genome-editing tool for therapeutic applications.

genomics↗

Unifying transcranial focused ultrasound and transcranial magnetic stimulation effects with calcium-dependent synaptic plasticity theory

Low-intensity transcranial focused ultrasound stimulation (TUS) is an emerging technology that shares features of both established invasive neurostimulation techniques such as deep brain stimulation (DBS) and noninvasive techniques such as transcranial magnetic stimulation (TMS). Like DBS, TUS can target non-superficial brain structures with millimeter-level precision. Like TMS, but unlike DBS, the most important physiological effect of TUS from a clinical perspective is its ability to induce lasting neuroplastic changes (long term potentiation/depression; LTP/LTD) from relatively short stimulation sessions. Thus follows the intriguing possibility that, although TUS and TMS have fundamentally different primary mechanisms of action -- acoustic versus electromagnetic -- they might nevertheless share a common secondary mechanism of plasticity induction through temporally patterned stimulation. A quantitative mathematical theory of this secondary mechanistic pathway could therefore have important explanatory and predictive value in both modalities. Two major challenges to the development of such a theory, however, are: i) experimental results showing contradictory plasticity effects between TUS and TMS for nominally similar stimulation parameters, and ii) the markedly different temporal structures of their stimulation waveforms (ranging from discrete pulses in TMS to continuous sinusoidal oscillations in TUS), even for highly aligned protocol designs such as continuous theta burst (cTB) stimulation. Here we show that a mathematical model of calcium-dependent synaptic plasticity in corticothalamic circuits, already developed extensively for TMS, can indeed provide such a unified description of stimulation effects across these two modalities. Numerical simulations using this model for a range of TUS and TMS protocols reproduced plasticity effects consistent with experimentally observed changes in cortical excitability. In particular, our model addresses both of the above challenges, by i) reconciling apparently contradictory results across modalities for the same stimulation parameters, and ii) introducing a simple algebraic approach, which we term the 'equivalent energy principle', for relating corresponding TMS and TUS waveforms. The ability of the model to account for differing effects across multiple stimulation modalities provides further support for the underlying general theory describing calcium-based regulation of stimulation plasticity effects, which spans multiple scales of system organization -- from ion channel kinetics to neural population activity. Our work also provides a foundation for future bidirectional exchange of new experimental observations and insights between experimental and theoretical TUS and TMS research, including strategies for model-based protocol optimization and discovery of novel plasticity-inducing TUS and TMS paradigms.

neuroscience↗