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Biology subjects

Zhao, X.

Publications and source records attributed to Zhao, X..

At least 127 records · Page 7Linked to original sources

Therapeutic Salmonella induces long-term protective trained immunity in NK cells against cancer metastasis

Trained immunity, a form of innate immune memory initially recognized in pathogen defense, has recently been reported to aid in combating cancer. Although trained immunity has been well-characterized in myeloid lineage cells, its presence in innate lymphoid cells, particularly natural killer (NK) cells, remains largely unexplored. Here, we report that a single dose of Salmonella YB1, an attenuated candidate anticancer vaccine strain, provides long-lasting protection against cancer metastasis in mice by inducing trained natural killer (NK) cells. Functional assays coupled with multiomics analysis revealed that Salmonella-trained NK (stNK) cells establish an enduring reprogrammed epigenome characterized by enhanced pro-survival signaling and immune effector functions, resulting in more potent IFN-{gamma} release and cytotoxicity upon secondary stimulation. We further revealed that IL-12 and IL-18 are essential but insufficient for this NK cell training effect. Crucially, stNK cells far outperform the common immune checkpoint therapies, including PD-1 and TIGIT blockade, in suppressing metastasis, underscoring the unique immunological mechanisms in combating metastasis. These findings uncover a novel long-term anti-metastatic function of trained immunity in NK cells, highlighting its potential as an effective antitumor strategy.

immunology↗

Tafazzin-Mediated Cardiolipin Remodeling Controls Metabolic Stress Response and Effector Function of Inflammatory T Cells

Clonal expansion and effector differentiation of T cells require extensive metabolic reprogramming. This includes the restructuring of the inner mitochondrial membrane (IMM) to enhance respiration by increasing chemiosmotic coupling efficiency. Cardiolipin, a unique phospholipid that is exclusively synthesized and localized in the IMM, modulates the biophysical properties of the electron transport chain (ETC) in tissues with high energy demands, such as cardiomyocytes and skeletal muscle. However, it remains unclear whether cardiolipin is also important for metabolic remodeling during T helper (Th) cell differentiation. In this study, we show that cardiolipin transacylation, catalyzed by the enzyme Tafazzin, supports the clonal expansion and effector function of inflammatory Th1 and Th17 cells in vitro and in models of autoimmune colitis and encephalomyelitis. At the molecular level, we demonstrate that loss of Tafazzin-mediated cardiolipin maturation induces a metabolic and transcriptional stress response in Th cells to compensate for impaired coupling efficiency of the ETC complexes and disrupted cellular redox homeostasis. However, the genetic program that restores cellular homeostasis and mitigates oxidative stress concurrently impairs the effector functions of inflammatory T cells, such as cytokine production. Our findings also provide insights into the complex clinical manifestation of patients with Barth syndrome (BTHS) caused by mutations in the human TAFAZZIN gene. BTHS is characterized by cardiac and skeletal myopathy as well as neutropenia and an increased susceptibility to infections. Although the molecular basis of the immunodeficiency remains poorly understood, our findings suggest that impaired Th cell function contributes to the immunopathology observed in BTHS patients.

immunology↗

C/EBPβ-mediated PARP1 Suppression Drives Tumor Progression of Aneuploid Cells

Aneuploidy--defined as gains and losses of chromosomes--is frequently observed in cancer and has been implicated in promoting tumor progression and metastasis. However, the molecular mechanisms underlying this phenomenon remain poorly understood. By generating new models of aneuploidy, we found that aneuploidy confers remarkable resistance to reactive oxygen species (ROS)-mediated cell death. This resistance is a general consequence of aneuploidy, independent of the specific chromosomes gained or lost. Mechanistically, Poly(ADP-Ribose) Polymerase 1 (PARP1) is suppressed in aneuploid cells, which inhibits PARP1-mediated cell death after ROS (parthanatos). We validated aneuploidy-associated PARP1 suppression across 15 cell models and human tumors, with pronounced effects in metastatic tumors. Importantly, decreased PARP1 levels promote tumor metastasis while increased PARP1 suppresses it. Through a genome-wide CRISPR screen and functional validation, we identified the transcription factor CCAAT/enhancer-binding protein beta (CEBPB) as a critical mediator of PARP1 downregulation and ROS resistance in aneuploid cells. Furthermore, we found that lysosomal dysfunction serves as the upstream mediator of CEBPB activation in aneuploid cells. We propose that aneuploidy-driven CEBPB activation promotes PARP1 suppression, fostering ROS resistance and cancer progression. HighlightsO_LIAneuploidy confers resistance to oxidative stress independent of p53 status, karyotype and cell lineage through inhibition of PARP1 expression and activity C_LIO_LISuppressed PARP1 enhances metastatic potential, while PARP1 restoration suppresses metastatic spread, revealing a novel mechanism linking aneuploidy to cancer progression. C_LIO_LIPARP1 suppression compromises DNA damage repair and cell death to multiple genotoxic stressors, including reactive oxygen species, alkylating agents, and UV radiation. C_LIO_LIA genome-wide CRISPR screen and a CRISPRa screen identifies CEBPB as a critical transcription factor mediating PARP1 regulation and ROS resistance. C_LIO_LINuclear CEBPB increases significantly after aneuploidization in experimental systems and in primary human cancers. C_LI O_FIG O_LINKSMALLFIG WIDTH=195 HEIGHT=200 SRC="FIGDIR/small/670212v2_ufig1.gif" ALT="Figure 1"> View larger version (63K): org.highwire.dtl.DTLVardef@1bf4edforg.highwire.dtl.DTLVardef@d3311eorg.highwire.dtl.DTLVardef@13daf25org.highwire.dtl.DTLVardef@b5e65f_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

Aberrant recursive splicing in a human disease locus

Recursive splice sites are rare motifs postulated to facilitate splicing across massive introns and shape isoform diversity, especially for long, brain-expressed genes. The necessity of this unique mechanism remains unsubstantiated, as does the role of recursive splicing (RS) in human disease. From analyses of rare copy number variants (CNVs) from almost one million individuals, we previously identified large, heterozygous deletions eliminating an RS site (RS1) in the first intron of CADM2 that conferred substantial risk for attention deficit hyperactivity disorder (ADHD) and other neurobehavioral traits. CADM2 encodes a neuronally expressed cell adhesion molecule that has repeatedly been associated with ADHD and numerous similar traits. To explore the molecular impact of RS ablation in CADM2, we used CRISPR to model patient deletions and to target a smaller region ([~]500 base pairs) containing RS1 in both human induced neurons (iNs) and rats. Transcriptome analyses in unedited iNs provided a catalog of CADM2 transcripts, including novel transcripts that retained RS exons. Intriguingly, ablating RS1 altered the gradient of RNA abundance across the first intron of CADM2, decreased the level of CADM2 expression, and impacted transcript usage. Decreased CADM2 expression was reflected in reduced exon usage downstream of the RS1 site and global alteration to genes involved in neuronal processes including synapse and axon development. Given the scale of our analyses and the widespread association of CADM2 with neurobehavioral traits, we sought to validate these findings using in vivo models and found that rodent models harboring Cadm2 RS1 deletions exhibited significant changes in relevant behaviors and functional brain connectivity. In summary, our analyses demonstrate a functional role for RS as a noncoding regulatory mechanism in a gene associated with a spectrum of neuropsychiatric and behavioral traits. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=140 SRC="FIGDIR/small/666599v1_ufig1.gif" ALT="Figure 1"> View larger version (44K): org.highwire.dtl.DTLVardef@171156borg.highwire.dtl.DTLVardef@13553baorg.highwire.dtl.DTLVardef@bee7forg.highwire.dtl.DTLVardef@156f19e_HPS_FORMAT_FIGEXP M_FIG Graphical Abstract C_FIG

genomics↗

Mediator Subunit MED16 Collaborates with UBP1-TFCP2 to Control Transcriptional Activation or Repression via Promoter Positional Specificity

The Mediator complex acts as a master transcriptional co-regulator, yet the mechanisms by which its individual subunits mediate gene-specific transcription remain incompletely defined. Here, we report that the Mediator subunit MED16 physically associates with the UBP1-TFCP2 heterodimer, which controls the context-dependent transcriptional activation or repression. Biochemical purification combined with mass spectrometry validated MED16 as a bona fide interactor of UBP1-TFCP2. Integrative transcriptomic analyses demonstrated that UBP1 recruits the Mediator complex through MED16 to activate a panel of silenced genes associated with lung homeostasis, angiogenesis and cell proliferation. By contrast, MED16-UBP1 co-occupancy at the HIV-1 transcription start site (TSS) represses viral transcription and sustains HIV latency by compromising pre-initiation complex assembly. Domain-mapping experiments revealed that MED16 must integrate into the intact Mediator complex to exert either activating or repressive function. Genomic analysis uncovered a positional regulatory logic: UBP1-TFCP2 binding motifs adjacent to the TSS promote transcription, while those overlapping the TSS elicit repression. Collectively, our work identifies an MED16-UBP1 regulatory module with dual transcriptional activity and highlights this signaling axis as a potential target for HIV-1 interventions.

biochemistry↗

A non-catalytic role for RFC in PCNA-mediated processive DNA synthesis

The ring-shaped sliding clamp PCNA enables DNA polymerases to perform processive DNA synthesis during replication and repair. The loading of PCNA onto DNA is catalyzed by the ATPase clamp loader RFC. Using a single-molecule platform to visualize the dynamic interplay between PCNA and RFC on DNA, we unexpectedly discovered that RFC continues to associate with PCNA after loading, contrary to the conventional view. Functionally, this clamp-loader/clamp complex is required for processive DNA synthesis by polymerase {delta} (Pol{delta}), as the PCNA-Pol{delta} assembly is inherently unstable. This architectural role of RFC is dependent on the BRCT domain of Rfc1, and mutation of its DNA-binding residues causes sensitivity to DNA damage in vivo. We further showed the FEN1 flap endonuclease can also stabilize the PCNA-Pol{delta} interaction and mediate robust synthesis. Overall, our work revealed that, beyond their canonical enzymatic functions, PCNA-binding proteins harbor non-catalytic functions essential for DNA replication and genome maintenance.

biophysics↗

Comparison and Dynamic interaction between Auditory Cortex and Prefrontal Cortex of Behaving Monkeys during Novelty Detection

The ability to detect deviations from expected sensory input is fundamental for adaptive behavior. We recorded electrocorticographic activity from the auditory (AC) and prefrontal (PFC) cortices of behaving macaques during an auditory oddball task to probe the cortical dynamics of predictive processing. Repetition of standard stimuli evoked suppression and facilitation in AC and strong low-frequency (2 Hz) enhancement in PFC, accompanied by bidirectional delta-band coupling indicative of a shared predictive state. Deviant stimuli triggered early AC responses followed by PFC activation and increased feedforward and feedback connectivity across delta, theta, and gamma bands. Behavioral engagement amplified both prediction and prediction error signals, strengthening cortical network coordination. Together, these findings reveal a hierarchical predictive network in which the AC encodes sensory regularities and violations, while the PFC integrates predictive context in a behaviorally dependent manner.

neuroscience↗

Walking Selectively Modulates Behaviorally Relevant Auditory Responses According to Stride Cycle Phase

Perception in natural environments unfolds while the body is in motion, yet how locomotion shapes cortical computations for fine-grained and dynamic scene analysis remains unclear. Here, we combined over-ground walking with mobile EEG and a transitional click-train paradigm to test how natural locomotion influences auditory processing in humans. Participants listened to two-segment click trains in which a subtle inter-click-interval (ICI) change signaled a pitch shift and performed a task-engaged change-detection task while either sitting or walking; an independent cohort also completed a passive-listening version. Walking elevated behavioral detection thresholds and slowed responses, indicating reduced sensitivity to fine temporal changes. Neurally, locomotion produced a response-component-specific attenuation: activity time-locked to the ICI transition--the change response previously linked to temporally integrative updating of an ongoing auditory object--was strongly reduced, whereas the offset response was largely preserved and onset responses were only modestly affected. Critically, this modulation persisted during passive listening and was selectively amplified near the perceptual threshold during task-engaged detection, revealing an interaction between motor state and cognitive demand. Thus, natural locomotion does not uniformly degrade hearing; instead, it preferentially down-weights a behaviorally critical, temporally demanding stage of auditory processing, offering a framework for understanding how motor-cognitive state shapes auditory scene analysis in the moving brain.

neuroscience↗

A molecular and spinal circuit basis for the functional segregation of itch and pain

Recent advances reveal an extensive cellular diversity within the dorsal horn. How this complexity processes distinct sensations, like itch and pain, remains a fundamental question. We discovered hidden within a population of neurons expressing the gastrin-releasing peptide receptor (Grpr+), thought to be itch-specific, are highly homologous yet functionally distinct subtypes distinguished by expression of Tachykinin-1 (Tac1). While the Tac1- subtype mediates itch, the Tac1+ subtype mediates mechanical allodynia across diverse pain states. Inhibitory populations and differential sensitivities to GRP serve as key modulators of the Grpr+ neuron subtypes, shaping modality specific output. Leveraging computationally designed genomic enhancers to silence the Tac1- population reverses itch while silencing the Tac1+ subtype reverses mechanical allodynia broadly. The work demonstrates the nuance of differential sensory modality coding within the dorsal horn and the power of genomic enhancer-based strategies for modality-specific targeting.

neuroscience↗

MViewEMA: Efficient Global Accuracy Estimation for Protein Complex Structural Models Using Multi-View Representation Learning

Estimation of model accuracy (EMA) is crucial for the reliable application of protein structure models in biological research. With the rapid advancement of protein structure prediction techniques and the explosive growth of predicted structural data, existing EMA methods struggle to balance computational efficiency with estimation performance. Here, we present MViewEMA, a single-model EMA method that leverages a multi-view representation learning framework to integrate residue-residue interaction features from micro-environment, meso-environment, and macro-environment levels for global accuracy assessment of protein complex models. Benchmark results demonstrate that MViewEMA outperforms state-of-the-art EMA methods in global accuracy assessment, achieving more than a 10-fold improvement in computational efficiency compared to our previous method, DeepUMQA3. This method enables efficient selection of high-quality protein complex models from large-scale structural datasets and achieved top performance in model selection tracks during the CASP16 blind test, demonstrating its potential to enhance the accuracy of complex structure prediction when integrated into modern frameworks such as AlphaFold-Multimer, AlphaFold3, and DiffDock-PP.

bioinformatics↗

Population-level super-pangenome reveals genome evolution and empowers precision breeding in watermelon

Pangenomes are increasingly critical for harnessing crop genetic diversity, yet their resolution and utility are often limited by insufficient sampling of high-quality genome assemblies. Here, we report a population-level watermelon super-pangenome constructed from 138 reference-grade assemblies, including 135 newly generated near-gapless genomes representing all seven watermelon species. The super-pangenome captures approximately one million structural variants (SVs), enabling accurate variant genotyping across ~900 watermelon accessions and substantially expanding variant discovery both across and within species. Broader sampling within the pangenome provides insights into genome evolution among watermelon species and sheds light on the origin of cultivated watermelon. SV-inclusive genome-wide association studies enhance trait mapping resolution and identify a copy number variation upstream of ClFCI1 that regulates flesh color intensity in a dosage-dependent manner. Leveraging this comprehensive variation map, we developed high-accuracy genomic prediction models for 18 agronomic traits. Together, our findings and genomic resources establish a foundational framework for dissecting complex traits and accelerating precision breeding in watermelon, while offering a valuable model for SV-resolved pangenomics in crop species.

plant biology↗

Graph pangenome reveals structural variation dynamics during cucumber breeding

Structural variants (SVs) represent a significant yet underexplored component of plant genome diversity. Analyzing SV dynamics is important for understanding their contributions to phenotypic variation and their influence on genome evolution. Here, we present a graph-based pangenome for cucumber, constructed from 39 reference-level genome assemblies. The pangenome captures 171,892 high-confidence SVs and enables genotyping of these SVs across 443 cucumber accessions, representing diverse geographic origins and spanning wild progenitors, landraces, and modern cultivars. Our analyses reveal that during cucumber domestication, a substantial portion of mildly deleterious SNPs are retained, whereas SVs are consistently purged, highlighting their potentially highly deleterious nature. During the geographic expansion of cucumber, a reduction in SV burden and a younger age of SVs than SNPs were observed, suggesting stronger purifying selection acting on SVs. Additionally, notable gene flow from wild population to African and European populations was detected, resulting in an increased SV burden, potentially due to hitchhiking effects. Importantly, incorporating SV burden into genomic prediction models improved the prediction accuracy for several agronomically important traits. This study illuminates the dynamics of SVs during cucumber domestication and improvement, highlights the complex interplay between SVs and selection pressures, and underscores the extensive implications of SVs for future cucumber breeding.

plant biology↗

An Unexpected Role of Molecular Chaperones in Regulating the Excited States and Activities of Folded Enzymes

Molecular chaperones are recognized for assisting protein folding. Emerging evidence suggests that chaperones also interact with natively folded proteins. Yet their functional impact on folded proteins remains unclear. Here, we show that chaperones can directly modulate the conformational dynamics and catalytic efficiency of enzymes in their native states. Spy and Hsp70 increased lysozyme activity by altering conformational exchanges, and this effect extended across other chaperones and enzymes. Hsp70, Spy, Hsp104, and Hsp20 enhanced the catalytic activities of multiple folded enzymes, including alkaline phosphatase, DNA polymerase Pfu, endonucleases Cas12a/Cas13a, and xylanase. These findings uncover an unanticipated function of chaperones in regulating enzyme function expanding their mechanistic scope beyond folding assistance and suggests opportunities in enzyme engineering, diagnostics, and cellular regulation.

molecular biology↗

Granulin+ macrophages promote lineage plasticity in prostate cancer through paracrine signaling loops

The role of tumor-infiltrating immune cells in driving phenotype switching remains unclear, despite the well-established association between lineage transition and drug resistance in prostate cancer. This study employed an integrated analysis of single-cell multiomics to investigate the dynamics of immune infiltration, transcriptional programs, and cell-cell communication in prostate cancer. Our results demonstrated that granulin (GRN) positive macrophages facilitated the transition from adenocarcinoma to a multilineage state with mesenchymal and stem-like traits by activating intra-tumoral NF-{kappa}B signaling. Subsequently, the multilineage clones induced macrophages to highly express granulin through the secretion of CSF1, forming a positive feedback cell communication loop. Next, we validated the biological function of granulin in mediating epithelial-mesenchymal transition in vitro. Additionally, organoids drug resistance assay demonstrated that granulin drove resistance to androgen receptor (AR)-targeted drug (enzalutamide). Moreover, pharmacologic blockade of the CSF-1/CSF-1R axis in TRAMP mouse models reduced the expression of GRN in macrophages and suppressed the formation of multilineage subclones in prostate malignant cells. Furthermore, multiplex immunofluorescence staining of tumor samples from TRAMP mouse models revealed the VIM lineages were spatially in close contact with macrophages. Meanwhile, Cytometry by Time-Of-Flight (CyTOF) analysis validated our findings at single-cell protein level in patients with castration-resistant prostate cancer. Besides, three distinct tumor-infiltrating subsets associated with disease relapse were identified, including DCN+ endothelial cells, CCL7+ fibroblasts, and IFIT1+ neutrophils. These results offer potential therapeutic targets to address lineage plasticity-driven resistance to AR-targeted therapy.

cancer biology↗

Biohybrid tendons enhance the power-to-weight ratio and modularity of muscle-powered robots

Biohybrid robots powered by tissue engineered skeletal muscle have historically relied on architectures in which muscle actuators are placed directly on skeletons, thus limiting the accessible design space for such machines. By contrast, native musculoskeletal architecture relies on tendons to bridge the interface between muscles and skeletons, enabling precise, space-efficient, and energy-efficient force transmission. In this study, we use a mathematical model of the muscle-tendon-skeleton interface to design a biohybrid muscle-tendon unit composed of tissue engineered muscle coupled to adhesive tough hydrogel tendons. We show how tuning tendon stiffness and pre-tension modulates actuator performance, measure fatigue characteristics of our actuators over >7000 cycles, and tune skeleton stiffness to increase force transmission muscles to skeletons by [~]29X. Furthermore, we demonstrate an [~]11X improvement in power-to-weight ratio of muscle-tendon units as compared to previous demonstrations of robots powered by muscles alone. This work validates a robust approach for designing, manufacturing, and deploying muscle-tendon actuators that promises to enhance the modularity and efficiency of biohybrid robots.

bioengineering↗

SMCHD1 compacts DNA directly in an ATP-regulated manner

Structural maintenance of chromosome (SMC) complexes play crucial roles in genome organization by DNA loop extrusion. SMCHD1 is a non-canonical SMC protein important for X-inactivation, imprinting and the silencing of specific autosomal genes. While it is known to be a repressor, little is known about its structure or mechanism of action. Here, we show that the SMCHD1 homodimer is flexible and dynamic in solution. This flexibility is conferred by its yet uncharacterized linker domain, which can alter its length by dynamically switching between compact and extended conformations. Interestingly, we observed that SMCHD1 can directly bridge and compact DNA, independently of other proteins, forming large protein-DNA clusters. SMCHD1 contains a GHKL ATPase domain and SMC hinge domain, however each domain alone is insufficient for DNA compaction. DNA compaction rate decreases when the linker domain is removed. The coiled-coil domain does not affect compaction rate but facilitates interaction with a partner protein LRIF1. Surprisingly, DNA compaction by SMCHD1 does not require ATP and paradoxically, compaction rate is reduced with the addition of ATP. Similarly, SMCHD1 forms clusters with reconstituted nucleosome arrays in the absence of ATP, and the addition of ATP results in a reduction in cluster sizes. Our data provides biophysical and mechanistic insights into the role of SMCHD1 in gene silencing and genome organization.

molecular biology↗

AAV-based temporal APOE4-to-APOE2 replacement reveals rebound adaptation and RAB24-mediated Aβ and cholesterol dysregulation

APOE-targeted gene therapy offers a promising strategy for modifying Alzheimers disease (AD) risk, yet the temporal dynamics and context-dependent effects of APOE isoform modulation remain poorly defined. Here, we developed a rapid AAV-based platform enabling inducible in vivo replacement of APOE4 with APOE2. In 5xFAD mice, sustained APOE4 expression exacerbated cognitive decline, A{beta} deposition (parenchymal and vascular), and glial activation, whereas long-term APOE2 expression--with concurrent APOE4 silencing--significantly reversed these pathological features and rescued cognitive function. In contrast, short-term APOE2 replacement conferred no benefit and unexpectedly worsened behavioral and pathological outcomes. Transcriptomic profiling revealed that APOE4-associated gene signatures were broadly reversed by long-term APOE2 expression, but paradoxically aggravated by short-term replacement. Among these, RAB24--a regulator of autophagic trafficking--was upregulated by APOE4 and short-term APOE2 but suppressed by long-term APOE2. RAB24 elevation impaired A{beta} clearance and cholesterol homeostasis via lysosomal retention in primary astrocytes and neurons. Together, these findings uncover a rebound-adaptation mechanism that shapes APOE2 therapeutic outcomes, identify RAB24 as a modifiable node in A{beta} and cholesterol metabolism, and establish a temporally controlled gene therapy platform to inform the design of future APOE-targeted interventions in AD.

neuroscience↗

Same-sex mounting in single-housed C57BL/6J female mice is not regulated by estrous state

Female-female mounting is widespread in mammals. Although the factors that regulate the display of female-female mounting likely vary according to species and to behavioral context, a large body of work has investigated the relationship of female-female mounting to female hormonal status. While this relationship has been well explored in ovariectomized and hormonally manipulated female rodents, less is known about the potential relationship between female-female mounting and estrous state in naturally cycling female rodents. Recent studies found that short-term social isolation robustly promotes same-sex mounting in C57BL/6J female mice. In the current study, we tested whether displays of female-female mounting by naturally cycling single-housed C57BL/6J females during interactions with naturally cycling, group-housed stimulus females depend on the estrous state of either female (n = 34 independent pairs). We found that the likelihood of mounting by single-housed females did not differ according to their estrous state. Moreover, single-housed females displayed mounting in trials that included receptive stimulus females, as well as in trials that included non-receptive stimulus females, and same-sex mounting was observed across all resident-stimulus female estrous state combinations. These findings indicate that same-sex mounting by single-housed C57BL/6J females is not coupled to the estrous state of either female in the pair. Future work remains to determine the factors that regulate the occurrence of female-female mounting in this species and behavioral context.

animal behavior and cognition↗