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Yang, C.

Publications and source records attributed to Yang, C..

At least 55 records · Page 3Linked to original sources

Complete elucidation and heterologous reconstruction of the biosynthetic pathway of camptothecin

Camptothecin derivatives are first-line anticancer drugs used worldwide for the treatment of diverse malignant tumors. However, the biosynthetic pathway of camptothecin has remained elusive for five decades. Here, we fully map its entire biosynthetic route. We discovered five key missing enzymes (OpCAR, OpSDR11, OpCS, OpGH1, and OpSTR) via the combination of MALDI mass spectrometry imaging, single-cell RNA sequencing and co-expression analysis. Meanwhile, we demonstrated a free flavin mononucleotide triggered the non-enzymatic 6-5-6 to 6-6-5 fused-ring skeleton rearrangement, filling the last gap in camptothecin biosynthesis. Finally, we validated this identified pathway and achieved the de novo biosynthesis of camptothecin in Saccharomyces cerevisiae. These discoveries uncover the long-standing mystery underlying camptothecin and pave the way for manufacturing camptothecin and its derivatives through synthetic biology approaches.

synthetic biology↗

Development and Analytical Validation of a Smartphone-Based Quantitative Lateral Flow Immunoassay for Serum Cystatin-C

Cystatin-C is an important renal function biomarker, and conventional quantification requires centralized laboratory analyzers, which limits timely testing in primary care and resource-limited settings. To address this need, we developed and validated a simple, rapid, and quantitative smartphone-based (SP) lateral flow immunoassay (LFIA) for measuring serum Cystatin-C. The SP-LFIA platform consists of a colorimetric LFIA strip and a custom SP reader with uniform LED illumination and macro lens for image capture. Quantitative image analysis of the colorimetric signal is performed by a dedicated application using a pre-defined third order polynomial calibration model. Following systematic optimization, the assay demonstrated a wide quantitative range of 0.32-8.00 mg/L, with a limit of detection of 0.15 mg/L. Analytical validation conducted according to CLSI guidelines showed excellent precision, with intra- and inter-assay coefficients of variation below 10%, and no significant interference from bilirubin, triglycerides, hemoglobin, or rheumatoid factor. Accelerated stability testing confirmed robust strip performance after storage at 50 {degrees}C for 28 days. Method comparison using 100 clinical serum samples showed high agreement with a commercial PETIA reference method (R{superscript 2} = 0.993) and minimal bias. These results indicate that the developed smartphone-based LFIA provides a reliable, cost-effective, and practical tool for point-of-care Cystatin-C monitoring.

biochemistry↗

Aberrant chromatin looping by NUP98-HOXA9 is constrained by CTCF and facilitated by cohesin

The acute myeloid leukemia (AML) fusion protein NUP98-HOXA9 (NHA9) drives leukemogenesis by promoting aberrant chromatin loop formation through phase separation, yet the mechanisms underlying these interactions remain unclear. To address this, we dissect the interplay between NHA9 and individual loop extrusion factors using in situ Hi-C, CUT&RUN, RNA-seq, and Auxin-inducible degradation of CTCF or RAD21. CTCF was found to be dispensable for NHA9 loop formation, although CTCF binding constrained a subset of loops that emerged only upon CTCF depletion. In contrast, cohesin played a distance-dependent role where short-range NHA9 loops formed independently of RAD21, while long-range loops were strongly cohesin-dependent. Despite this requirement, RAD21 showed minimal enrichment at NHA9 loop anchors, indicating that NHA9 does not function as a canonical cohesin barrier. Instead, these findings support a non-canonical model in which cohesin transiently facilitates interactions between distal NHA9-bound loci, which are subsequently stabilized through NHA9 phase separation. Together, this work reveals a distinct mechanism of oncogenic chromatin looping in which NUP98-HOXA9 cooperates with canonical loop extrusion machinery to reprogram genome architecture in AML.

Molecular Biology↗

Buffered sweat microfluidics with AI-enabled translation for clinically actionable blood urea estimation and renal risk stratification

Kidney-function assessment relies on blood urea as a clinically informative metabolic marker; however, its dependence on venipuncture and centralised laboratory testing limits high-frequency monitoring and delays timely clinical intervention. Here, we report an integrated platform combining a wearable buffered microfluidic patch with a physiology-informed, data-driven calibration framework for real-time, non-invasive estimation of blood urea from microlitre-scale sweat volumes (4.79 L). By precisely regulating the release kinetics of internal buffer salts, the device stabilises the local reaction microenvironment, mitigating variability in sweat pH and flow to ensure reproducible measurement. The resulting signals are processed through an artificial intelligence (AI)-enabled analysis pipeline that integrates sweat urea with patient-specific physiological information to generate clinically interpretable outputs. In multicentre studies, sweat urea shows a strong association with blood urea across diverse cohorts, but with nonlinear and time-lagged relationships that limit direct use. The AI-enabled calibration model compensates for these effects, enabling high-fidelity estimation of blood urea (r = 0.945 versus gold-standard measurements) at clinically relevant concordance levels. The platform further identifies kidney injury with 89.1% accuracy and stratifies disease severity with 83.2% accuracy. Notably, these results demonstrate that the integration of physicochemical stabilisation and AI-enabled data-driven translation establishes sweat as a clinically actionable surrogate for renal monitoring, supporting population-level estimation and highlighting the potential for personalised longitudinal assessment, and enabling a scalable, non-invasive strategy for high-frequency kidney disease management.

biophysics↗

cuBayes: GPU accelerated FreeBayes that achieves 1-minute whole-genome SNV calling while maintaining algorithmic semantics

Next-generation sequencing now produces whole-genome data in hours, but downstream variant calling remains a multi-hour to multi-day bottleneck that excludes genomic analysis from time-critical clinical settings. GPU acceleration offers a natural path forward -- variant calling is inherently parallelizable across genomic positions -- yet open-source infrastructure for porting existing algorithms to GPU hardware remains limited, leaving many widely-used tools without accelerated implementations. FreeBayes, a haplotype-based variant caller central to the 1000 Genomes Project and to multi-sample tumor evolution analyses, exemplifies this gap: it is natively single-threaded despite its algorithmic suitability for parallelization. We present cuBayes, a CUDA implementation of FreeBayes germline SNV calling that completes HG002 and HG004 2x250bp Illumina 60x whole-genome analysis in one minute (as opposed to hours if not days with manual region-based CPU parallelization) on a single NVIDIA RTX 6000 Ada GPU, while producing variant calls with 99.97% concordance to the CPU reference. cuBayes is structured around an atom/molecule architecture in which reusable functional units (BAM decompression, position-wise pileup, batch coordination) are cleanly separated from algorithm-specific logic, providing a foundation intended to support acceleration of additional sequence analysis algorithms without redundant low-level engineering.

bioinformatics↗

Lineage Memory and Convergent Adaptation Dictate the Single-Cell and Spatial Architecture of Brain Malignancies

How diverse cancer lineages navigate the draconian central nervous system environment--whether constrained by ancestral ontogeny or driven by convergent adaptation--remains a fundamental biological paradox. To decode this, we integrated extensive in-house and public resources to construct the largest single-cell atlas of primary and secondary brain malignancies (>550,000 cells). We demonstrate that malignant cells balance strict lineage imprinting with shared brain-adaptive programs, powerfully converging upon a dominant pan-cancer mesenchymal (MES)-like state alongside a SYT1+ pioneer subpopulation exploiting neuronal mimicry. Concurrently, the microenvironment undergoes lineage-constrained divergence. The myeloid landscape shifts from a resident-dominated architecture in gliomas to extensive blood-borne infiltration in metastases. Lymphoid responses parallel this, crowning laryngocarcinoma as an ultra-hot subtype and revealing that massive T cell influx in highly infiltrated niches is paradoxically driven into terminal exhaustion, contrasting with severe immune exclusion in cold tumors. Furthermore, stromal-vascular adaptation couples pro-angiogenic tip-endothelial activation with a dynamic opposition between structural extracellular matrix (ECM) deposition and focal proteolytic degradation. Anchored by the pan-cancer MES adaptation, we leveraged subcellular spatial transcriptomics to redefine the microenvironment around four MES-like architectural niches, mapping an evolutionary trajectory from perivascular entry to immunosuppressive stromal remodeling. Finally, projecting these architectures onto independent clinical cohort establishes the MES-S2 proliferative niche as the primary driver of severe clinical deterioration across both transcriptomic and proteomic dimensions.

Cancer Biology↗

Combinatorial docking and molecular generation to navigate over 100-billion molecules for prospective ligand discovery

Commercially available make-on-demand libraries now exceed 100 billion compounds, requiring over 50 years to screen on 2,000 CPU cores using conventional docking. We present two complementary approaches to address this challenge. CombiDOCK, a combinatorial docking framework, enables exhaustive screening at the 100-billion scale within 40 days. MINT-Dock, a generative framework, accelerates navigation of this space by integrating CombiDOCK with Monte Carlo Tree Search. Benchmarked on 46 diverse targets, CombiDOCK matched full-molecule docking accuracy, and MINT-Dock achieved a 4,800-fold enrichment over random selection. Compared with prior billion-scale brute-force campaigns against {sigma}2, VMAT2, and VAChT, prospective CombiDOCK screens of the 100-billion-molecule library yielded higher hit rates and more potent ligands, while MINT-Dock achieved comparable outcomes across single- and multi-target objectives with >20-fold computational cost reductions. Docking-predicted poses of the best VAChT-binding compounds were confirmed by cryo-EM structures. These methods provide exhaustive and generative paths for navigating the trillion-molecule frontier of drug discovery.

bioinformatics↗

Distinguishing Photoacoustic and Photothermal Neuron Stimulation Through Quantitative Mapping Spatiotemporal Field Evolution

Neuromodulation is a rapidly advancing strategy for modulating brain function and treating neurological disorders, yet the mechanisms of optical neural stimulation remain incompletely understood. A central challenge is that photoacoustic (PA) and photothermal (PT) effects are typically generated simultaneously and evolve on overlapping spatial and temporal scales, making their contributions to neuronal activation difficult to distinguish. Here, we overcome this limitation by integrating two carbon-based emitters with a spatial-offset pump-probe imaging platform to distinguish PA and PT neuromodulation through direct mapping of spatiotemporal field evolution. The two emitters produce nearly identical thermal fields while exhibiting a 26-fold difference in acoustic output, enabling decoupled comparison of thermal and acoustic contributions. To directly characterize the physical fields, we establish a spatial-offset pump-probe imaging system capable of visualizing both temperature and pressure evolution, confirming matched thermal profiles between the two emitters. Neuronal stimulation experiments further show that neurons are markedly more responsive to PA stimulation than to PT stimulation. Beyond resolving a longstanding mechanistic question, this work demonstrates the enhanced efficiency of PA stimulation and provides general guidance for designing high-performance optical neural interfaces.

neuroscience↗

Linezolid Acts as a Selective Inhibitor of the JAK2V617F Mutation

The JAK2V617F (JAK2VF) driver mutation is found in 95% of patients with polycythemia vera (PV), a progressive myeloproliferative neoplasm. Current treatments suppress excessive hematopoiesis but lack specificity for targeting JAK2VF cells, are unable to deplete mutant stem/progenitor cells and ultimately result in drug resistance. We discovered that the FDA-approved antibiotic, linezolid (LZD), ameliorates the PV phenotype across multiple model systems. LZD suppressed cell proliferation and STAT5 signaling, altered the cell cycle, and increased apoptosis of JAK2VF-harboring human erythroleukemia cells, but not in wild-type acute leukemia cells. Computational modelling indicated that LZD interacts specifically with mutant JAK2VF but not with wild-type JAK2 protein. We further showed that, in JAK2VF mice that faithfully recapitulate human PV, LZD mitigates disease burden by selectively targeting JAK2VF stem cells thereby normalizing spleen size and blood counts. LZD also inhibited hematopoietic colony formation by patient-derived peripheral blood mononuclear cells, with the more primitive progenitors being preferred targets. Importantly, LZD selectively decreased JAK2VF+ colony numbers, without impacting wild-type JAK2 colonies. In all, the data provide a firm foundation for evaluating LZD-like molecules as an effective therapy for PV and other myeloproliferative neoplasms. Key pointsO_LILinezolid acts as a JAK2V617FIZselective inhibitor in PV mouse models and PV patient samples while sparing wildIZtype hematopoiesis. C_LIO_LILinezolid acts directly on JAK2V617F hematopoietic stem cells. C_LI

cancer biology↗

Combinatorial screening of nanoparticles for nose-to-brain RNA delivery to modulate neuroinflammation after traumatic brain injury

Traumatic brain injury (TBI)-induced neuroinflammation can evolve over weeks or months, contributing to ongoing secondary damage and worsening neurological recovery. RNA-based therapeutics hold great potential to regulate inflammatory signaling, but delivery to the brain remains challenging because of the blood brain barrier. Intranasal administration offers a direct non-invasive route for brain access but is often limited by low delivery efficiency. Here we constructed a combinatorial library of DNA-barcoded 103 lipid nanoparticles by varying lipid components with diverse headgroup chemistries and bioreactive moieties. A high throughput screening of these nanoparticles in vivo following intranasal administration led to the identification of top candidates with highest brain accumulation. Intranasal delivery of an antagomir targeting microRNA-9-5p loaded nanoparticle effectively reduced cerebral microRNA-9-5p levels, suppressed inflammatory markers, and improved neurological outcomes in TBI. These results demonstrate a systematic approach for optimizing intranasal lipid nanoparticle design and support the feasibility of RNA delivery to modulate neuroinflammation after brain injury.

bioengineering↗

An oncolytic adenovirus armed with anticancer prodrug-activating enzyme offers enhanced tumor killing and antitumor immunity.

Oncolytic viruses are most commonly administered via intratumoral injection; however, their clinical efficacy in achieving tumor eradication remains limited by several challenges, including insufficient penetration into all tumor cells and the inability to elicit robust systemic antitumor immune responses capable of eliminating metastatic microtumors. Here, we report an oncolytic adenovirus, OAd-2B6, with an engineered adenoviral E1 region for tumor selectivity and carrying the prodrug- activating enzyme cytochrome P450 2B6 (CYP2B6) to activate the anticancer prodrug cyclophosphamide (Cytoxan, CTX). OAd-2B6 alone induced dose-dependent tumor cell killing across multiple human tumor cell lines and exhibited strong synergistic antitumor effects when combined with CTX. Importantly, OAd-2B6-mediated local activation of CTX resulted in a potent bystander killing effect that eliminated tumor cells not directly infected by the virus. In a H1299 lung cancer xenograft nude mouse model, intratumoral injection of OAd-2B6 combined with CTX significantly inhibited tumor growth and even achieved complete tumor regression, with markedly superior efficacy compared with monotherapy. In immunocompetent mice bearing 4T1 breast cancer xenografts, OAd-2B6 alone inhibited tumor growth and was accompanied by upregulation of IFN-{gamma} and GzmB expression in the tumor-infiltrated T cells. CTX combination therapy further enhances this anti-tumor immune response, promoting the activation of T cells to suppress non-injected tumors at a distal site. Collectively, this study demonstrates that OAd-2B6 exerts potent antitumor effects through multiple mechanisms, including direct oncolysis, intratumoral prodrug activation leading to bystander killing, and enhancement of systemic antitumor immunity. These findings provide a promising strategy for improving the therapeutic efficacy of oncolytic therapy.

cancer biology↗

STAT: A multi-agent framework for integrated and interactive spatial transcriptomics analysis

Spatial transcriptomics analysis often involves a myriad of computational methods across diverse platforms, leading analysts to spend excessive time on data assembly rather than deriving biological insights. Current AI solutions tend to either oversimplify spatial data into generic single-cell tables or operate autonomously without opportunities for intermediate review, thus hindering the visual and iterative analyses essential for spatial biology. In response to these challenges, we introduce STAT, a multi-agent framework designed to make spatial analysis more conversational and user-friendly while maintaining transparency and control. STAT integrates a persistent session, a shared interactive tissue viewer, and a staged skill-aware pipeline, enabling a more intuitive analytical experience. In a comprehensive benchmark evaluation encompassing eleven analytical task categories across three spatial platforms and both cell- and spot-resolution data, STAT demonstrates superior performance compared to a vanilla large language model and existing autonomous spatial analysis agents, excelling in task completion, analytical quality, and token efficiency. Notably, STAT enables multi-task spatial analysis of a mixed-resolution breast cancer cohort and successfully reproduces key findings from a published Visium HD colorectal cancer study using natural language prompts alone. STAT thus facilitates trustworthy and scientifically rigorous spatial transcriptomics analysis, allowing researchers to focus more on biological interpretation.

bioinformatics↗

Coordinated phase separation and phase transition underlie synaptic ribbon condensate formation and plasticity

Mesoscale molecular apparatuses with diverse functions are widespread in cells. How mesoscale cellular apparatuses are formed and regulated is poorly understood. The synaptic ribbon in sensory neurons, which can dynamically adjust its size and shape in response to light or sound, is a mesoscale molecular assembly. In this study, we demonstrate that RIBEYE, the backbone protein of synaptic ribbons, via combined ordered and disordered interactions, forms micron-sized dynamic molecular assemblies. Integrated cryo-electron microscopy and tomography studies revealed that the N-terminal SAM domain and the C-terminal B domain of RIBEYE form distinct nanoscale filaments and further assemble into ribbon-like architectures via phase transition. Unexpectedly, the N-terminal intrinsically disordered region of RIBEYE softens the solid mesoscale ribbon structures via phase separation. The mesoscale size and shape of the RIBEYE condensate are bidirectionally tuned by physiological modulators such as Piccolino and CtBP1, linking synaptic ribbon structural plasticity to functional adaptability. Thus, our study demonstrates that combined phase transition and phase separation of nanoscale protein oligomers can build mesoscale functional cellular apparatuses.

biochemistry↗

Controlled linking of AAV capsids enables coordinated multi-vector delivery

Adeno-associated virus (AAV)-based delivery of large genetic systems splits cargo across vectors, but functional reconstitution depends on stochastic co-delivery and often requires high viral doses. Here, we present a multi-capsid linking strategy that enables coordinated delivery of AAV vectors carrying distinct or split genetic cargos. Using a substrate-confined linking process, we suppress uncontrolled higher-order aggregation while enabling programmable nanoscale capsid coupling via oligonucleotide linkers. These linkers further enable efficient downstream purification of linked AAVs and recycling of unlinked vectors, yielding [~]70% AAV dimers and trimers in <24 hours. By enforcing coordinated delivery, linked AAVs achieve co-transduction at reduced viral doses and with greater expression uniformity than conventional dual-AAV approaches. This improved coordination enhances reconstitution of split genetic systems and increases targeted prime editing efficiency in vitro and in the mouse brain. This capsid coupling strategy expands the functional scope of AAVs toward dose-efficient and uniform delivery of large genetic systems.

bioengineering↗

Ramping-up hippocampal ripples and their neocortical coupling support human visual short-term memory

Emerging evidence suggests that the hippocampus contributes to visual short-term memory (VSTM). However, the neural mechanisms through which hippocampal activity supports the maintenance of VSTM representations remain largely unknown. Here, using intracranial EEG recordings from human participants performing a delayed match-to-sample task for naturalistic objects, we investigated the role of hippocampal ripple activity--brief high-frequency oscillations associated with memory replay--in VSTM maintenance and hippocampal-neocortical communication. We found that hippocampal ripple rates progressively ramped up during the maintenance period and supported successful VSTM. More critically, hippocampal ripples were temporally coupled with the ripples in the lateral temporal lobe (LTL), and these coupled ripples were associated with memory reactivation in the LTL. These findings provide direct evidence that hippocampal-neocortical interaction via coupled ripples supports VSTM, extending the role of hippocampal ripples from long-term consolidation to short-term mnemonic processes and offering new insights into the dynamic coding mechanisms of working memory. Impact StatementHippocampal ripple ramping-up and neocortical coupling support a dynamic coding mechanism for visual short-term memory maintenance

neuroscience↗

Mitochondrion-IMC contact sites are critical for cofactor biosynthesis and egress signaling in Toxoplasma gondii

Toxoplasma gondii is a single-celled parasite belonging to the Apicomplexa phylum. Toxoplasmas single mitochondrion is highly dynamic, changing its morphology as the parasite undergoes egress and invasion. Recently, we have demonstrated that mitochondrial morphology is driven by a protein named Lasso Maintenance Factor 1 (LMF1). This protein interacts with IMC10, a protein present at the parasites inner membrane complex (IMC), mediating a unique membrane contact site between the IMC and mitochondrion. Interestingly, parasites lacking either LMF1 or IMC10 have abnormal mitochondrial morphology, cell division defects, and delayed propagation in tissue culture. Although both components of the tether were identified, the functions of this contact site remain unknown. In this work, we show that {Delta}lmf1 parasites exhibit upregulation of egress signaling and downregulation in folate metabolism and pantothenate biosynthesis. {Delta}lmf1 parasites exhibit increased intracellular calcium levels, leading to greater sensitivity to ionophore-induced egress and microneme secretion. We have confirmed that parasites have decreased levels of tetrahydrofolate and coenzyme A, showing a limitation in cofactor production. Interestingly, the {Delta}lmf1 parasites prefer glutamine instead of glucose as a catabolic substrate. Accordingly, we demonstrate for the first time that proper mitochondrial positioning is crucial for folate and Coenzyme A metabolism as well as egress signaling. IMPORTANCEToxoplasma gondii is the causative agent of Toxoplasmosis, a disease that affects a third of the worlds population. This parasite has a single, highly dynamic mitochondrion. The parasites mitochondrion changes shape depending on environmental conditions (inside or outside the host cell) or on stressors, such as drugs. Our laboratory characterized the proteins involved in regulating mitochondrial dynamics in the parasite, but the functional importance of these mitochondrial changes has not yet been described. Here, we show that the shape of Toxoplasmas mitochondrion is important for the synthesis of key cofactors, such as folates and coenzyme A. We show that mitochondrial shape in this parasite is important for signaling the parasites exit from the host cell, a critical process in its life cycle. These findings review a previously unknown function of a parasite-specific organelle contact site, providing new insights into the importance of mitochondria for these parasites.

microbiology↗

Intercellular communication is a heritable dimension of human tissue architecture

Methods that map genetic risk to cells do not directly test whether spatially organized ligand-receptor (LR) gene annotations carry conditional heritability association. Here we introduce EdgeMap, which scores each gene by the spatial activity of its LR contexts in spatial transcriptomics data, maps these scores alongside cell-intrinsic annotations to SNP-level LD scores, and tests both jointly against GWAS summary statistics. Across 17 traits and five human tissues, edge z-scores are systematically higher in biologically matched tissues: all 15 traits with both matched and unmatched tissue classes show this ordering (median{Delta} z = 1.51; sign P = 3.1 x 10-5), and 11 of 13 nominal-positive associations concentrate in the biologically matched set (P = 1 x 10-4). The pattern survives broad LR-gene-class and cell-type composition controls. Donor-level cross-section summaries, independent GWAS replication for LDL and CAD, and cell-segmented Visium HD liver data provide convergent support. A secondary analysis prioritizes constituent genes within active LR contexts; sixteen of 31 prioritized genes are absent from standard gene-level methods. These results establish spatially weighted LR-gene annotations as a complementary layer for interpreting complex-trait genetic architecture.

genetics↗

Evaluating codon optimization strategies for mammalian glycoprotein production with an open-source expression vector

Efficient production of human proteins for the development of tool compounds and biologics depends on a detailed understanding of the protein expression machinery in mammalian cells. Codon optimization is widely believed to enhance protein yield, yet its impact in homologous mammalian systems remains poorly defined. Here, we systematically compare five codon usage strategies reflecting common assumptions about rare codons, RNA stability, and synthesis efficiency. We developed pTipi, an efficient open-source mammalian expression vector, and evaluated its performance in antibody production. We generated plasmids for common epitope tag antibodies such as V5, anti-biotin and anti-His for distribution by Addgene. To compare codon usage schemes, we performed a bake-off of 18 human and murine Wnt pathway glycoproteins in mammalian cells. Small-scale expression screens revealed that codon optimization did not provide a general advantage over native coding sequences, while strategies prioritizing RNA stability consistently reduced expression. Interestingly, a skewed codon scheme using the most abundant codons produced yields comparable to native sequences and occasionally enhanced protein output. To enable flexible evaluation of codon strategies, we implemented a Golden Gate-compatible pTipi platform for efficient synthetic gene incorporation. We conclude that native codons are sufficient for robust homologous mammalian expression of glycoproteins, while selective codon skewing can be beneficial for some targets.

molecular biology↗