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Tang, L.

Publications and source records attributed to Tang, L..

At least 37 records · Page 2Linked to original sources

Age-related changes in the gut microbiota of a long-lived seabird suggest divergence from mammalian models

Gut microbiota plays key roles in shaping host development, immunity, and physiology. The assembly of vertebrate gut microbiota during early life follows relatively predictable trajectories across several mammalian species, largely driven by maternal transmission routes. However, birds lack these transmission mechanisms due to their oviparity, potentially leading to different age-related microbiota patterns. Here, we investigate gut microbiota variation in Atlantic puffin (Fratercula arctica) chicks and adults across six British populations using 16S rRNA amplicon sequencing. We find that chick microbiotas show strong population-level structuring that disappears in adults, with spatial patterns particularly pronounced in anaerobic bacteria. Puffin microbiotas become increasingly individualised and aerotolerant with age, while taxonomic richness remains stable - patterns that contrast with the convergent, richness-increasing trajectories observed in several mammalian species. Our results suggest that environmental exposure drives early-life microbiota assembly in birds, highlighting the value of avian systems for understanding vertebrate microbiota development beyond mammals.

ecology↗

A Potential Beta-hydroxybutyrate Therapy for Duchenne Muscular Dystrophy in Disease Models

Duchenne muscular dystrophy (DMD) is a common and lethal muscular degenerative disorder caused by mutations in the Dystrophin gene. Patients with DMD suffer progressive motor and respiratory decline over time and exhibit mitochondria defects at the cellular level, contributing to their reduced life expectancy. Despite extensive efforts, effective treatments for DMD remain unavailable. This study aims to explore a dietary approach to treat DMD, by precisely utilizing ketone bodies, an alternative fuel and signaling molecule for the mitochondria. As the experimental design, beta-hydroxybutyrate (BHB), the ketone body that is most abundant and stable in mammals, was supplemented in the drinking water of DMD disease model mice (mdx mice) as well as wild type mice. The results show that exogenous BHB supplementation in mdx mice led to significant decreases in plasma creatine kinase (CK) levels compared to chow-fed mdx mice, indicating mitigation of muscle damages. Functional tests also show that BHB improved muscle strength and endurance in mdx mice, while histological analyses revealed muscle health restoration, evidenced in uniform fiber diameter. BHB supplementation did not adversely affect the growth and overall health in either wild type or mdx mice. These findings may provide the proof-of-principle evidence for the use of BHB as a potential dietary approach for DMD treatment.

physiology↗

Bayesian inference of lineage trees by joint analysis of single-cell multimodal lineage-tracing data with BiLinT

The advent of single-cell lineage-tracing technologies has enabled simultaneous measurement of gene expression and lineage barcodes. However, integrating these modalities for high-resolution lineage reconstruction has remained challenging due to limitations of methods that analyze modalities separately. In response, we present BiLinT, a Bayesian framework for reconstructing high-resolution cell lineage trees by jointly modeling single-cell multimodal lineage-tracing data. BiLinT integrates lineage barcode evolution (modeled via a continuous-time Markov chain) and gene expression dynamics (modeled via an Ornstein-Uhlenbeck process) within a unified probabilistic model. Applications to synthetic and real datasets demonstrate improved accuracy and reveal developmental fate biases.

bioinformatics↗

Rational design of chemically responsive cytokines for cancer immunotherapy

Cytokines are key signal mediators of the immune system, playing essential roles in regulating central immunological processes. Despite their unique ability to modulate the immune system, the translation of cytokine-based therapies to the clinic has been significantly hindered by severe toxicities resulting from the pleiotropy and off-target effects of many cytokines. Here, we present a general strategy for the design of switchable cytokines that enables precise control over cytokine activity using the clinically approved drug, Venetoclax. We rationally designed self-inhibited Switchable InterLeukins (SwILs) by embedding the chemically controlled interface (Bcl-2: BIM-BH3) into the cytokines structure, resulting in conditional cytokines activated by Venetoclax. We showed the broad applicability of this strategy across various cytokines, including IL-2, IL-15, and IL-10. In vivo studies with IL-15 demonstrated that the SwILs achieved Venetoclax-dependent tumor control comparable to that of the native cytokine. Additionally, we showed that this strategy can be expanded to respond to other tumor-intrinsic stimuli, such as tumor-specific proteases. Overall, SwILs offer control of cytokine activity, enhancing the safety and clinical applicability of cytokine-based therapeutics.

bioengineering↗

Role of Speed Regulation and Speed Modulation in Velocity-Field Based Control

The velocity vector field (flow) controller is a well-established control strategy for lower limb exoskeletons. In this paper, we analyze this controller and propose modifications to improve its performance. We demonstrate that flow control acts as a variable proportional-derivative error regulator, where the parameter {Gamma} represents the desired norm of the hip-knee joint velocity vector (path speed). Based on this, we introduce two modifications to {Gamma}: (1) a constant {Gamma} set to the mean desired path speed, and (2) a variable {Gamma} that mimics natural path speed during unassisted walking. We compared the modified flow controllers with a slow-{Gamma} version in experiments involving seven participants walking on a treadmill at 0.6m/s, 0.8m/s, and 1.0m/s. Compared to the slow-{Gamma} controller, the RMS tracking error decreased by 30.7{+/-} 11.3% and the range of motion of the knee increased by 48.2 {+/-} 5.5% for the mean-{Gamma} controller, while the variable-{Gamma} controller had 32.4 {+/-} 14.7% smaller RMS error and 50.5 {+/-} 6.5% larger range of motion of the knee. Additionally, the slow-{Gamma} controller consistently applied resistive power, whereas participants reported more comfortable and natural gait with the modified controllers. We also compared them with the original tuning of flow controller, with results indicating superior performance from the proposed modifications. These findings demonstrate effectiveness across different walking speeds and offer a tuning strategy for future flow controller use.

bioengineering↗

An evolutionary leap in plant reproduction: From archegonia and motile sperm to embryo sacs and pollen tubes

The transition of plants from water to land marks a pivotal step in their evolutionary history, with the change in reproductive mode being the most fundamental. This change freed plant reproduction from aquatic dependence, fostering terrestrial lifes prosperity. Key to the shift from archegonial to embryo sac reproduction are pollen tube emergence and female gametophyte changes, though their evolutionary trajectories and mechanisms remain unclear. Ginkgo, a basal gymnosperm, occupies a pivotal position in this transition, retaining motile sperm, simplified archegonia, and primitive pollen tubes, making it an ideal model. To study how the transition between these two reproductive modes occurred, we collected transcriptome data from the reproductive organs of Ginkgo and evolutionarily representative species. Our findings reveal the MYB98-CRP-ECS module- critical for angiosperm pollen tube guidance--in Ginkgos mature archegonia, with pollen tubes containing guidance components. While egg cells are transcriptionally and functionally conserved across land plants, changes in the cell fate of other female gametophyte component cells drove the shift from archegonia to embryo sacs. Pollen tubes may originate from fern male gametophyte internalization and modification. These findings clarify the evolutionary path and molecular basis of this major reproductive transition.

plant biology↗

Humanized Caffeine-Inducible Systems for Controlling Cellular Functions

Current cell therapies are limited by the lack of tools for controlling gene expression using humanized systems responsive to non-toxic stimuli. Starting from nanobodies that homodimerize in response to caffeine, we computationally designed inducible heterodimers and humanized the best-performing pairs. We used the resulting caffeine-inducible domains in engineered cytokine receptors for caffeine-inducible STAT3 signaling and in split transcription factors (caff-TFs) containing human-derived zinc-finger proteins. Heterodimerization of split transcription factors drastically enhanced their performance compared to homodimerization. We demonstrate that caff-TFs are compatible with lentiviral and retroviral delivery to Jurkat T-cells and enable inducible expression of therapeutic genes such as chimeric antigen receptors (CARs) in response to caffeine concentrations consistent with normal coffee consumption. By using the common, non-toxic molecule caffeine, and exclusively humanized protein components, these systems promise to be a safer alternative to existing systems and may be used in synthetic biology applications and for safer, more effective cell therapies.

synthetic biology↗

Rational Design of Immunogenic Nanoparticles as a Platform for Enhanced Ovarian Cancer Immunotherapy in Mice

Ovarian cancer immunotherapy remains a challenge based on the "cold" tumor microenvironment. Herein we present a rational design to create immunogenic nanoparticles as a multi-agent platform that promotes immune response in a mouse model of ovarian cancer. The hybrid lipid-silica nanosystem is capable of co-loading four types of cargo molecules including a model antigen, nucleic acid-based adjuvant Cytosine-p-linked to Guanine (CpG, TLR3/9 agonist), lipid-based adjuvant (MPLA, TLR4 agonist) integrated into the lipid coat, and optionally a small molecule drug, such as the chemotherapeutic agent oxaliplatin, a well-established treatment for ovarian cancer. The optimization of the nanoplatform in terms of lipid composition, functionalized silica dendritic core formation, and final charge, as well as their compatibility with the complex loading profile highlights an opportunity for enhanced survival of mice with advanced ovarian cancer compared to monotherapy. Furthermore, intraperitoneal administration led to preferential accumulation within tumor-burdened tissues with selective accumulation in myeloid cells. High myeloid cell cytotoxicity negated the benefits of oxaliplatin. The inclusion of CpG in the nanoparticle formulation enhanced the survival of mice with ovarian cancer. To interpret these outcomes and guide future design, we also developed a mathematical model of nanoparticle-driven immune activation, which quantified treatment efficacy and identified key parameters governing tumor response. The presented hybrid nanoparticle i tunable, enabling delivery of alternative molecules therefore, thereby highlighting a promising platform for the treatment of peritoneal cancers. Graphical TOC O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=69 SRC="FIGDIR/small/657862v1_ufig1.gif" ALT="Figure 1000"> View larger version (26K): org.highwire.dtl.DTLVardef@1434599org.highwire.dtl.DTLVardef@18e79e6org.highwire.dtl.DTLVardef@e5285corg.highwire.dtl.DTLVardef@bcc604_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

Towards Unmanned Proteomics Data Generation: A Fully Automated Sample-to-Data System for Proteomic Experiments

The {pi}-HuB project requires proteomic measurements of millions of low-input samples that are challenging with current technology. Here, we introduce a pilot {pi}-HuB data factory that features a fully automated sample-to-data system to enable high-throughput digitization of human samples. Our platform, as a proof-of-concept towards unmanned proteomics, was demonstrated to show longitudinal robustness and applied for spatial proteomics and the profiling of plasma and cell lines, thereby serving as the workhorse to drive {pi}-HuB.

biochemistry↗

NanoLoop: A deep learning framework leveraging Nanopore sequencing for chromatin loop prediction

Chromatin loops play a crucial role in gene regulation and cellular function, providing key insights into understanding the three-dimensional structure of the genome and its impact on cellular homeostasis. Nanopore sequencing technology, with its advantages in simultaneously detecting sequences and methylation patterns, brings new opportunities for studying three-dimensional genome structures. We introduce NanoLoop, the first algorithmic framework attempting to predict genome-wide chromatin interactions using Nanopore data. In experiments across four human lymphoblastoid cell lines, NanoLoop demonstrated excellent predictive performance and cross-cell line generalization capabilities. We also discovered four distinct methylation patterns at loop anchors that influence histone modification levels and determine various loop types. NanoLoop further predicted previously uncharacterized long-range chromatin loops, highlighting DNA methylations role in three-dimensional genome regulation and providing new insights into the complex regulatory relationships between epigenetic modifications and three-dimensional genome organization.

bioinformatics↗

DNA Methylation in Sex Chromosomes and Genes under Selection Underpins the Emergence of Sexual Size Dimorphism

Sexual size dimorphism (SSD) refers to the differences in body size between males and females. Epigenetics such as methylation contribute to shaping phenotypes, nevertheless, their role in SSD is still unclear. Here, we used Cynoglossus semilaevis, a species with larger females known as female-biased SSD, as a model to investigate the role of methylation in the emergence and regulation of SSD. Methylomes and transcriptomes were constructed in four tissues (brain, liver, muscle, and gonad) from three key life stages: juveniles (3-months post fertilization), male mature stage (1-year post fertilization; ypf), and female mature stage (3 ypf). In 1 ypf and 3 ypf females showed lower methylation, while the number of differentially methylated regions between sexes increased during the lifetime. Genes at the top of the growth hormone/insulin-like growth factor (GH/IGF) axis and hypothalamus-pituitary-gonadal axis (gh1, igf1, gnrhr2r-like, err{gamma}, etc.) showed differential methylation between sexes, consistent with sex-related differences in growth. The female-specific W chromosome showed higher methylation than the autosomes or the Z chromosome. Genes of the IGF signaling network that negatively regulate growth and located on W chromosome were hyper-methylated than their Z homologs. Furthermore, genes with a faster evolutionary rate in C. semilaevis exhibited lower methylation levels than the background genes, suggesting an important evolutionary role for DNA methylation in shaping SSD. Our results provide a comprehensive depiction of methylation regulation of SSD in vertebrates, and improve our understanding of how methylation regulation can help organisms to respond to natural selection, and allocate resources between the sexes.

developmental biology↗

Loss of Kmt2c/d promotes gastric cancer initiation and confers vulnerability to mTORC1 inhibition and anti-PD1 immunotherapy

KMT2C and KMT2D (KMT2C/D) are frequently mutated in gastric adenocarcinoma, yet their function in cancer initiation remains poorly understood. In this study, based on the observation that loss-of-function mutations of KMT2C and KMT2D are enriched and co-occur in gastric adenocarcinoma, we developed genetically engineered mouse models to selectively knock out Kmt2c and Kmt2d in gastric epithelial cells with Tmprss2-CreERT2. Through histological staining and single-cell RNA sequencing, we observed that Kmt2c/d loss led to nuclear dysplasia and expansion of cells with mixed gastric lineage markers. When combined with Pten deletion, Kmt2c/d loss drove rapid development of muscle-invasive gastric adenocarcinoma as early as 3 weeks post Cre-mediated gene deletion. The adenocarcinoma exhibited decreased expression of gastric lineage markers and increased expression of intestinal differentiation markers, phenocopying human gastric adenocarcinoma. Kmt2c/d knockout reduced protein synthesis but upregulated transcription of ribosomal proteins, rendering sensitivity to mTORC1 inhibitors. Additionally, Kmt2c/d knockout increased MHC-I molecule expression and enhanced antigen presentation. Combination of mTROC1 inhibition and anti-PD1 immunotherapy significantly suppressed tumor growth in immune-competent mice. Together, these findings reveal the role of Kmt2c/d loss in gastric cancer initiation and suggest the potential therapeutic strategies for KMT2C/D-deficient gastric cancer.

cancer biology↗

Metabolic reinvigoration of NK cells by IL-21 enhances immunotherapy against MHC-I deficient solid tumors

Natural killer (NK) cells, a type of potent cytotoxic lymphocytes, are particularly promising for the treatment of cancers that lose or downregulate major histocompatibility complex class I (MHC-I) expression to evade T cell-mediated immunotherapy. However, the hostile and immune suppressive tumor microenvironment (TME) greatly hinders the function of tumor-infiltrating NK cells limiting the therapeutic efficacy against solid tumors. Here, we show that a fusion protein of interleukin-21 (IL-21-Fc), as a direct in vivo intervention, can safely and effectively reprogram NK cell metabolism and enhance their effector function in the TME. Our research demonstrates that combining IL-21-Fc with IL-15 superagonist (IL-15SA) or NK cell transfer leads to the eradication of MHC-I-deficient tumors and confers durable protection in syngeneic and xenograft tumor models. Mechanistically, we uncover that IL-21-Fc enhances NK cell effector function by upregulating glycolysis in a lactate dehydrogenase A (LDHA)-dependent manner. These findings not only underscore the considerable potential of IL-21-Fc as an in vivo therapeutic intervention to bolster NK cell-based immunotherapy, but also unveil an innovative strategy of metabolic reprogramming for NK cell rejuvenation within tumors. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=183 SRC="FIGDIR/small/643961v2_ufig1.gif" ALT="Figure 1"> View larger version (57K): org.highwire.dtl.DTLVardef@daf24forg.highwire.dtl.DTLVardef@5a5029org.highwire.dtl.DTLVardef@144c978org.highwire.dtl.DTLVardef@106ed1c_HPS_FORMAT_FIGEXP M_FIG C_FIG HIGHLIGHTSO_LINK cells display functional exhaustion in MHC-I deficient solid tumors C_LIO_LIIL-21-Fc as an in vivo-applicable and safe immunotherapy reinvigorates intratumoral NK cells for enhanced effector function C_LIO_LIIL-21-Fc enhances NK cell function by elevating glycolysis in a LDHA-dependent manner C_LIO_LICombining IL-21-Fc with low-dose IL-15SA or NK cell transfer eradicates syngeneic and xenografted solid tumors C_LI

cancer biology↗

Single-cell RNA-seq reveals altered plasma cell subsets and decreased cytotoxicity of NK cells in patients with Kawasaki diseas

AimThe pathogenesis and therapeutic strategies of Kawasaki disease (KD) are worth further exploring. Using single-cell RNA sequencing (scRNA-seq), our study aimed to explore the landscape of peripheral blood mononuclear cells (PBMCs) in patients with KD. MethodsWe analyzed the scRNA-seq data of three patients with KD and three healthy controls from the GSE168732 dataset. Additionally, we explored the immune profiles and immune cell subtypes of patients with KD. ResultsSignificantly increased B cells and decreased NK cells were observed in the KD group compared with that in the control group. Furthermore, six B cell subsets were identified in the PBMCs of patients with KD. Particularly, plasma cells (CD9+ and S100A9+ B cell clusters) distinctly increased in the KD group. CD9+ B cell cluster was characterized by vascular endothelial growth factor (VEGF) signaling-associated marker genes and DEGs. Meanwhile the S100A9+ B cell cluster was characterized by platelet aggregation marker genes. As for NK cells, CD16+CD56dim NK cells were enriched in the KD group. Cytotoxicity-related activating receptors (KLRD1,KLRC3) and cytotoxicity-associated genes (PRF1, NKG7, GZMA, GZMH, GNLY) were downregulated in the KD group. ConclusionCD9+ and S100A9+ plasma cells may contribute to CALs in KD by upregulating VEGF and activating platelet. In addition, decreased cytotoxicity of NK cells mediated by KLRD1/KLRC3 receptor may play a vital role in the development of KD. Our results suggested that plasma cells and NK cells could be promising targets for the treatment of KD.

immunology↗

Lower spatial turnover of rare fungal taxa dominantly shaped by stochastic processes in grassland soils

The spatial pattern and community assembly of soil microbial taxa have notable meanings for biodiversity shaping and maintaining mechanisms. Rare fungal taxa may exhibit distinct patterns and assembly mechanisms compared to abundant taxa, but such information is limited, especially at large scales. Here, we investigated distance-decay patterns and underlying assembly mechanisms for abundant and rare fungal taxa in 129 soil samples collected across 4,000 km in Chinese Northern grasslands, based on high-throughput sequencing data. A total of 208 abundant OTUs (relative abundance > 0.1%, 2.73% of entire OTUs) and 5,779 rare OTUs (relative abundance < 0.01%, 75.85% of entire OTUs) were identified. Both abundant and rare fungal taxa showed significant distance-decay relationships (P < 0.001), but the turnover rate for rare taxa (0.0024 per 100 km) was nearly half that of abundant taxa (0.0054 per 100 km) based on the binary Bray-Curtis distance. The lower turnover of rare fungal taxa was likely due to their community assembly mechanism dominated by stochastic processes, which were less influenced by environmental gradients. In contrast, abundant taxa assembly was dominated by deterministic factors like soil variables and plant traits, which varied significantly along the geographic distance. Consistently, rare fungal taxa were also less sensitive to environmental changes, with a lower turnover rate by environmental distance (0.0027 vs. 0.0099) than abundant taxa. In summary, our findings revealed that rare fungal taxa, shaped mainly by stochastic processes, had lower spatial turnover compared to abundant taxa, dominated by deterministic processes, enhancing our understanding of rare microbial biogeography.

ecology↗

Food pairing independently associated with cardiometabolic traits beyond dietary patterns across western and eastern populations

Cardiometabolic health is closely linked to diet. Both specific food choices and dietary indices are commonly used to guide cardiometabolic protection strategies. However, the balance between foods may also significantly impact cardiometabolic health. Here, we explore the balance and imbalance in long-term dietary food intake to quantify food pairing patterns (FPs), providing insights beyond conventional dietary indices and single-food intake frequencies. Using data from our GGMP (n = 6,994) and the NHANES (n = 7,350) cohorts, we observed that long-term food pairing patterns are independent of single food intake frequency and dietary indices. We identified 1,759 and 306 cardiometabolic-related long-term food pairing patterns from two cohorts (FDR < 0.05), respectively. Notably, around 80% of these pairing foods not individually associated with cardiometabolic traits, and food pairing pattern associations with cardiometabolic traits at hyper food group level were consistent across Eastern and Western populations. Besides, mediation analysis revealed that 72.7% of long-term food pairing patterns affected cardiometabolic traits through 31 microbial genera, with Clostridiumsensustricto1 playing a predominant role. Moreover, multi-step mediation analysis found that microbes mediated the impact of long-term food pairing patterns on cardiometabolic traits primarily through their metabolic pathways, such as pyruvate fermentation to propanoate and ergothioneine biosynthesis pathways. Our data suggest that balance between dietary foods is broadly associated with cardiometabolic traits by modulating gut microbial functionalities, in contrast to the lower occurrence when considering individual foods in isolation. These results offer a novel perspective for designing personalized dietary strategies beyond present dietary indices to enhance cardiometabolic health.

microbiology↗

The genetic diversity and populational specificity of the human gut virome at single nucleotide resolution

Large-scale characterization of gut viral genomes provides strain-resolved insights into host-microbe interactions. However, existing viral genomes are mainly derived from Western populations, limiting our understanding of global gut viral diversity and functional variations necessary for personalized medicine and addressing regional health disparities. Here, we introduce the Chinese Gut Viral Reference (CGVR) set, consisting of 120,568 viral genomes from 3,234 deeply sequenced fecal samples collected nationwide, covering 72,751 viral species-level clusters (VSCs), nearly 90% of which are absent from current databases. Analysis of single nucleotide variations (SNVs) in 233 globally prevalent VSCs revealed that 18.9% showed significant genetic stratification between Chinese and non-Chinese populations, potentially linked to bacterial infection susceptibility. The predicted bacterial hosts of population-stratified viruses exhibit distinct genetic components associated with health-related functions, including multidrug resistance. Additionally, viral strain diversity at the SNV level correlated with human phenotypic traits, such as age and gastrointestinal issues like constipation. Our analysis also indicates that the human gut bacteriome is specifically shaped by the virome, which mediates associations with human phenotypic traits. This foundational resource underscores the unique genetic makeup of the gut virome across populations and emphasizes the importance of recognizing gut viral genetic heterogeneity for deeper insights into regional health implications.

microbiology↗

Identification of Ephrin type-B receptor 4 as a critical mediator of tissue fibrosis

Pulmonary fibrosis (PF) is a pathology associated with interstitial lung diseases (ILDs), including idiopathic pulmonary fibrosis (IPF). Fibrosis promotes continual secretion of extracellular matrix (ECM), producing non-functional scar tissue and causing organ failure. This study investigated the tyrosine kinase receptor Ephrin type-B receptor 4 (EphB4) as a mediator of PF. To this end, we generated mice with conditional Col1a2-driven deletion of Ephb4 and used a preclinical mouse model of PF, total and single nuclei RNA (snRNA) sequencing, NanoString, previously published single cell data, computational analysis, and functional assays of mouse and human healthy control and IPF lung fibroblasts. Col1a2-CreERT-driven Ephb4 deletion, or EphB4 inhibition via NVP-BHG712, markedly protected against bleomycin-induced PF. Total RNA-sequencing of fibroblasts isolated from Ephb4-deficient fibrotic mouse lungs exhibited reduced expression of ECM, ER Cargo, and protein trafficking-related genes. NVP-BHG712 reduced expression of these identified genes in mouse lung fibroblasts under fibrotic conditions in vitro. SnRNA sequencing of mouse lungs treated with NVP-BHG712 identified transcriptomic changes of ECM genes in specific fibroblast subpopulations. RNA sequencing, computational, and functional assays using mouse and human IPF fibroblasts identified elastin as a key mediator involved in EphB4 signaling. Combined, our data show that EphB4 is a crucial mediator of PF.

pathology↗