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Biology subjects

Ding, G.

Publications and source records attributed to Ding, G..

At least 19 recordsLinked to original sources

Brain State Dynamics and Developmental Differences in Reading Comprehension

Reading comprehension is a complex cognitive task that involves dynamic interactions between the brain and external information. Previous studies on reading development primarily focused on localized or static brain activities. However, it remains an enigma how brain state dynamics evolve with development underlying reading comprehension. This study aims to address this issue by combining functional magnetic resonance imaging (fMRI) with Hidden Markov Model (HMM) to explore brain state dynamics. A total of 35 typically developing children and 31 adults were scanned while reading a story. Our results demonstrated a tripartite brain state organization, characterized respectively by high activities in the visual (State #1), language (State #2), and default mode network (DMN, State #3) regions. Children exhibited significantly longer dwell time in the DMN state (State #3) compared to adults, along with a higher probability of transitioning from the language state (State #2) to the DMN state (State #3). In addition, adults exhibited greater flexibility in state transitions during reading comprehension. Finally, the alignment between the dynamic states of children and the average states of adults was a significant positive predictor of their reading comprehension performance. This study provides a novel, intuitive perspective on how brain state dynamics evolve during the development of reading comprehension.

neuroscience↗

Hidden genetic diversity in 320 nearly-complete East Asian genome assemblies

East Asian populations, representing over 20% of the global population, remain critically underrepresented in human genomic studies, limiting our understanding of population-stratified genetic variation and its implications for health and disease. Here we present the first phase of the Asian Pan-Genome project (APG), comprising 320 nearly complete, fully phased haploid genome assemblies from 160 East Asian individuals. These assemblies achieve unprecedented quality, with an average contig N50 of 144.3 megabase pairs and an average quality value of 64.5. Leveraging these superior assemblies, we reveal previously uncharacterized diversity in human repeatome, including population-stratified patterns in centromere satellites and rDNA arrays. Compared to existing global human genome assemblies, the newly generated genomes supplement 152 million base pairs of novel sequences, 355 gene gains, 18,300 structural variation loci and 26 large euchromatic inversions missing from current human pangenomes. We perform population stratification analyses of structural variations, and further resolve the structural haplotypes of complex genomic regions such as Major Histocompatibility Complex and Survival Motor Neuron loci across global pangenomes, exemplifying tandem-duplicate and inversion-rich complex locus architectures in the human genome, respectively. This resource provides a critical foundation for human genetic studies, especially for East Asian populations, promoting more accurate variant discovery, reducing bias, and ultimately advancing the equity and efficacy of genomic medicine.

genomics↗

Learning to read a second language establishes a parallel L2 representation alongside the native one in the VWFA

Learning to read a second language requires the brain to incorporate a new writing system into an already established native-language reading network, yet how this process reshapes the Visual Word Form Area (VWFA) remains poorly understood. Using fMRI with a passive viewing paradigm, we systematically investigated how VWFA responses to Chinese (L1) and English (L2) words evolved across three groups of native Mandarin-speaking children at distinct stages of L2 literacy acquisition: L2 pre-readers, L2 beginning readers, and L2 advanced readers. We combined univariate activation analyses, representational similarity analysis, and supervised machine learning classification to investigate two theoretical accounts of VWFA reorganization: the Overlay Model, which predicts stable L1 responses as L2 responses emerge, and the Competing Model, which predicts competitive reallocation of neural resources from L1 to L2. We found that although the VWFA already exhibited robust selective responses to L1 words, L2-word selectivity was absent in L2 pre-readers but emerged robustly in beginning readers, with L1-word selectivity remaining stable throughout. Representational similarity analysis further revealed that robust L2 word representations within the VWFA emerged only after children began learning to read L2, while L1 word representations remained stable across all three groups. Finally, supervised machine learning analyses successfully discriminated among the three L2 literacy groups on the basis of L2 but not L1 activation patterns, indicating that VWFA responses to L2 alone were sufficient to capture childrens stages of L2 literacy acquisition, whereas responses to L1 were insensitive to L2 learning experience, providing no support for the Competing Models prediction of competitive neural reallocation away from L1. Together, these findings support the Overlay Model, demonstrating that the VWFA incorporates a new writing system within its existing cortical resources without compromising L1 print processing.

neuroscience↗

SPEND-hSRS imaging of fumarate uncovers mitochondrial metabolic heterogeneity

Mitochondria, acting as the energy powerhouse, biosynthetic center, and reductive equivalent hub of the cell, participate in cellular metabolic activities. However directly imaging mitochondrial chemical content and quantifying metabolic activity in living cells remain challenging. Here, by Self-PErmutation Noise2noise Denoiser enhanced Hyperspectral Stimulated Raman Scattering (SPEND-hSRS) microscopy, we demonstrate fingerprint-region metabolic imaging of fumarate, a key intermediate in the tricarboxylic acid (TCA) cycle, with sub-millimolar sensitivity. In chemotherapy-stressed bladder cancer cells, fumarate imaging revealed two mitochondrial subpopulations with divergent TCA metabolic preferences quantified by ratio metric analysis. Pixel-wise least absolute shrinkage and selection operator (LASSO) spectral unmixing further reconstructs fumarate and lipid maps, uncovering localized fumarate enrichment in protrusions. Extending to CH-window hyperspectral SRS imaging, we uncover the interplay between mitochondria and lipid droplets (LDs) in protrusions, where fatty acid is found to be released from LDs, to fuel the TCA cycle. Together, our work establishes SPEND-hSRS as high-resolution platform for linking fumarate to mitochondrial heterogeneity. Our results provide new insights into how mitochondrial heterogeneity and interaction with LDs drive cancer cell adaptation to stress.

cancer biology↗

Characterization of programmed cell death pathways activated in Mycobacterium tuberculosis-infected human macrophages

Mycobacterium tuberculosis (Mtb) primarily infects human lung macrophages, which serve as its major replication niche. Mtb can manipulate host macrophage cell death pathways to its advantage by inhibiting apoptosis and inducing necrotic cell death. However, the specific necrotic cell death pathway activated in human macrophages after Mtb infection remains unclear. Here, we used the THP-1 cell line and primary human monocyte-derived macrophage (hMDM) to analyze multiple programmed cell death pathways during days 1-3 after Mtb infection. Confocal microscopic analysis demonstrates that Mtb-infected THP-1 cells or hMDMs rarely exhibited apoptosis. Immunoblotting shows that Mtb induces significant CASP3 and GSDME activation in THP-1 cells, but not in hMDMs. We show that Mtb, in THP-1 cells but not hMDM, induces a significant increase in GSDMD cleavage, a hallmark of pyroptosis. MLKL phosphorylation was not observed in THP-1 cells or hMDMs during Mtb infections, indicating an absence of necroptosis. No changes in ferroptosis markers such as GPX4 expression or lipid peroxidation levels were detected. Time-lapse live-cell imaging revealed no lysosomal membrane permeabilization prior to plasma membrane rupture (PMR). However, we observed DNA release from Mtb-infected THP-1 cells and hMDMs after PMR. The DNA released from THP-1 cells exhibits low levels of myeloperoxidase and histone H3 citrullination. High-resolution confocal imaging shows that Mtb is associated with the released DNA. We demonstrate that pyroptosis induction in THP-1 cells is dispensable for the DNA release and cell death induction. In conclusion, our results reveal that Mtb-triggered cell death in hMDMs bypasses canonical cell death pathways like apoptosis, pyroptosis, necroptosis, and ferroptosis. Instead, cell death in both THP-1 cells and hMDMs correlates with DNA release, potentially through a pathway similar to NETosis in neutrophils.

cell biology↗

lncRNAs contribute to caste differentiation as a regulatory layer in ants

Caste differentiation in ants represents one of the major evolutionary transitions and provides a unique model for studying developmental mechanisms underlying division of labor. Genetically identical individuals follow divergent epigenetically-regulated developmental trajectories that give rise to morphologically distinct phenotypes and specialized roles. While long non-coding RNAs (lncRNAs) are emerging as key epigenetic regulators across diverse biological systems, their specific contributions to caste development in social insects remain largely unexplored. Here, we conducted comprehensive transcriptomic analyses across major developmental stages of two evolutionarily and ecologically distinct ants Monomorium pharaonis and Acromyrmex echinatior, identifying over 10,000 lncRNAs. We demonstrated that lncRNAs exhibit dynamic, caste-specific expression patterns throughout development. We also identified a subset of lncRNAs displaying canalized expression patterns, characterized by progressively increasing caste bias and decreasing within-caste variation as development proceeds. Co-expression analyses revealed that canalized lncRNAs are functionally linked to canalized protein-coding genes, which are crucial regulators for caste differentiation. These canalized lncRNAs show striking tissue-specific enrichment consistent with canalized protein-coding genes. Functional validation through RNA interference revealed that canalized lncRNAs directly regulate caste-specific traits. Furthermore, juvenile hormone treatment capable of redirecting worker lncRNA expression profiles toward gyne-like patterns, with similar expression changes and tissue specificity to JH-responsive protein-coding genes, linking lncRNA regulation to established hormonal pathways controlling caste fate. Our findings establish lncRNAs as active architects of caste differentiation in social insects, demonstrating that these rapidly-evolving regulatory molecules contribute to the evolution and maintenance of social phenotypes through tissue-specific regulation of caste-associated developmental programs.

developmental biology↗

Cholesterol metabolism modulation facilitates CAR-T induced killing of ovarian cancer

Ovarian cancer is one of the most lethal gynecological cancers worldwide and has one of the highest recurrence rates. Recently developed Chimeric Antigen Receptor T (CAR-T) cell therapy has shown potent clinical efficacy against hematological malignancies. However, solid tumors, including ovarian cancer, possess several mechanisms that hinder T cell activity, and metabolic alteration of cancer cells has been shown to contribute to resistance to immune cell attack against solid tumors. Here, we explored the metabolic response of ovarian cancer cells to CAR-T cell attack using label-free high-content hyperspectral stimulated Raman scattering (h2SRS) imaging. Utilizing visible h2SRS imaging with much improved spatial resolution, we found an altered cholesterol metabolism, featured by increased storage of cholesteryl ester in lipid droplets and free cholesterol, in ovarian cancer cells that survived the CAR-T treatment. Administration of Avasimibe, an inhibitor of cholesteryl esterification, further enhanced CAR-T cytotoxicity. Our study shows the promise of implementing metabolic modulation to facilitate CAR-T cell treatment of solid tumors. Significance StatementOvarian cancer is a major global health challenge, mainly due to relapse driven by chemotherapy resistance development. Meanwhile, immunotherapies such as CAR-T have revolutionized treatment for blood cancers, but their application in solid tumors like ovarian cancer is hindered by limited efficacy. This study uses high-content stimulated Raman scattering (SRS) imaging to reveal metabolic adaptations that help ovarian cancer cells survive CAR-T-mediated cytotoxicity. Guided by these insights, we apply metabolic interventions that enhance CAR-T cytotoxicity efficacy. This approach reveals therapeutic vulnerabilities in ovarian cancer and demonstrates an investigative strategy applicable for overcoming resistance in solid tumors.

cell biology↗

Prenatal liver is resistant to low glucose-induced inhibition of mTORC1

Prenatal development may adopt unique patterns of metabolic responses to different nutrient supplies. AMPK and mTOR are two central metabolic regulators, with AMPK acting to slow down and mTOR to promote anabolism. Typically, low glucose inhibits TRPVs, leading to AMPK activation and mTOR complex I (mTORC1) inhibition. Here, we observed surprisingly that mTORC1 in the foetal liver remains active in low glucose, although AMPK is effectively activated in an AMP-dependent manner. Mechanistically, we found that TRPV4, a key liver TRPV, is acetylated at K608, disabling its inactivation by fructose-1,6-bisphosphate (FBP)-unoccupied aldolase. Mutation of K608 to arginine renders TRPV4 able to respond to low glucose in foetal hepatocytes. Consistently, embryonic liver-specific expression of acetylation-defective TRPV4-K608R mutant led to mTORC1 inhibition, and caused abnormal intrauterine development or even foetal death. Our findings reveal that the TRPV-mediated resistance of mTORC1 inhibition in low glucose acts as a safeguard for normal foetal development.

biochemistry↗

Mid-Infrared Photothermal Imaging of Fatty Acid Desaturation Reaction in Cancer Cells

Direct visualization of metabolic conversions within living systems is essential for understanding metabolic activities yet challenging due to the absence of reaction-specific reporters and the limited sensitivity of current imaging modalities. Herein, we report an approach to monitor fatty acids (FAs) desaturation, primarily catalyzed by stearoyl-CoA desaturase, in cancer cells using deuterium (D)-labeled palmitic acid (PA-d31) as the reaction-specific reporter and mid-infrared photothermal (MIP) microscopy as the bond-selective imaging modality. The desaturation of PA-d31 produced a peak at 2246 cm-1 in the cell-silent region, corresponding to the stretching vibration of unsaturated C-D bonds (D-C=C-D) in unsaturated fatty acids. Penalized least squares fitting was employed to remove water background for enhancing the visibility of this peak. Our study revealed heterogeneous spatial distributions of both saturated FAs and their desaturated metabolites within lipid droplet pools in cancer cells. Furthermore, we observed an increase in fatty acid unsaturation level in OVCAR5 cells under cisplatin-induced stress. By directly visualizing fatty acid desaturation, this study offers new insights into fatty acid metabolism and opens avenues for evaluating new therapeutic strategies targeting fatty acid metabolism.

biochemistry↗

Population-specific brain charts reveal Chinese-Western differences in neurodevelopmental trajectories

Human brain charts provide unprecedented opportunities for decoding neurodevelopmental milestones and establishing clinical benchmarks for precision brain medicine 1-7. However, current lifespan brain charts are primarily derived from European and North American cohorts, with Asian populations severely underrepresented. Here, we present the first population-specific brain charts for China, developed through the Chinese Lifespan Brain Mapping Consortium (Phase I) using neuroimaging data from 43,037 participants (aged 0-100 years) across 384 sites nationwide. We establish the lifespan normative trajectories for 296 structural brain phenotypes, encompassing global, subcortical, and cortical measures. Cross-population comparisons with Western brain charts (based on data from 56,339 participants aged 0-100 years) reveal distinct neurodevelopmental patterns in the Chinese population, including prolonged cortical and subcortical maturation, accelerated cerebellar growth, and earlier development of sensorimotor regions relative to paralimbic regions. Crucially, these Chinese-specific charts outperform Western-derived models in predicting healthy brain phenotypes and detecting pathological deviations in Chinese clinical cohorts. These findings highlight the urgent need for diverse, population-representative brain charts to advance equitable precision neuroscience and improve clinical validity across populations.

neuroscience↗

Neural trajectories reveal orchestration of cortical coding underlying natural language composition

Language is a hierarchically structured system that enables humans to communicate complex meanings. Despite recent advances, the neurocomputational mechanism underlying the composition of natural language remains unclear. Building on the neural population theory, we investigated how neural trajectories in latent spaces underpin natural language composition that integrates diverse lexical content and syntactic relations. We found that neural trajectories derived from human neocortical responses show an orchestration of distinct coding strategies during naturalistic story comprehension. Neural latent geometry is primarily associated with syntactic relations and exhibits more efficient compression relative to lexical content. We further demonstrate that these trajectories can be simulated by brain-inspired computing systems with near-critical dynamics and a preference for historical information. Overall, by positioning structure-based integration as a key computation of natural language comprehension, our findings provide a novel perspective on the mechanism underlying real-world language use and emphasize the importance of contextual information in the development of brain-inspired intelligent systems.

neuroscience↗

Tissue-wide profiling of human lungs reveals spatial sequestration of macrophages in tuberculosis

The immune response to human tuberculosis (TB), particularly in the context of complex lung pathology, remains incompletely understood. Here, we employed whole-slide spatial proteomics to map immune cell organization in TB-affected human lung tissues. Our analysis revealed pronounced spatial segregation of major immune cell populations in non-necrotizing TB lesions. At the tissue level, macrophages and lymphocytes formed distinct cellular communities associated with specific pathological features. At the lesion level, macrophages and B cells showed an inverse relationship in both abundance and spatial distribution. Proinflammatory T cells preferentially accumulated in macrophage-rich lesions but remained largely separated from macrophages. Interestingly, lesions exhibiting clear segregation between T cells and macrophages were more common in subclinical TB than in active disease. These findings suggest that spatial isolation of macrophages from effector lymphocytes may help temper inflammation and potentially prevent lesion progression to necrosis, while also enabling immune evasion by Mycobacterium tuberculosis. One Sentence SummaryXiao et al. reveal spatial segregation of immune cells in TB-lung tissue and link the microenvironmental dynamics to disease states of tuberculosis.

immunology↗

Inhibition of DHODH Activates Pyroptosis and cGAS-STING Pathways to Enhance NK cell Infiltration Mediated Anti-tumor Immunity in Melanoma

Cancer cells are heavily reliant on de novo pyrimidine synthesis. Suppression of pyrimidine metabolism directly inhibits tumor growth and fosters immune activation within the tumor microenvironment. Dihydroorotate dehydrogenase (DHODH), a crucial enzyme governing de novo pyrimidine synthesis, is a critical player in this context. Inhibition of DHODH not only reverses immunosuppression but also instigates a mild innate immune response. However, the impact of DHODH inhibition on natural killer (NK) cells remains unexplored. In this study, we found that inhibition of DHODH efficiently promotes NK cells infiltration in tumors. Suppression of DHODH led to increased oxidative stress in mitochondria, the release of mtDNA, and activation of caspase 3, which in turn activated the cGAS-STING pathway and pyroptosis in cancer cells, respectively, contributing to NK cells induced antitumor immune responses in melanoma. Additionally, we developed EA6, a novel DHODH inhibitor with higher efficacy in promoting NK cells infiltration. In summary, this study underscores that modulation of pyrimidine metabolism can effectively trigger antitumor immune responses, with a specific emphasis on NK cells. This finding opens new avenues for enhancing the efficacy of targeted nucleotide metabolism in cancer therapy. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=141 SRC="FIGDIR/small/644471v1_ufig1.gif" ALT="Figure 1"> View larger version (60K): org.highwire.dtl.DTLVardef@88d4fcorg.highwire.dtl.DTLVardef@156fe1aorg.highwire.dtl.DTLVardef@448086org.highwire.dtl.DTLVardef@152079c_HPS_FORMAT_FIGEXP M_FIG C_FIG The anti-tumor mechanisms of DHODH inhibition. Inhibition of DHODH activates cGAS-STING pathways to enhance NK cell infiltration. And the tumor-infiltrating NK cells facilitate melanoma cells pyroptosis which providing a positive feedback mechanism for DHODH-mediated anti-tumor immunity.

cancer biology↗

The Neurocognitive Mechanisms Underlying Narrative Schematic and Paraphrastic Transmission

Narrative transmission serves multiple crucial functions, such as cultural preservation, knowledge accumulation, and consensus building, in human society. However, our understanding of its neurocognitive mechanisms remains limited. In this study, we combined a social transmission chain design with fMRI to investigate the dynamic changes of different narrative components occurring throughout transmission chains and to uncover the factors driving fidelity and distortion. A total of 58 participants were scanned as they listened to and subsequently recalled a story within a social transmission chain. We distinguished two types of transmission modes: schematic transmission, which prioritizes preserving the structural framework of the information, and paraphrastic transmission, which entails rephrasing the content while conveying its meaning. Behavioral results revealed a pattern in which paraphrastic transmission led to distortion and divergence, whereas schematic transmission remained more stable and convergent. Neural findings indicated that the transmission of story structure and content involved subsystems of the Default Mode Network (DMN) and specific subregions of the Hippocampus (HPC). While neural reinstatement between narrative listening and speaking failed to predict across-generation fidelity of content and structure, functional connectivity pattern similarity analysis showed that the DMN and HPC work as an episodic memory system supporting transmission performance. These findings highlight that narrative transmission is supported by distinct neurocognitive representations within episodic memory subsystems, which work collaboratively to sustain the transmission of narratives.

neuroscience↗

Newly discovered and conserved role of IgM against viral infection in an early vertebrate

IgM emerged in jawed vertebrates 500 Mya and remains the most evolutionarily conserved antibody class. However, despite extensive studies on IgM as an ancient antiviral weapon in warm-blooded vertebrates, its role and mechanisms in combating viral infections in early vertebrates remain poorly understood. Here, we found that significant virus-specific sIgM titers were generated in serum and gut mucus of teleost fish that survived infection, and fish lacking sIgM were more susceptible to viral infection. These results challenge the paradigm that IgM and IgT are specialized to systemic and mucosal immunity, respectively. More crucially, our study provides further insight into the role of sIgM in viral neutralization and firstly clarified the mechanism through which teleost sIgM blocks viral infection by directly targeting viral particles. From an evolutionary perspective, our findings indicate that sIgM in both primitive and modern vertebrates follow conserved principles in the development of specialized antiviral immunity.

immunology↗

Revolutionizing large-scale DNA synthesis with microchip-based massive in parallel synthesis system

DNA synthesis serves as the fundamental enabling technology of engineering biology, aiming to provide DNA molecules of designed composition, length, and complexity at scale and low cost. Current high-throughput DNA synthesis technologies rely on intricate chip manufacturing and microfluidic systems to provide large-scale synthetic oligonucleotides, at the expense of low concentration and limited compatibility in the processing of longer DNA constructs assembly. Here, we report a microchip-based massive in parallel synthesis (mMPS), pioneering an "identification-sorting-synthesis-recycling" iteration mechanism to microchips for high throughput DNA synthesis. In comparison to microarray-based methods, we demonstrate that our method can increase the DNA product concentration by 4 magnitudes (to picomole-scale per sequence) and greatly simplifies the downstream processes for large-scale gene synthesis construction. By the construction of 1.97 million-diversity variant libraries that cover 1,254 human protein domains, we demonstrated the uniformity of the constructed variant libraries using mMPS-derived oligos is greatly improved, with amino acid distribution highly consistent as designed. In addition, by synthesizing 285 1kb-to-3kb genes with varying degrees of sequence complexity from previously reported strains A501 and 3DAC, potential ancestor of early archaea and bacteria, our result shows that the overall gene assembly success rate using mMPS-derived oligos is increased by 10-fold in comparison to other methods. Our mMPS technology holds the potential to close the gap between the quality and cost of writing DNA in increasing demand across many sectors of research and industrial activities.

synthetic biology↗

A tumor-secreted protein utilizes glucagon release to cause host wasting

Tumor-host interaction plays a critical role in malignant tumor-induced organ wasting across multiple species. Despite known regulation of regional wasting of individual peripheral organs by tumors, whether and how tumors utilize critical host catabolic hormone(s) to simultaneously induce systemic host wasting, however, is largely unknown. Using the conserved yki3SA-tumor model in Drosophila, we discovered that tumors increase the production of adipokinetic hormone (Akh), a glucagon-like catabolic hormone, to cause systemic host wasting, including muscle dysfunction, lipid loss, hyperglycemia, and ovary atrophy. We next integrated RNAi screening and Gal4-LexA dual expression system to identify that yki3SA-gut tumors secrete Pvf1 to remotely activate its receptor Pvr in Akh-producing cells (APCs), ultimately promoting Akh production. The underlying molecular mechanisms involved the Pvf1-Pvr axis that triggers Mmp2-dependent ECM remodeling of APCs and enhances innervation from the excitatory cholinergic neurons. Interestingly, we also confirmed the similar mechanisms governing tumor-induced glucagon release and organ wasting in mammals. Blockade of either glucagon or PDGFR (homolog of Pvr) action efficiently ameliorated organ wasting in the presence of malignant tumors. Therefore, our results demonstrate that tumors remotely promote neural-associated Akh/glucagon production via Pvf1-Pvr axis to cause systemic host wasting.

physiology↗

Ultrasensitive in vivo infrared spectroscopic imaging via oblique photothermal microscopy

In vivo IR spectroscopy faces challenges due to poor sensitivity in reflection mode and low resolution at micrometer scale. To break this barrier, we report an oblique photothermal microscope (OPTM) to enable ultrasensitive IR spectroscopic imaging of live subjects at sub-micron resolution. Classic photothermal measurement captures only a small fraction of probe photons through a pinhole to extract the photothermal signal. Instead, OPTM uses a differential split detector placed on the sample surface to collect 500-fold more photons and suppress the laser noise by 12 fold via balanced detection. Leveraging its improved sensitivity, OPTM enables low-dose IR imaging of skin without photodamage. Depth-resolved in vivo OPTM imaging of metabolic markers beneath mouse and human skin is shown. Furthermore, we demonstrate in vivo OPTM tracking of topical drug contents within mouse and human skin. Collectively, OPTM presents a highly sensitive imaging platform for in vivo and in situ molecular analysis.

bioengineering↗