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Pang, Y.

Publications and source records attributed to Pang, Y..

At least 19 recordsLinked to original sources

Cancer cells hijack mitochondria from Bhlhe40+ T cells for immune evasion

Cancer cells hijack mitochondria from T cells via tunneling nanotubes (TNTs) to promote immune evasion, yet the underlying mechanisms of mitochondrial-loss remain poorly understood. Here, through targeted screening of relevant genes, we demonstrated that CD38 is a potent regulator of TNT formation through interaction with its cognate ligand, CD31. Conditional knockdown of Cd38 in murine models leads to CD8+ T cell-dependent tumor shrinkage. Single-cell RNA sequencing of tumor-infiltrating T cells revealed that cancer cells preferentially target the Bhlhe40+ effector subset. Bhlhe40 is a transcription factor that upregulates the expression of S100a4, a reported chemoattractant of nanotubes. Bhlhe40 upregulation creates mitochondrial-loss vulnerability for tumor neoantigen-specific T cells. Dual mitochondria transfer blockade with Cd38 knockdown and S100a4 inhibitor trifluoperazine markedly suppressed tumor growth. Collectively, our findings identified the Bhlhe40-S100a4 cascade as a critical regulator of cancer/T cell mitochondrial transfer, providing insights for the development of new cancer immunotherapies.

immunology↗

Antigen-aware TCR embeddings reveal conserved immune patterns for personalized immune monitoring

T cell receptor (TCR) repertoires are highly individualized, while technical variation further complicates comparisons across individuals and cohorts. Here, we present TCRmeta, an antigen-aware framework that integrates population-scale repertoire relationships with experimentally defined antigen specificity to establish a shared space for repertoire analysis. TCRmeta predicted mutation-induced changes and captured antigen-related relationships in TCR specificity. Despite extensive sequence diversity, TCRmeta revealed a conserved repertoire landscape, enabling construction of a healthy reference for quantifying repertoire dispersal. Across cohorts, aging was associated with conserved V gene changes and progressive dispersal, with greater dispersal in CMV-positive individuals. Longitudinal analysis showed that repertoires progressively shifted toward the healthy reference following bone marrow transplantation or antiretroviral therapy. To directly compare repertoires in TCRmeta space, we developed Energy Shift, a pairwise measure robust to technical variation and HLA background while remaining sensitive to biological differences. Together, TCRmeta enables quantitative cross-individual and longitudinal immune monitoring.

bioinformatics↗

A durably colonizing engineered native symbiont enables sustained intestinal delivery for metabolic dysfunction and colitis

BackgroundEngineered bacterial therapeutics represent a promising strategy for sustained intestinal delivery of therapeutic molecules, but their efficacy is limited by inefficient colonisation, safety concerns and the need for repeated administration or auxiliary delivery systems. ObjectiveTo develop a safety-optimised native bacterial chassis capable of long-term gut colonisation and sustained therapeutic delivery for intestinal inflammatory and metabolic diseases. DesignNative murine Escherichia coli isolates were screened for antibiotic susceptibility, genetic tractability and long-term intestinal colonisation. The selected strain, MEc30, was further optimised by deleting the putative virulence-associated clb and irp loci. MEc30 was then engineered to deliver murine interleukin-10 (MEc30-mIL-10) or produce nicotinic acid (MEc30-NA), and therapeutic efficacy was evaluated in Il10-/- colitis and high-fat diet-induced metabolic dysfunction models. ResultsMEc30 achieved stable lifelong colonisation of the murine intestine after a single oral administration, without antibiotic preconditioning or auxiliary delivery systems, and did not detectably disturb host physiology or gut microbial ecology. Deletion of clb and irp abolished potential colibactin- and yersiniabactin-associated biosafety risks while preserving bacterial growth and colonisation capacity. MEc30-NA continuously produced nicotinic acid in the gut, activated epithelial GPR109a-associated barrier signalling, improved glucose and lipid metabolism, reduced systemic inflammation and avoided the sharp peak exposure associated with conventional nicotinic acid administration. MEc30-mIL-10 enabled sustained intestinal IL-10 delivery, suppressed inflammatory macrophage activation, improved barrier integrity and alleviated spontaneous colitis in Il10-/- mice. ConclusionThis study identifies MEc30 as a durable and safety-optimised native E. coli chassis for sustained intestinal therapeutic delivery. Engineered native symbionts may provide a long-acting live biotherapeutic strategy for chronic intestinal inflammatory and metabolic diseases.

microbiology↗

foxQ2 marks fast-acting brain interneurons including a subset of dopaminergic neurons innervating mushroom bodies and central complex in the beetle Tribolium castaneum

The brain is one of the most complex animal organs and the development of the many different neuron types remains enigmatic. A set of brain-specific transcription factors is involved in brain patterning but their specific contributions mostly remain to be elucidated, including foxQ2II. This transcription factor is conserved in anterior neuroectodermal patterning of most animals while it has been lost from vertebrates. The contribution of foxQ2II-positive neurons to the adult brain has remained enigmatic. Here, we use our enhancer trap, immunostainings and our newly established beetle brainbow system to categorize Tc-foxQ2II-positive neurons into nine clusters with different projection patterns. All clusters contain neurons with the fast-activating neurotransmitters acetylcholine and glutamate while no Tc-foxQ2II positive neuron is GABA-ergic or serotonin-positive. Interestingly, we found that many dopaminergic neurons were Tc-foxQ2II positive and we homologize them with dopaminergic neurons of the PPL2c, PPM1 and PPL1 cluster described in the Drosophila brain. Our results show that Tc-foxQ2II marks subsets of fast-acting interneurons contributing to the higher order brain centers mushroom bodies and central complex. Taken together, our work expands the known functional range of foxQ2 genes from sensory and neurosecretory cell specification to interneurons involved in the function of higher order brain centers.

neuroscience↗

A near-complete lamprey genome illuminates ancestral vertebrate innovations

The origin of vertebrates is characterized by a suite of phenotypic innovations, yet the underlying genetic mechanisms remain poorly understood. As a living representative of jawless vertebrates, the lamprey serves as a pivotal model for investigating the genomic basis of early vertebrate evolutioin. Here, we report a near telomere-to-telomere (T2T) genome assembly of the reissner lamprey (Lethenteron reissneri), generated from sperm DNA that is not subject to programmed genome rearrangement. The 1.25 Gb assembly resolves over 97% of chromosome sequences into single contigs, enabling reconstruction of previously inaccessible genomic regions. Centromeres display highly diversified, lamprey-specific repeat units and structural architectures, whereas telomeres contain both conserved and lineage-specific satellite repeats. Deep transcriptomic profiling across representative organs and developmental stages substantially improved genome annotation. Comparative genomic analyses revealed a major expansion of 1,562 gene families at the base of the vertebrate lineage, and they are significantly enriched for functions related to neural development, skeletal formation, and cardiac function, echoing the known phenotypic innovations in vertebrates. Notably, the CDH2 gene family underwent vertebrate-specific copy number expansion and acquired conserved cis-regulatory elements (CREs), highlighting its potential role in shaping the early vertebrate circulatory system. Histological analyses and functional knockout experiments demonstrated that one CDH2 paralog (CDH2_H) is essential for lamprey heart development and chamber formation, playing a critical role in the emergence of the closed circulatory system in early vertebrates. This high-quality lamprey genome provides a foundational resource for dissecting the genetic basis of key innovations that shaped vertebrate evolution.

genomics↗

Bridging Language Markers and Pathology: Correlations Between Digital Speech Measures and Surrogate CSF Biomarkers in Alzheimer's Disease

BackgroundDigital language markers show promise in detecting early cognitive impairment related to Alzheimers disease (AD), yet their relationship with cerebrospinal fluid (CSF) biomarkers of AD pathology remains unclear mainly due to the lack of data with both CSF and language markers. ObjectiveThis study aims to build links between digital language markers and fluid biomarkers through surrogate CSF biomarkers. MethodsUsing NACC clinical data as anchor variables, language makers in the I-CONECT study were linked to NACC CSF data. Surrogate CSF biomarkers were created for I-CONECT subjects using machine learning models from common NACC clinical variables. Correlations assessed associations between CSF and language markers. ResultsLower predicted amyloid-{beta} correlated significantly with reduced syntactic complexity and shorter speech responses. Higher predicted total tau and phosphorylated tau correlated with reduced syntactic complexity. ConclusionsThis study demonstrates novel links between language markers and fluid biomarkers, highlighting conversational language as a potential accessible, non-invasive approach for early detection and monitoring of Alzheimers pathology.

bioinformatics↗

Transcription factors SP5 and SP8 drive primary cilia formation

While specific transcription factors are known to regulate cell fate decisions, the degree to which they can stimulate formation of specific cell organelles is less clear. We used a multi-omics comparison of the transcriptomes of ciliated and non-ciliated embryonic cells to identify transcription factors upregulated in ciliated cells, and conditional genetics in mouse embryos and stem cells to demonstrate that SP5/8 regulate cilia formation and gene expression. In Sp5/8 mutant embryos primary and motile cilia are shorter than normal and reduced in number across cell types, contributing to situs inversus and hydrocephalus. Moreover, expression of SP8 is sufficient to induce primary cilia in unciliated cells. This work opens new avenues for studying cilia assembly using stem cell models and offers new insights into human ciliopathies.

developmental biology↗

Comparing Orientation-Dependent Transverse Relaxation at 3T and 7T: Deciphering Anisotropic Relaxation Mechanisms in White Matter

Purpose: This work aims to elucidate the mechanisms underlying orientation-dependent transverse relaxation in human brain white matter (WM), which have long been ambiguous. Methods: We analyzed publicly available 3T and 7T DTI datasets (b-values = 1000 and 2000 s/mm2) from 25 young adults participating in the Human Connectome Project. Orientation-dependent transverse relaxation R2 profiles from whole brain WM were generated from T2-weighted images (b-value = 0) and characterized using a previously developed cone model based on the generalized magic angle effect (MAE). Derived anisotropic R2 or R2a values were compared between different magnetic fields. Similar comparisons were also conducted for the derived R2a values from whole brain WM and two fiber tracts, based on gradient-echo signals reported in the literature. Classical relaxation theories predict that the ratio of (R2a (7T))/R2a (3T)) will be unity or (7/3)^2 (i.e., approximately 5.4) if the measured orientation-dependent R2 arises exclusively from MAE or from the previously proposed susceptibility effect, respectively. Results: Fitted model parameters were comparable for DTI datasets with b-values of 1000 and 2000 (s/mm2). The fitted R2a increased, on average, from 3.6{+/-}1.1 (1/s) at 3T to 5.4{+/-}1.5 (1/s) at 7T for DTI datasets with a b-value=1000 s/mm2. The measured ratio of (R2a (7T))/(R2a (3T)) was thus approximately 1.5. However, based on gradient-echo signals, this ratio essentially became unity within the measurement precision. Conclusion: This study suggests that MAE is the primary mechanism for the observed orientation-dependent transverse relaxation at 3T in human brain WM, offering a different perspective from previous literature.

biophysics↗

Unifying Orientation-Dependent Relaxation and Diffusion Around Axonal Fibers from DTI: Characterizing Fiber-Tract-Specific Anisotropic R2 Profiles of the Corpus Callosum

This work aims to characterize fiber-tract-specific orientation-dependent R2 from the seven callosal segments (CC1-CC7) based on human brain Connectome high-resolution DTI datasets. WM voxels from each segment were masked by the thresholds of FA and mode of anisotropy. Encoded in T2W images (b-value = 0), an orientation-dependent R2 profile was constructed based on voxel-wise fiber orientations and characterized by a "cone" model. This allowed [Formula], an orientation-dependent or anisotropic R2, to be separated from its orientation-independent or isotropic counterpart. Except for [Formula], no discernible differences were found for the fits between the two b-values. On average, [Formula] increased from 2.4{+/-}0.2 (1/s) to 3.2{+/-}0.3 (1/s) as the b-value increased. Furthermore, [Formula] showed an increasing trend from CC1 to CC7 and the open angle of the cone fluctuated around 65{degrees}. As usual, FA was found increasing from CC1 to CC7 and from a higher to a lower b-value. In conclusion, we have shown that fiber-tract-specific Anisotropic R2 profiles from the callosal segments can be characterized by a cone model. The proposed method offers a unique opportunity to reevaluate existing clinical DTI studies and optimize new ones for characterizing specific WM tracts in both healthy and diseased subjects.

biophysics↗

Enhanced Temporal-Resolution CEST Imaging method for reliable mapping of muscle OXPHOS

PurposeTo develop and validate a novel chemical exchange saturation transfer (CEST) MRI method to map skeletal muscle OXPHOS (Oxidative Phosphorylation CEST or OXCEST). Theory and MethodsOur proposed OXCEST method acquires creatine (Cr)-weighted CEST maps by applying RF saturation (B1) at only two frequency offsets: +1.8 ppm (targeting the Cr amine resonance) and -1.8 ppm (to calculate MTRasym at 1.8 ppm). The pre-exercise MTRasym is modeled as a second-order polynomial function (f) of B0. Next, the post-exercise alteration in MTRasym is hypothesized to be affected by both an exercise-induced increase in Cr and changes in B0 inhomogeneity. By inputting post-exercise B0 values into f, the change in MTRasym due to B0 variation alone was estimated. Thus, the Cr-related post-exercise MTRasym could be isolated and quantified. OXCEST and 31P-MRS were performed in seven subjects across two sessions to compare the OXCEST-derived Cr recovery time constant (TCr) with the ground-truth phosphocreatine recovery time constant (TPCr). ResultsA second-order polynomial function f could reliably describe the relationship between pre-exercise MTRasym and B0 (R2=0.87{+/-}0.07 in the lateral gastrocnemius (LG); R2=0.98{+/-}0.01 in the medial gastrocnemius (MG); R2=0.96{+/-}0.03 in the soleus). The mean pre-exercise MTRasym was approximately 6-7% for all muscle groups. Following exercise, MTRasym increased by 11.4{+/-}4.5% in LG and 8{+/-}2.4% in MG, and showed mono-exponential recovery (R2>0.97). The combined TCr of LG and MG was found to be significantly correlated with TPCr (R{superscript 2}=0.83, p=0.005). ConclusionOXCEST enables reliable assessment of post-exercise Cr recovery and demonstrated strong agreement with 31P-MRS.

bioengineering↗

Effects of Exercise and Konjac on Lipid Metabolism and Mechanism in Obese Rats

ObjectiveTo study the effects of exercise and konjac on body weight and lipid metabolism in obese rats, and the possible mechanism of exercise combined with konjac on body weight and lipid metabolism. MethodsFifty male Sprague Dawley rats were randomly divided into 5 groups. After six weeks of intervention, blood lipid, body weight, liver weight, inflammatory factors, oxidative stress markers and proteins were measured. ResultsWeight and liver weight in HFD group were significantly higher (P<0.05, P<0.01) than those in CON group. Compared with HFD group, blood lipid index in intervention group were significantly decreased; The levels of MDA (P<0.01, P<0.05, P<0.05) and SOD (P<0.05) in intervention group were significantly decreased; the GSH levels in HAE group and HKE group were significantly increased(P<0.01, P<0.05); the levels of IL-6, TNF-, and leptin in HAE group (P<0.05, P<0.05, P<0.01) and HKE group (P<0.01, P<0.01, P<0.05) were significantly decreased; ApoA5 in intervention group was significantly increased (P<0.01), SREBP-1c and LXR was significantly decreased (P<0.01). ConclusionKonjac or exercise alone can improve the lipid metabolism, and the comprehensive effect is better. The mechanism of regulating lipid metabolism may be related to the expression of LXR, SREBP-1c and ApoA5.

biochemistry↗

Measuring Longitudinal Genome-wide Clonal Evolution of Pediatric Acute Lymphoblastic Leukemia at Single-Cell Resolution

Approximately 15-20% of children with acute lymphoblastic leukemia (pALL) are not cured despite years of treatment with more than ten chemotherapeutic agents, yet bulk sequencing reveals minimal somatic variation that could explain genetic treatment resistance. Using error-corrected bulk sequencing, and primary template-directed amplification (PTA)-enabled single-cell exome and whole-genome sequencing, we discovered much more genetic diversity in pALL. Individual leukemic cells harbor 3.7-fold more mutations (mean 3,553) than detected in bulk samples (mean 965). Many ETV6-RUNX1 patients harbor multiple independent ras-mutated clones, and we also identified convergent evolution of JAK2 mutations as well as copy number alterations. PTA-based phylogenetic analysis of over 150 single-cell genomes linked heritable phenotypes to specific genetic alterations and identified low-frequency clones harboring mutations in treatment resistance-associated genes (ITGA9, NTRK3, SULF2) that increased in frequency during treatment. These findings reveal extensive hidden genetic diversity in pALL while providing a framework for the early detection of high-risk leukemic populations.

cancer biology↗

Roles of Cro2 and CI2 binding to OR operators in controlling lysogeny stability during prophage induction

The lysogeny-lysis switch in bacteriophage lambda serves as a model for understanding cell fate decisions. The molecular network controlling this switch has been explored through extensive experimental and computational studies. Yet, the specific role of protein-DNA interactions, like the binding of CI2 and Cro2 proteins to operator sites, in regulating lysogeny stability during prophage induction remains less under-stood. This study employs a minimalistic model and the Accurate Chemical Master Equation (ACME) method to construct detailed probability landscapes of the networks behavior under varying conditions, such as different dissociation and CI2 degradation rates which simulate UV irradiation effects. Our findings indicate that Cro2 binding at OR3 and CI2 at OR1 significantly influence lysogeny stability, with the former destabilizing and the latter stabilizing it. Conversely, interactions at OR1 by Cro2 and OR3 by CI show minimal impact on this stability. Through the ACME approach, we could examine the networks global behavior under conditions unapproachable by conventional stochastic simulations. This study highlights the critical roles of specific protein-DNA interactions in maintaining lysogeny and provides insight into the broader dynamics of the lysogeny-lysis switch under various physiological stresses.

systems biology↗

Genome-wide Mapping Eukaryotic Open Chromatin Regions with Double-Stranded DNA Deaminase

A variety of methods such as ATAC-seq and CUT&Tag have been developed for probing chromatin states. However, enzymatic cleavage of DNA in these methods hinders their multi-omics integration with other DNA profiling techniques. Here, by extending our use of dsDNA deaminase (FOOtprinting with DeamInasE, FOODIE), we introduce two new methods for mapping Chromatin Open region by DeamInasE (ChrODIE) and histone modification by ANtibody-associated DeamInasE (ANDIE), respectively. Unlike cleavage-based methods, both ChrODIE and ANDIE leave genomic DNA after deamination unfragmented and amplifiable. This offers the potential for simultaneous or downstream integration with other genomic profiling methods, such as mapping 3D genome interactions.

genomics↗

Single-cell proteomics of pre-implantation mouse embryos uncovers distinct asymmetry of certain proteins among early blastomeres

During pre-implantation mouse embryonic development, blastomeres undergo division and differentiation, reaching a distinctive level of heterogeneity, hence the completion of the first cell fate determination. However, when the initial asymmetry emerges and how this heterogeneity amplifies, particularly at the protein level, remain elusive. Here, by mass spectrometry-based single-blastomere proteomics, we identified proteins exhibiting significant heterogeneity in abundance among mouse blastomeres as early as the 2-cell stage. Differential gene expression among blastomeres, as indicated by intra-embryo variation in RNA abundance detected through single-cell RNA sequencing, was insufficient to fully explain the corresponding disparities in protein abundance. Instead, the asymmetric distribution of protein molecules during cell division was observed, serving as another mechanism contributing to protein heterogeneity, independent of RNA expression.

developmental biology↗

Single-cell analysis of the somatic mutational landscape in human chondrocytes during aging and in osteoarthritis

Somatic mutation is now recognized as a cause of multiple human diseases other than cancer. Osteoarthritis (OA), a highly prevalent age-related disease, has been associated with increased chromosomal abnormalities in articular cartilage of OA patients. Thus far no systematic attempt has been made to characterize the somatic mutational landscape of chondrocytes during normal aging and in affected cartilage of OA patients. Here we used single-cell whole genome sequencing to quantitatively analyze single-nucleotide variants (SNVs) and small insertions and deletions (InDels) in 100 single chondrocytes isolated from the cartilage of hip femoral heads of 17 subjects aged from 26 to 90 years, including 9 OA patients and 8 non-OA donors. Both SNVs and InDels were found to accumulate with age in chondrocytes with a clock-like mutational signature. Surprisingly, the age-related accumulation rate of these mutations was found to be lower in OA chondrocytes compared with chondrocytes from non-OA control subjects.

genomics↗

Enhanced spatially resolved transcriptomics analysis by matching between expression profiles and spatial topology

Spatially resolved transcriptomics (SRT) quantifies gene expression covering contextual heterogeneity for the tissue section. Exploratory data analysis using SRT data sheds light on diverse biomedical research fields. We propose STForte, a pairwise graph autoencoding-based approach for SRT data analysis, which is capable of matching the information between expression profiles and spatial topology in the latent space. STForte benefits from the designed framework to provide encodings with justifiable spatial correlations for the down-stream analysis of both homogeneous and heterogeneous SRT data. Moreover, STForte can unravel the biological patterns of unobserved locations or recover deficient measurements to enable spatial enhancement. Latent encodings generated by STForte can be used to perform spatial region identification or other downstream tasks to gain biological insights and elucidate biological processes. In this work, we presented various analyses to show that STForte is scalable for analyzing SRT data under different scenarios with considerable performance.

bioinformatics↗

PRISM: Multiplexed Profiling of RNA In-Situ through Single-round of Imaging in Three-Dimensional Tissue

Spatial RNA imaging has not been widely adopted because conventional fluorescence microscopy is limited to only a few channels, and the cyclic reactions needed to increase multiplexing in techniques such as sequential fluorescence in-situ hybridization (FISH) require sophisticated instrumentation. Here, we introduce Profiling of RNA In-situ through Single-round iMaging (PRISM), a method that expands coding capacity through color intensity grading. Using a radius vector filtering strategy to ensure the distinguishability of codewords in color space, PRISM achieves up to 64-plex color-barcoded RNA imaging in a single imaging round with conventional microscopes. We validate PRISMs versatility across various tissues by generating a 3D atlas of mouse embryonic development from E12.5 to E14.5, a quasi-3D tumor-normal transition landscape of human hepatocellular carcinoma (HCC), and a 3D cell atlas and subcellular RNA localization landscapes of mouse brain. Additionally, we show the critical role of cancer-associated fibroblasts (CAFs) in mediating immune infiltration and immune response heterogeneity within and between tumor microenvironments.

bioengineering↗