ABSTRACT
Regulatory T (Treg) cells are critical for immune tolerance but also form a barrier to antitumor immunity. As therapeutic strategies involving Treg cell depletion are limited by concurrent autoimmune disorders, identification of intratumoral Treg cell-specific regulatory mechanisms is needed for selective targeting. Epigenetic modulators can be targeted with small compounds, but intratumoral Treg cell-specific epigenetic regulators have been unexplored. Here, we show that JMJD1C, a histone demethylase upregulated by cytokines in the tumor microenvironment, is essential for tumor Treg cell fitness but dispensable for systemic immune homeostasis. JMJD1C deletion enhanced AKT signals in a manner dependent on histone H3 lysine 9 dimethylation (H3K9me2) demethylase and STAT3 signals independently of H3K9me2 demethylase, leading to robust interferon-γ production and tumor Treg cell fragility. We have also developed an oral JMJD1C inhibitor that suppresses tumor growth by targeting intratumoral Treg cells. Overall, this study identifies JMJD1C as an epigenetic hub that can integrate signals to establish tumor Treg cell fitness, and we present a specific JMJD1C inhibitor that can target tumor Treg cells without affecting systemic immune homeostasis.
Subject(s)
Autoimmune Diseases , Humans , Cytokines , Epigenomics , Histone Demethylases , Homeostasis , Oxidoreductases, N-Demethylating , Jumonji Domain-Containing Histone Demethylases/geneticsABSTRACT
Increasing evidence suggests that transcriptional control and chromatin activities at large involve regulatory RNAs, which likely enlist specific RNA-binding proteins (RBPs). Although multiple RBPs have been implicated in transcription control, it has remained unclear how extensively RBPs directly act on chromatin. We embarked on a large-scale RBP ChIP-seq analysis, revealing widespread RBP presence in active chromatin regions in the human genome. Like transcription factors (TFs), RBPs also show strong preference for hotspots in the genome, particularly gene promoters, where their association is frequently linked to transcriptional output. Unsupervised clustering reveals extensive co-association between TFs and RBPs, as exemplified by YY1, a known RNA-dependent TF, and RBM25, an RBP involved in splicing regulation. Remarkably, RBM25 depletion attenuates all YY1-dependent activities, including chromatin binding, DNA looping, and transcription. We propose that various RBPs may enhance network interaction through harnessing regulatory RNAs to control transcription.
Subject(s)
Chromatin/metabolism , RNA-Binding Proteins/metabolism , RNA/metabolism , Transcription, Genetic/genetics , YY1 Transcription Factor/metabolism , Binding Sites , Gene Expression Regulation , Genome, Human/genetics , Hep G2 Cells , Humans , K562 Cells , Nuclear Proteins , Promoter Regions, Genetic/genetics , Protein Binding , RNA-Binding Proteins/genetics , RNA-Seq , Transcriptome , YY1 Transcription Factor/geneticsABSTRACT
Chemerin is an adipokine with chemotactic activity to a subset of leukocytes. Chemerin binds to 3 G protein-coupled receptors, including chemokine-like receptor 1 (CMKLR1), G protein-coupled receptor 1 (GPR1), and C-C chemokine receptor-like 2 (CCRL2). Here, we report that GPR1 is capable of Gi signaling when stimulated with full-length chemerin or its C-terminal nonapeptide (C9, YFPGQFAFS). We present high-resolution cryo-EM structures of Gi-coupled GPR1 bound to full-length chemerin and to the C9 peptide, respectively. C9 insertion into the transmembrane (TM) binding pocket is both necessary and sufficient for GPR1 signaling, whereas the full-length chemerin uses its bulky N-terminal core for interaction with a ß-strand located at the N-terminus of GPR1. This interaction involves multiple ß-strands of full-length chemerin, forming a ß-sheet that serves as a "lid" for the TM binding pocket and is energetically expensive to remove as indicated by molecular dynamics simulations with free energy landscape analysis. Combining results from functional assays, our structural model explains why C9 is an activating peptide at GPR1 and how the full-length chemerin uses a "two-site" model for enhanced interaction with GPR1.
Subject(s)
Chemokines , Receptors, G-Protein-Coupled , Animals , Humans , Adipokines/metabolism , Binding Sites , Chemokines/metabolism , Cryoelectron Microscopy , HEK293 Cells , Intercellular Signaling Peptides and Proteins/metabolism , Protein Binding , Receptors, CCR/metabolism , Receptors, Chemokine/metabolism , Receptors, Chemokine/chemistry , Receptors, G-Protein-Coupled/metabolism , Receptors, G-Protein-Coupled/chemistry , Signal TransductionABSTRACT
Chemerin is a processed protein that acts on G protein-coupled receptors (GPCRs) for its chemotactic and adipokine activities. The biologically active chemerin (chemerin 21-157) results from proteolytic cleavage of prochemerin and uses its C-terminal peptide containing the sequence YFPGQFAFS for receptor activation. Here we report a high-resolution cryo-electron microscopy (cryo-EM) structure of human chemerin receptor 1 (CMKLR1) bound to the C-terminal nonapeptide of chemokine (C9) in complex with Gi proteins. C9 inserts its C terminus into the binding pocket and is stabilized through hydrophobic interactions involving its Y1, F2, F6, and F8, as well as polar interactions between G4, S9, and several amino acids lining the binding pocket of CMKLR1. Microsecond scale molecular dynamics simulations support a balanced force distribution across the whole ligand-receptor interface that enhances thermodynamic stability of the captured binding pose of C9. The C9 interaction with CMKLR1 is drastically different from chemokine recognition by chemokine receptors, which follow a two-site two-step model. In contrast, C9 takes an "S"-shaped pose in the binding pocket of CMKLR1 much like angiotensin II in the AT1 receptor. Our mutagenesis and functional analyses confirmed the cryo-EM structure and key residues in the binding pocket for these interactions. Our findings provide a structural basis for chemerin recognition by CMKLR1 for the established chemotactic and adipokine activities.
Subject(s)
Adipokines , Chemokines , Receptors, Chemokine , Humans , Cell Membrane , Chemokines/metabolism , Cryoelectron Microscopy , Receptors, Chemokine/metabolismABSTRACT
The early stages of human development are increasingly acknowledged as pivotal in laying the groundwork for subsequent behavioral and cognitive development. Spatiotemporal (4D) brain functional atlases are important in elucidating the development of human brain functions. However, the scarcity of such atlases for early life stages stems from two primary challenges: (1) the significant noise in functional magnetic resonance imaging (fMRI) that complicates the generation of high-quality atlases for each age group, and (2) the rapid and complex changes in the early human brain that hinder the maintenance of temporal consistency in 4D atlases. This study tackles these challenges by integrating low-rank tensor learning with spectral embedding, thereby proposing a novel, data-driven 4D functional atlas generation framework based on spectral functional network learning (SFNL). This method utilizes low-rank tensor learning to capture common functional connectivity (FC) patterns across different ages, thus optimizing FCs for each age group to improve the temporal consistency of functional networks. Incorporating spectral embedding aids in mitigating potential noise in FC networks derived from fMRI data by reconstructing networks in the spectral space. Utilizing SFNL-generated functional networks enables the creation of consistent and highly qualified spatiotemporal functional atlases. The framework was applied to the developing Human Connectome Project (dHCP) dataset, generating the first neonatal 4D functional atlases with fine-grained temporal and spatial resolutions. Experimental evaluations focusing on functional homogeneity, reliability, and temporal consistency demonstrated the superiority of our framework compared to existing methods for constructing 4D atlases. Additionally, network analysis experiments, including individual identification, functional systems development, and local efficiency assessments, further corroborate the efficacy and robustness of the generated atlases. The 4D atlases and related codes will be made publicly accessible (https://github.com/zhaoyunxi/neonate-atlases).
Subject(s)
Atlases as Topic , Connectome , Magnetic Resonance Imaging , Humans , Magnetic Resonance Imaging/methods , Infant, Newborn , Connectome/methods , Male , Female , Brain/diagnostic imaging , Brain/physiology , Brain/growth & development , Infant , Image Processing, Computer-Assisted/methods , Machine Learning , Nerve Net/diagnostic imaging , Nerve Net/physiology , Nerve Net/growth & developmentABSTRACT
Clinically, a considerable number of non-small cell lung cancer (NSCLC) patients are unable to receive or resist chemotherapy, and the efficacy of non-chemotherapy treatment strategies based on anti-angiogenic agents combined with immune checkpoint blockade is still unsatisfactory. Neoantigen vaccine, based on personalized tumor DNA mutations, could elicit tumor specific T cell infiltration into the tumor site, exerting potent anti-tumor efficacy. Here, we evaluated the feasibility and safety of a new antitumor strategy by adding neoantigen vaccine to the regimen of bevacizumab and anti-PD-1 antibody. Firstly, 7 novel immunogenic neoantigen peptides were identified and developed for neoantigen vaccine (LLCvac), which can elicit strong antitumor immune response in vivo. Then, in orthotopic lung cancer model, LLCvac further combining with bevacizumab and anti-PD-1 antibody exerted a stronger antitumor effect, exhibiting significant decrease of tumor volume without obvious toxicity. Furthermore, tumor immune microenvironment assessment also showed that the proportion of neoantigen-specific T cells in blood could be induced dramatically by the combined therapy. And a large amount of neoantigen-specific Ki67-positive CD8+ T cells were found in tumor tissues, which infiltrated tumor tissues effectively to kill tumor cells expressing identified neoantigens. Overall, these results suggested that this combined therapy could safely induce robust antitumor efficacy, serving as an effective chemotherapy-free strategy for NSCLC treatment.
Subject(s)
Cancer Vaccines , Carcinoma, Non-Small-Cell Lung , Lung Neoplasms , Humans , Antigens, Neoplasm , Bevacizumab/therapeutic use , Cancer Vaccines/pharmacology , Cancer Vaccines/therapeutic use , Carcinoma, Non-Small-Cell Lung/drug therapy , CD8-Positive T-Lymphocytes , Lung Neoplasms/drug therapy , Tumor MicroenvironmentABSTRACT
The direct application of liquid marbles in electromagnetic wave (EMW) absorption is challenging due to their poor stability, susceptibility to gravitational collapse, and shaping difficulties. To address this issue, a novel strategy is proposed to incorporate liquid marble microstructures (NaCl/nano-SiO2) encapsulated in organic phases (Octadecane) into the rubber-matrix (SEBS) using the ultrasound-assisted emulsion blending method. The resulting NaCl/SiO2/Octadecane microstructures anchored to SEBS offer a substantial solid-liquid interface consisting of NaCl solution and SiO2. When subjected to an alternating electromagnetic (EM) field, the water molecules and polysorbate within SiO2 exhibit heightened responsiveness to the EM field, and the movement of Na+ and Cl- within these microstructures leads to their accumulation at the solid-liquid interface, creating an asymmetric ion distribution. This phenomenon facilitates enhanced interfacial polarization, thereby contributing to the material's EMW absorption properties. Notably, the latex with 16 wt% SEBS (E-3), exhibiting a surface morphology similar to human cell tissues, achieves complete absorption of X-band (fE = 4.20 GHz, RLmin = -33.87 dB). Moreover, the latex demonstrates light density (0.78 g cm-3) and environmental stability. This study not only highlights the predominant loss mechanism in rubber-based wave-absorbing materials but also provides valuable insights into the design of multifunctional wave-absorbing materials.
ABSTRACT
Macrophages have recently been discovered to assume a significant role in the progression of cryptococcosis. However, the potential involvement of macrophage-derived exosomes in the pathogenesis of cryptococcosis remains uncertain. In this study, we investigated the changes of microRNAs in macrophage exosomes (exo-miRNAs) in cryptococcal infections and the role of markedly altered exo-miRNAs in the modulation of Human Umbilical Vein Endothelial Cells (HUVEC) permeability and ROS accumulation and pyroptosis in Human Bronchial Epithelioid Cells (BEAS-2B). Techniques such as microarray analysis and real-time quantitative PCR were used to detect different exo-miRNAs and to screen for the most highly expressed exo-miRNAs. Then its mimics were transfected into HUVEC to study its effect on the monolayer permeability of HUVEC. Finally, the relationship between this exo-miRNAs and the ROS accumulation and pyroptosis was verified by bioinformatics analysis. The results showed that five exo-miRNAs were overexpressed and two exo-miRNAs were reduced, among which, exo-miR-4449 was expressed at the highest level. Exo-miR-4449 could be internalized by HUVEC and enhanced its monolayer permeability. Moreover, exo-miR-4449 was found to promote ROS accumulation and pyroptosis in BEAS-2B through HIC1 pathway. Thus, exo-miR-4449 plays an important role in the pathogenesis of cryptococcosis and holds promise as a significant biomarker for treatment.
Subject(s)
Cryptococcosis , Cryptococcus , MicroRNAs , Humans , Human Umbilical Vein Endothelial Cells/metabolism , Pyroptosis/genetics , Cryptococcus/metabolism , Reactive Oxygen Species/metabolism , MicroRNAs/genetics , MicroRNAs/metabolism , Macrophages/metabolism , Cryptococcosis/metabolism , Cryptococcosis/pathology , Kruppel-Like Transcription FactorsABSTRACT
Soybean domestication has significantly changed key agronomic traits, yet its impact on leaf photosynthetic phosphorus-use efficiency (PPUE) and its underlying traits remain poorly known. Further information on this would be important to increase soybean P-use efficiency. To address this gap, 48 soybean accessions (16 wild relatives, 16 landraces and 16 cultivars) were used to compare leaf anatomical traits, foliar chemical P fractions, P allocation and PPUE under two P levels. The results showed that the cultivars had higher area-based and mass-based photosynthesis rates, PPUE, metabolite P concentration, and its percentage of leaf total P, as well as a greater percentage of lipid P, nucleic acid P and residual P. Conversely, wild relatives tended to have higher leaf P concentration, palisade:spongy thickness ratio, and concentrations of inorganic P, nucleic acid P, lipid P and residual P. PPUE was negatively correlated with leaf inorganic P concentration and its percentage relative to leaf total P, while it was positively correlated with the concentration and percentage of metabolite P. We concluded that soybean domestication increased PPUE, as a result of both increased photosynthesis rate and decreased leaf P concentration; domestication reduced the palisade:spongy thickness ratio coupled with increased allocation of P to P-containing metabolites, thereby contributing to faster photosynthesis and higher PPUE. This study shed light on the significance of leaf P allocation and anatomical traits affecting PPUE during soybean domestication, offering a mechanistic understanding to further enhance soybean P-use efficiency.
ABSTRACT
In standard quantum weak measurements, preselection and postselection of quantum states are implemented in the same photon. Here we go beyond this restrictive setting and demonstrate that the preselection and postselection can be performed in two different photons, if the two photons are polarization entangled. The Pancharatnam-Berry phase metasurface is incorporated in the weak measurement system to perform weak coupling between probe wave function and spin observable. By introducing nonlocal weak measurement into the microscopy imaging system, it allows us to remotely switch different microscopy imaging modes of pure-phase objects, including bright-field, differential, and phase reconstruction. Furthermore, we demonstrate that the nonlocal weak-measurement scheme can prevent almost all environmental noise photons from detection and thus achieves a higher image contrast than the standard scheme at a low photon level. Our results provide the possibility to develop a quantum nonlocal weak-measurement microscope for label-free imaging of transparent biological samples.
ABSTRACT
The latest advancements in nuclear medicine indicate that radioactive isotopes and associated metal chelators play crucial roles in the diagnosis and treatment of diseases. The development of metal chelators mainly relies on traditional trial-and-error methods, lacking rational guidance and design. In this study, we propose the structure-aware transformer (SAT) combined with molecular fingerprint (SATCMF), a novel graph transformer network framework that incorporates prior chemical knowledge to construct coordination edges and learns the interactions between chelating agents and metal ions. SATCMF is trained on stability data collected from metal ion-ligand complexes, leveraging the SAT network to extract structural features relevant to the binding of ligands with metal ions. It further integrates molecular fingerprint features to refine the prediction of the stability constants of the chelating agents and metal ions. The experimental results on benchmark data set demonstrate that SATCMF achieves state-of-the-art performance based on four different graph neural network architectures. Additionally, visualizing the learned molecular attention distribution provides interpretable insights from the prediction results, offering valuable guidance for the development of novel metal chelators.
Subject(s)
Chelating Agents , Metals , Chelating Agents/chemistry , Metals/chemistry , Neural Networks, Computer , Ligands , Ions/chemistry , Coordination Complexes/chemistryABSTRACT
BACKGROUND: Limited data regarding the correlation between oxidative balance score (OBS) and hyperuricemia highlights the necessity for thorough investigations. This study aims to examine the link between OBS, which incorporates dietary and lifestyle factors, and the occurrence of hyperuricemia. METHODS: We conducted a cross-sectional study involving 13,636 participants from the 2007-2018 National Health and Nutrition Examination Survey (NHANES). The oxidative balance score (OBS) was determined based on four lifestyle factors and sixteen dietary nutrients. We assessed the levels of serum uric acid (SUA) and the occurrence of hyperuricemia as outcomes. Weighted logistic regression and linear models were used for statistical analysis, using Restricted Cubic Splines (RCS) to examine potential nonlinear associations. Subgroup analysis and sensitivity assessments were performed to identify any variations and ensure the robustness of the findings. RESULTS: Higher OBS was consistently correlated with decreased SUA levels and a reduced prevalence of hyperuricemia. RCS highlighted a significant negative nonlinear association, particularly in females. Subgroup analysis revealed gender-based differences and interactive correlation, providing additional insights regarding OBS and hyperuricemia relationship. CONCLUSION: This study underscores a robust negative correlation between OBS and SUA levels as well as the incidence of hyperuricemia, emphasizing the importance of dietary and lifestyle factors. Incorporating RCS, subgroup analysis, and sensitivity assessments enhances the depth of our findings, providing valuable insights for further research.
Subject(s)
Diet , Hyperuricemia , Life Style , Nutrition Surveys , Uric Acid , Humans , Hyperuricemia/blood , Hyperuricemia/epidemiology , Female , Male , Cross-Sectional Studies , Nutrition Surveys/methods , Nutrition Surveys/statistics & numerical data , Middle Aged , Adult , Uric Acid/blood , Diet/methods , Diet/statistics & numerical data , Oxidative Stress , Prevalence , AgedABSTRACT
INTRODUCTION: Developmental delay at an early age indicates the probability of continued problems after school age. Hypertensive disorders of pregnancy (HDP) are associated with developmental delays in offspring, with inconsistent outcomes. Neonatal outcomes vary according to HDP exposure and are relevant to development in later years. Here we aimed to clarify the relationship between HDP and developmental delay in offspring and whether neonatal outcomes mediate this association. MATERIAL AND METHODS: We used data from 5934 mother-child pairs from the Tohoku Medical Megabank Project Birth and Three-Generation Cohort Study, a prospective cohort study conducted in Japan between July 2013 and March 2017. The Ages and Stages Questionnaires, third edition, at 24 and 42 months of age, measured developmental delay in five areas. We performed multivariate quasi-Poisson regression and causal mediation analysis by neonatal outcomes. RESULTS: At 24 months of age, compared to offspring born from normotensive mothers, offspring born from HDP-affected mothers were more likely to experience developmental delay (risk ratio [RR] 1.29, 95% confidence interval [CI]: 1.09-1.52) in the areas of communication (RR 1.21, 95% CI: 1.00-1.45) and personal-social (RR 1.15, 95% CI: 1.03-1.28). This association was mediated by neonatal outcomes: preterm birth, neonatal asphyxia, NICU admission, and neonatal small head circumference. No association was observed between HDP and developmental delay at 42 months of age. CONCLUSIONS: Exposure to HDP during fetal life is associated with offspring developmental delay. This association is partly mediated by neonatal outcomes.
Subject(s)
Developmental Disabilities , Hypertension, Pregnancy-Induced , Humans , Female , Pregnancy , Developmental Disabilities/epidemiology , Japan/epidemiology , Hypertension, Pregnancy-Induced/epidemiology , Prospective Studies , Adult , Male , Infant, Newborn , Child, Preschool , Cohort Studies , Prenatal Exposure Delayed Effects , Pregnancy Outcome/epidemiologyABSTRACT
Orbital angular momentum (OAM) mode division multiplexing (MDM) systems can support large-capacity and high-speed rate information transmission, in which the OAM mode conversion devices play an important role. In this paper, the mode conversion principle of magneto-optical fiber-based long-period grating (MOF-LPG) is analyzed for further developing new magneto-optical (MO) OAM mode converters, including three types of C P 01 to O A M ±1,1, O A M ±1,1 to O A M ±2,1, and O A M ±1,1 to C P 02. It is shown that the magnetic tunability of the mode converters through the propagation constants of the eigenmodes is useful for compensating for process errors and increasing the operating wavelength range. The implementation of MOF-LPGs is also discussed from the aspect of the prospective experiments.
ABSTRACT
As one of the fundamental physical quantities, temperature is extremely important in various fields. In order to study the temperature sensing characteristics of dual-emitting center phosphors, Bi3+-doped and Bi3+/Sm3+-doped Sr2Ga2GeO7 phosphors were synthesized by high-temperature solid-phase method. Under 312 nm excitation, the Sr2Ga2GeO7:Bi3+ phosphor exhibits a blue broadband emission corresponding to the 3P1 â 1S0 transition of Bi3+ ions. By testing the temperature change spectrum of phosphors, it was found that Bi3+ exhibited strong thermal sensitivity. However, due to the fact that single ion doped phosphors are easily affected by other factors when applied to the field of temperature sensing, based on the thermal sensitivity of Bi3+, Sm3+ with low temperature sensitivity was selected as the co-doped ion, and it was found that the two ions had different thermal quenching characteristics when the temperature change spectrum was tested. Using the temperature detection method based on the fluorescence intensity ratio (FIR) of the dual emission centers, it was found that the best absolute sensitivity Sa was 3.125% K-1 and the maximum relative sensitivity Sr was 1.275% K-1 in the range of 303-423 K. These results show that Sr2Ga2GeO7:Bi3+/Sm3+ phosphors have broad application prospects in the field of optical temperature sensing.
Subject(s)
Gallium , Luminescence , Luminescent Agents , Samarium , Strontium , Temperature , Strontium/chemistry , Samarium/chemistry , Luminescent Agents/chemistry , Luminescent Agents/chemical synthesis , Gallium/chemistry , Bismuth/chemistry , Germanium/chemistry , Luminescent MeasurementsABSTRACT
Identifying the primary source of heavy metals (HMs) pollution and the key pollutants is crucial for safeguarding eco-health and managing risks in industrial vicinity. For this purpose, this investigation was carried out to investigate the pollution area identification with soil static environmental capacity (QI), receptor model-oriented critical sources, and Monte Carlo simulation (MCS) based probabilistic environmental and human health hazards associated with HMs in agricultural soils of Narayanganj, Bangladesh. The average concentration of Cr, Ni, Cu, Cd, Pb, Co, Zn, and Mn were 98.67, 63.41, 37.39, 1.28, 23.93, 14.48, 125.08, and 467.45 mg/kg, respectively. The geoaccumulation index identified Cd as the dominant metal, indicating heavy to extreme contamination in soils. The QI revealed that over 99% of the areas were polluted for Ni and Cd with less uncertain regions whereas Cr showed a significant portion of areas with uncertain pollution status. The positive matrix factorization (PMF) model identified three major sources: agricultural (29%), vehicular emissions (25%), and industrial (46%). The probabilistic assessment of health hazards indicated that both carcinogenic and non-carcinogenic risks for adult male, adult female, and children were deemed unacceptable. Moreover, children faced a higher health hazard compared to adults. For adult male, adult female, and children, industrial operations contributed 48.4%, 42.7%, and 71.2% of the carcinogenic risks, respectively and these risks were associated with Ni and Cr as the main pollutants of concern. The study emphasizes valuable scientific insights for environmental managers to tackle soil pollution from HMs by effectively managing anthropogenic sources. It could aid in devising strategies for environmental remediation engineering and refining industry standards.
Subject(s)
Metals, Heavy , Soil Pollutants , Soil , Metals, Heavy/analysis , Soil Pollutants/analysis , Soil/chemistry , Humans , Environmental Monitoring , Bangladesh , Risk Assessment , Environmental Pollution , Agriculture , Monte Carlo MethodABSTRACT
BACKGROUND: The cellular and molecular dynamics of human prepuce are crucial for understanding its biological and physiological functions, as well as the prevention of related genital diseases. However, the cellular compositions and heterogeneity of human prepuce at single-cell resolution are still largely unknown. Here we systematically dissected the prepuce of children and adults based on the single-cell RNA-seq data of 90,770 qualified cells. RESULTS: We identified 15 prepuce cell subtypes, including fibroblast, smooth muscle cells, T/natural killer cells, macrophages, vascular endothelial cells, and dendritic cells. The proportions of these cell types varied among different individuals as well as between children and adults. Moreover, we detected cell-type-specific gene regulatory networks (GRNs), which could contribute to the unique functions of related cell types. The GRNs were also highly dynamic between the prepuce cells of children and adults. Our cell-cell communication network analysis among different cell types revealed a set of child-specific (e.g., CD96, EPO, IFN-1, and WNT signaling pathways) and adult-specific (e.g., BMP10, NEGR, ncWNT, and NPR1 signaling pathways) signaling pathways. The variations of GRNs and cellular communications could be closely associated with prepuce development in children and prepuce maintenance in adults. CONCLUSIONS: Collectively, we systematically analyzed the cellular variations and molecular changes of the human prepuce at single-cell resolution. Our results gained insights into the heterogeneity of prepuce cells and shed light on the underlying molecular mechanisms of prepuce development and maintenance.
Subject(s)
Endothelial Cells , Gene Expression Regulation , Adult , Humans , Cell Communication/genetics , Gene Regulatory Networks , Single-Cell Analysis , Bone Morphogenetic ProteinsABSTRACT
The innovation of liquid biopsy holds great potential to revolutionise cancer management through early diagnosis and timely treatment of cancer. Integrative analysis of different tumour-derived omics data (such as genomics, epigenetics, fragmentomics, and proteomics) from body fluids for cancer detection and monitoring could outperform the analysis of single modality data alone. In this review, we focussed on the discussion of early cancer detection and molecular residual disease surveillance based on multi-omics data of blood. We summarised diverse types of tumour-derived components, current popular platforms for profiling cancer-associated signals, machine learning approaches for joint analysis of liquid biopsy data, as well as multi-omics-based early detection of cancers, molecular residual disease monitoring, and treatment response surveillance. We also discussed the challenges and future directions of multi-omics-based liquid biopsy. With the development of both experimental protocols and computational methods dedicated to liquid biopsy, the implementation of multi-omics strategies into the clinical workflow will likely benefit the clinical management of cancers including decision-making guidance and patient outcome improvement.
Subject(s)
Multiomics , Neoplasms , Humans , Genomics/methods , Proteomics , Neoplasms/pathology , Epigenomics , Computational Biology/methodsABSTRACT
Multi-omics allows the systematic understanding of the information flow across different omics layers, while single omics can mainly reflect one aspect of the biological system. The advancement of bulk and single-cell sequencing technologies and related computational methods for multi-omics largely facilitated the development of system biology and precision medicine. Single-cell approaches have the advantage of dissecting cellular dynamics and heterogeneity, whereas traditional bulk technologies are limited to individual/population-level investigation. In this review, we first summarize the technologies for producing bulk and single-cell multi-omics data. Then, we survey the computational approaches for integrative analysis of bulk and single-cell multimodal data, respectively. Moreover, the databases and data storage for multi-omics, as well as the tools for visualizing multimodal data are summarized. We also outline the integration between bulk and single-cell data, and discuss the applications of multi-omics in precision medicine. Finally, we present the challenges and perspectives for multi-omics development.
Subject(s)
Computational Biology/methods , Precision Medicine/methods , Humans , Single-Cell Analysis/methodsABSTRACT
PURPOSE: Bone health and body composition share several common mechanisms like oxidative stress and inflammation. Anthocyanins have antioxidant and anti-inflammatory properties. We have reported that anthocyanins are associated with better body composition in children, but the associations with bone health have not been elucidated. We aimed to explore the association of anthocyanins with bone mineral content (BMC) and bone mineral density (BMD) at multiple sites in children. METHODS: In this cross-sectional study, 452 Chinese children aged 6-9 years were recruited. A validated 79-item food frequency questionnaire was used to collect dietary information. BMC and BMD at multiple sites (whole body; whole body excluding head, WBEH; limbs; arms; legs) were measured by dual-energy X-ray. RESULTS: Higher dietary intake of total anthocyanidins (per one standard deviation increase) was associated with a 1.28-13.6 g (1.31-1.60%, compared to median) higher BMC at all sites and a 3.61-6.96 mg (0.65-0.90%) higher BMD at the whole body, WBEH, and arm sites after controlling for a number of possible covariates. The results were similar and more pronounced for cyanidin, but not for delphinidin and peonidin. Higher dietary intake of cyanidin (per one standard deviation increase) was associated with a 1.33-15.4 g (1.48-1.68%) higher BMC at all sites and a 4.15-7.77 mg (0.66-1.00%) higher BMD at all sites except the legs. No statistically significant associations with BMC or BMD were found for dietary intake of delphinidin and peonidin. CONCLUSIONS: Higher dietary intake of total anthocyanidins and cyanidins were associated with higher BMC and BMD in Chinese children.