The hypergraph neural network (HGNN) is an emerging powerful tool for modeling and learning complex, high-order correlations among entities upon hypergraph structures. While existing HGNN-based approaches excel in modeling high-order correlations among data using hyperedges, they often have difficulties in distinguishing diverse semantics ( e.g.
View Article and Find Full Text PDFBackground: China is an aging society, and the older population is at a higher risk of influenza infection and influenza-related mortality. However, there is limited knowledge regarding the aging of influenza epidemics, which is crucial for estimating the disease burden.
Methods: We collected weekly influenza surveillance data from 2005/06 to 2016/17, and quantified the aging of influenza-like illness (ILI) and influenza virus-positive cases in China via the mean age of the influenza cases and the proportion of individuals aged 65 and above among the influenza cases.
Intervening in mitochondrial oxidative phosphorylation (OXPHOS) has emerged as a potential therapeutic strategy for certain types of cancers. Employing kinome-based CRISPR screen, we find that knockout of dual-specificity tyrosine phosphorylation-regulated kinase 1A (DYRK1A) synergizes with OXPHOS inhibitor IACS-010759 in liver cancer cells. Targeting DYRK1A combined with OXPHOS inhibitors activates TGF-β signaling, which is crucial for OXPHOS-inhibition-triggered cell death.
View Article and Find Full Text PDFProc Natl Acad Sci U S A
January 2025
Ferroptosis, a unique form of iron-dependent cell death triggered by lipid peroxidation accumulation, holds great promise for cancer therapy. Despite the crucial role of GPX4 in regulating ferroptosis, our understanding of GPX4 protein regulation remains limited. Through FACS-based genome-wide CRISPR screening, we identified MALT1 as a regulator of GPX4 protein.
View Article and Find Full Text PDFTumor-initiating cells (TICs) possess the ability to evade anti-tumor immunity, potentially explaining many failures of cancer immunotherapy. Here, we identify CD49f as a prominent marker for discerning TICs in hepatocellular carcinoma (HCC), outperforming other commonly used TIC markers. CD49f-high TICs specifically recruit tumor-promoting neutrophils via the CXCL2-CXCR2 axis and create an immunosuppressive milieu in the tumor microenvironment (TME).
View Article and Find Full Text PDFBackground: Gallbladder cancer (GBC) is the most common and lethal malignancy of the biliary tract that lacks effective therapy. In many GBC cases, infiltration into adjacent organs or distant metastasis happened long before the diagnosis, especially the direct liver invasion, which is the most common and unfavorable way of spreading.
Methods: Single-cell RNA sequencing (scRNA-seq), spatial transcriptomics (ST), proteomics, and multiplexed immunohistochemistry (mIHC) were performed on GBC across multiple tumor stages to characterize the tumor microenvironment (TME), focusing specifically on the preferential enrichment of neutrophils in GBC liver invasion (GBC-LI).
Neutrophils, the most abundant and efficient defenders against pathogens, exert opposing functions across cancer types. However, given their short half-life, it remains challenging to explore how neutrophils adopt specific fates in cancer. Here, we generated and integrated single-cell neutrophil transcriptomes from 17 cancer types (225 samples from 143 patients).
View Article and Find Full Text PDFBackground & Aims: Despite the increasing number of treatment options available for liver cancer, only a small proportion of patients achieve long-term clinical benefits. Here, we aim to develop new therapeutic approaches for liver cancer.
Methods: A compound screen was conducted to identify inhibitors that could synergistically induce senescence when combined with cyclin-dependent kinase (CDK) 4/6 inhibitor.
Shotgun phosphoproteomics enables high-throughput analysis of phosphopeptides in biological samples. One of the primary challenges associated with this technology is the relatively low rate of phosphopeptide identification during data analysis. This limitation hampers the full realization of the potential offered by shotgun phosphoproteomics.
View Article and Find Full Text PDFIEEE Trans Pattern Anal Mach Intell
April 2024
The traditional 3D object retrieval (3DOR) task is under the close-set setting, which assumes the categories of objects in the retrieval stage are all seen in the training stage. Existing methods under this setting may tend to only lazily discriminate their categories, while not learning a generalized 3D object embedding. Under such circumstances, it is still a challenging and open problem in real-world applications due to the existence of various unseen categories.
View Article and Find Full Text PDFExploring the relative importance of different routes in SARS-CoV-2 transmission is crucial in infection prevention. However, even in the same environmental setting, the relative importance of different routes has varied in different studies. We hypothesize that respiratory aerosol size and number distribution might play a key role.
View Article and Find Full Text PDFOrganoid models have the potential to recapitulate the biological and pharmacotypic features of parental tumors. Nevertheless, integrative pharmaco-proteogenomics analysis for drug response features and biomarker investigation for precision therapy of patients with liver cancer are still lacking. We established a patient-derived liver cancer organoid biobank (LICOB) that comprehensively represents the histological and molecular characteristics of various liver cancer types as determined by multiomics profiling, including genomic, epigenomic, transcriptomic, and proteomic analysis.
View Article and Find Full Text PDFUnlabelled: KRAS mutations are causally linked to protumor inflammation and are identified as driving factors in tumorigenesis. Here, using multiomics data gathered from a large set of patients, we showed that KRAS mutation was associated with a specific landscape of alternative mRNA splicing that connected to myeloid inflammation in intrahepatic cholangiocarcinoma (iCCA). Then, we identified a negative feedback mechanism in which the upregulation of interleukin 1 receptor antagonist (IL1RN)-201/203 due to alternative splicing confers vital anti-inflammatory effects in KRAS-mutant iCCA.
View Article and Find Full Text PDFWhat Is Already Known About This Topic?: The first nationwide wave of coronavirus disease 2019 (COVID-19), driven by the Omicron variant, has largely subsided. However, subsequent epidemic waves are inevitable due to waning immunity and the ongoing evolution of the severe acute respiratory syndrome coronavirus 2.
What Is Added By This Report?: Insights gleaned from other nations offer guidance regarding the timing and scale of potential subsequent waves of COVID-19 in China.
Shotgun phosphoproteomics enables high-throughput analysis of phosphopeptides in biological samples, but low phosphopeptide identification rate in data analysis limits the potential of this technology. Here we present DeepRescore2, a computational workflow that leverages deep learning-based retention time and fragment ion intensity predictions to improve phosphopeptide identification and phosphosite localization. Using a state-of-the-art computational workflow as a benchmark, DeepRescore2 increases the number of correctly identified peptide-spectrum matches by 17% in a synthetic dataset and identifies 19%-46% more phosphopeptides in biological datasets.
View Article and Find Full Text PDFcld-CASP3: cleaved caspase 3; cld-PARP: cleaved PARP; DTP: drug tolerant persister; GO: Gene Ontology; GTEx: The Genotype-Tissue Expression; HCC: hepatocellular carcinoma; HCQ: hydroxychloroquine; IC50: half maximal inhibitory concentration value; KEGG: Kyoto Encyclopedia of Genes and Genomes; LAPTM5: lysosomal protein transmembrane 5; NT: non-targeting; PDC: patient-derived primary cell lines; PDO: patient-derived primary organoid; TCGA: The Cancer Genome Atlas.
View Article and Find Full Text PDFBackground: Immune microenvironment is well recognized as a critical regulator across cancer types, despite its complex roles in different disease conditions. Intrahepatic cholangiocarcinoma (iCCA) is characterized by a tumor-reactive milieu, emphasizing a deep insight into its immunogenomic profile to provide prognostic and therapeutic implications.
Methods: We performed genomic, transcriptomic, and proteomic characterization of 255 paired iCCA and adjacent liver tissues.
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant has become the dominant lineage worldwide. Experimental studies have shown that SARS-CoV-2 Omicron variant is more stable on various environmental surfaces than the ancestral strains of SARS-CoV-2. However, the influences on the role of the contact route in SARS-CoV-2 transmission are still unknown.
View Article and Find Full Text PDFGraph Neural Networks have attracted increasing attention in recent years. However, existing GNN frameworks are deployed based upon simple graphs, which limits their applications in dealing with complex data correlation of multi-modal/multi-type data in practice. A few hypergraph-based methods have recently been proposed to address the problem of multi-modal/multi-type data correlation by directly concatenating the hypergraphs constructed from each single individual modality/type, which is difficult to learn an adaptive weight for each modality/type.
View Article and Find Full Text PDFIEEE Trans Pattern Anal Mach Intell
February 2023
Graph-based semi-supervised learning methods have been used in a wide range of real-world applications, e.g., from social relationship mining to multimedia classification and retrieval.
View Article and Find Full Text PDFIntrahepatic cholangiocarcinoma (iCCA) is a highly heterogeneous cancer with limited understanding of its classification and tumor microenvironment. Here, by performing single-cell RNA sequencing on 144,878 cells from 14 pairs of iCCA tumors and non-tumor liver tissues, we find that S100P and SPP1 are two markers for iCCA perihilar large duct type (iCCA) and peripheral small duct type (iCCA). S100P + SPP1- iCCA has significantly reduced levels of infiltrating CD4 T cells, CD56 NK cells, and increased CCL18 macrophages and PD1CD8 T cells compared to S100P-SPP1 + iCCA.
View Article and Find Full Text PDFHydrogen sulfide (HS) is an active physiological molecule, and its intracellular level has great significance to life functions. In this study, an effective and sensitive method was developed for HS sensing with dark field microscopy (DFM). The proposed method employed AuNPs as the signal source, DFM as the readout system, and an intelligence algorithm as the image processing and output systems, respectively.
View Article and Find Full Text PDFThe continuous emergence of drug-target interaction data provides an opportunity to construct a biological network for systematically discovering unknown interactions. However, this is challenging due to complex and heterogeneous correlations between drug and target. Here, we describe a heterogeneous hypergraph-based framework for drug-target interaction (HHDTI) predictions by modeling biological networks through a hypergraph, where each vertex represents a drug or a target and a hyperedge indicates existing similar interactions or associations between the connected vertices.
View Article and Find Full Text PDFIn this work, an auto-identify sensor was constructed for rapid and high-precision detection of L-histidine. The proposed strategy is based on the auto-identify algorithm and the aggregation of alkynyl and azide functionalized gold nanoparticles induced by the Cu catalyzed azides and alkynes cycloaddition (CuAAC) reaction. Specially, the color of scattering light spots for the aggregated gold nanoparticle (AuNPs) caused by CuAAC reaction was quite different from that of the monomers.
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