Artificial cell shells can achieve protection, identification, measurement, and manipulation of cells, but most cell encapsulation methods fail to control shell thickness, directly limiting the shell function in practical applications. The in-situ polymerization method has the potential to control the encapsulation shell but lacks chemical driving forces to enable shell thickness from nanoscale to micrometer-scale. The micrometer-scale shell can enhance the functionality in cell encapsulation and extend its applications to broader fields. In this work, we utilized the efficient and mild thiol-alkene click reaction to construct a micrometer-scale shell and encapsulate microbial cells into large-sized polymer microspheres. The encapsulated microbial cells are larger than the coexisting emulsion colloids and particulate impurities, thereby achieving "Convert microbial cell detection to polymer particle counting" and providing a new perspective for the application of micrometer-scale artificial cell shells.

Urinary tract infection (UTI) is one of the most common diseases during pregnancy, caused by multiple microbial pathogens and posing significant risks to both maternal and fetal outcomes. Current diagnostic methods are limited by prolonged detection times or require a certain degree of sample preprocessing, making it difficult to meet the needs of personalized at-home testing for pregnant patients. To more effectively address this requirement, we developed an intelligent point-of-care (POC) testing platform based on the composite microspherebased optical signature-enhanced detection (CMOSED), enabling highly sensitive and real-time personalized diagnosis of three major bacterial pathogens. The platform employs four carboxyl-functionalized polystyrene (PS) microsphere size classes, including three small antigen-coded microspheres and one large antibody-carrying microsphere. Through the synergistic interaction between the microsphere lensing effect and the photonic nanojet (SIMLN), the system achieves high-precision target recognition even within complex urinary matrices; through the dynamic response of microsphere assemblies to varying target concentrations, it enables accurate detection of analyte levels; through the AI-assisted diagnostic system for Urinary Tract Infections in Pregnancy (AID-UTIP), it achieves rapid, personalized home-based testing. The system achieves high sensitivity and specificity detection for the three major UTI pathogens within 30 min at a cost below $1.5 per test. A prospective clinical evaluation (n = 25) demonstrated detection accuracies of 96% for UPEC, 92% for Klebsiella pneumoniae, and 92% for Enterococcus faecalis. By integrating diverse antigen-antibody combinations, this method offers a rapid, cost-effective, and extensible strategy for multi-pathogen detection, representing a promising paradigm for intelligent, decentralized infectious disease diagnostics in home-based pregnancy care.

In recent years, prostate cancer (PCa) has been one of the most prevalent malignancies, significantly impacting men's health and quality of life. The concentration of sarcosine in clinical urine samples serves as an early indicator of PCa, facilitating the screening of individuals with the disease. This paper presents a portable and lowcost handheld fluorescence detector for the on-site detection of sarcosine. The device employs an orthogonal optical path configuration, utilizing a 365 nm light-emitting diode (LED) as the excitation light source, and a Si PIN photodiode coupled with an AS7341 spectral sensor for photoelectric conversion, enabling straightforward analysis of fluorescence intensity and wavelength. With overall dimensions of 9.4 & times; 6.5 & times; 5.0 cm3, the total cost of the device is only $27. Methodologically, green fluorescent CdZnTeS quantum dots (QDs), which exhibit high sensitivity to H2O2, were selected as the substrate probe. Sarcosine oxidase (SOx) catalyzes the oxidation of sarcosine, generating H2O2, which subsequently quenches QDs. Under optimal experimental conditions, the probe demonstrated a strong linear relationship with sarcosine concentrations ranging from 1 to 100 mu M, achieving a detection limit of 0.72 mu M. It also demonstrates favorable selectivity and anti-interference capability. Furthermore, the device has been successfully applied to the quantitative detection of sarcosine in real samples. It effectively distinguishes PCa patients from healthy individuals, indicating its broad application prospects in disease screening.

Respiratory pathogens jeopardize population health, particularly high-risk groups. CRISPR-Cas systems, as novel nucleic acid detection platforms, offer timely identification and have become a major research focus. This study presents a novel diagnostic workflow that combines recombinase polymerase amplification (RPA) for pre-amplification of pathogen nucleic acids with CRISPR-based detection. By combining microfluidic technology and portable imaging devices, this study developed a multiplex assay capable of simultaneously detecting seven clinically relevant pathogens in a single sample, including influenza A virus (FluA), influenza B virus (FluB), respiratory syncytial virus (HRSV) A and B, mycoplasma pneumoniae (MP), adenovirus (HAdv), and parainfluenza virus (HPIVs). Utilizing the POCT-CRISPR platform, simultaneous detection of seven respiratory pathogens can be achieved within approximately 30 min, achieving detection limits of 0.1-1 fM. This method streamlines the detection process, significantly reducing both the complexity of operations and the overall detection time. Clinical cohort validation demonstrated a detection efficiency of 99.63% sensitivity and 100% specificity. These results confirm the effectiveness and reliability of the detection method. Additionally, the 7-virus panel is estimated at approximately $32 per sample, a cost competitive with commercial multiplex qPCR detection kits ($15-$110 per sample) and substantially more economical than integrated cartridge-based syndromic platforms. The platform features simple operation, cost-effectiveness, short turnaround time, and reliable detection performance, making it highly suitable for point-of-care testing (POCT) at the grassroots level.

Cancer-associated fibroblasts (CAFs) play a crucial role in the tumor microenvironment (TME) by influencing tumor progression, metastasis, and therapy resistance. Accumulating evidence suggests that CAFs undergo senescence, which can impact their effects on the TME. Here, we developed a machine learning-based prediction model, the Cellular Senescence Prediction Model (CSPM), to accurately identify senescent CAFs (sCAFs) based on single-cell RNA sequencing data. In colorectal cancer (CRC), the abundance of sCAFs strongly correlated with impaired chemotherapy responsiveness and poor prognosis. In preclinical models, including subcutaneous tumors, patient-derived organoids (PDOs), patient-derived organoid xenografts (PDOXs), and orthotopic tumors, sCAFs mediated chemoresistance through the senescence-associated secretory phenotype (SASP), with IL6 and CXCL12 being key contributors. Macrophage-derived IL1B triggered CAF senescence through the IL1B-IL1R1 interaction, promoting the accumulation of sCAFs in tumors. Spatial transcriptomics and multiplex immunohistochemistry revealed colocalization of IL1B+ macrophages and IL1R1+ sCAFs in the tumor stroma. Functional studies using fibroblast-specific Il1r1 knockout mice further confirmed that macrophage-derived IL1B induces CAF senescence via IL1R1, leading to SASP-driven chemotherapy resistance. These findings highlight the critical role of sCAFs in CRC chemoresistance and suggest that targeting the IL1B-IL1R1 axis may offer a promising strategy to enhance chemotherapy efficacy in CRC.

BackgroundMicrovascular invasion (MVI) is closely related to the recurrence and metastasis of hepatocellular carcinoma (HCC), but the underlying cellular mechanism remains largely elusive. This study aims to elucidate the regional cellular discrepancy between MVI-positive (MVI+) and MVI-negative (MVI-) HCC by integrating Spatial transcriptomics (ST) and spatial metabolomics (SM).Methods and findingsST and SM were performed on six tissue samples from four patients (including 2 MVI+, 2 MVI-, and 2 paratumor tissues), with the integration of 79 public single-cell RNA sequencing datasets of HCC. Patient identity was used as a covariate in the linear equation for regional differentially expressed gene analysis with the ST data. Clinical validation was conducted through multiplex immunofluorescence staining in 79 patients, together with external validation in the cancer genome atlas (TCGA)-liver hepatocellular carcinoma (LIHC) cohort (n = 299) and an independent microarray dataset (n = 62). For cell-type-specific metabolic profiling, spatial transcriptomic-metabolic registration was performed. The functional roles of key metabolites were further validated in vitro using inflammatory cancer-associated fibroblasts (iCAFs) derived from hepatic stellate cells (HSCs) and primary CAFs through co-culture models and various functional assays assessing cell proliferation, migration, and invasion. In the tumor lesion, a malignant STMN1+HMGN2+GPC3+ cell subtype enriched in MVI+ HCC was identified, which exhibited enhanced proliferative activity and was associated with poor prognosis. This finding was further confirmed in a local cohort of 79 patients, where multiplex immunofluorescence staining for the three genes (STMN1, HMGN2, and GPC3) showed significantly higher expression in the MVI+ group than in the MVI- group (p = 0.046). Integrated SM analysis further revealed that this cell population underwent metabolic reprogramming characterized by suppressed glycerolipid metabolism. In the tumor capsule, iCAFs-related genes were downregulated in MVI+ cases, and iCAFs were located distally from the tumor boundary. Spatial metabolite mapping showed a strong correlation between taurine and iCAFs, and functional assays demonstrated that taurine promotes HCC proliferation and migration by suppressing iCAF activity. One limitation of this study is the small sample size of spatial omics data, which hinders a more complete molecular functional analysis of the STMN1+HMGN2+GPC3+ cell subtype and iCAFs in MVI+ HCC. Larger-scale ST cohorts are required to further validate and expand the findings of this study.ConclusionsThis integrative spatial atlas proposes a hypothesis that there exists a highly proliferative and metabolically reprogrammed malignant cell subtype in the tumor lesion of MVI+ HCC, and that taurine in the tumor capsule modulates iCAF activity to influence tumor progression. The exploratory results provide mechanistic insights into MVI-related HCC progression and offer potential avenues for targeted therapeutic intervention of MVI+ HCC.

Patient-derived xenograft (PDX) models constructed by noninvasively accessible circulating tumor cells (CTCs) serve as pivotal and invaluable tools for oncology research and precision medicine. However, the rarity of CTCs in blood and their limited proliferation ability present significant challenges for establishing patient CTC-derived xenograft (CDX) models. In this study, a novel 3D cellulose scaffold is developed for efficient isolation and in situ culture of CTCs, with the aim of constructing CDX models. Characterized by a macroporous and flexible structure, the 3D cellulose scaffold achieves high-efficiency CTC capture while maintaining cell viability. Its excellent biocompatibility and permeability further promote the rapid and in situ growth of CTCs. Importantly, the self-supporting and biodegradable scaffold allows for direct implantation into immunodeficient mice without leaving any residual material. This 3D cellulose scaffold has been successfully employed to construct CDX models from breast cancer patients. The application of this platform may enhance our understanding of metastasis mechanisms and offer significant benefits for cancer therapy.

Abstract Quantifying CD11b in whole blood from patients with sepsis is analytically challenging because conventional preprocessing can perturb activation state and bias the measured surface-marker abundance. To address this limitation, we report a biomimetic-acoustic cooperative platform for rapid CD11b-based neutrophil activation readout. CD11b expression is transduced into a quantitative microsphere-depletion signal using a competitive microsphere format, and residual microspheres are identified and counted by an object-detection model assisted by frequency-domain image-quality features to improve robustness during tilted-chip readout. A lotus-leaf-replica ceiling establishes pump-free transport within the flow-velocity window required for acoustic enrichment. In an expanded prospective pilot cohort of 36 clinical samples, the assay showed exploratory discrimination between qSOFA-defined groups, with an AUC of 0.92 (95% CI, 0.80–0.99) and a sample-to-answer time of around 40 min. These results establish an analytical proof of concept for this biomimetic-acoustic cooperative platform and provide preliminary evidence of clinical feasibility.

Background: The tumor-resident microbiome plays a pivotal role in shaping the tumor immune microenvironment; however, its relationship with the host transcriptome and the response to immune checkpoint inhibitors (ICIs) remains largely uncharacterized in non-small cell lung cancer (NSCLC). This study aimed to elucidate the relationship between tissue-resident microbiota, host transcriptomic alterations, and immunotherapy response in NSCLC. Methods: Paired tumor (T) and paracancerous tissue (PT) samples from patients with NSCLC were analyzed using 2bRAD-M and bulk RNA sequencing to generate comprehensive microbiome and transcriptome profiles. The conditional mutual information algorithm was employed to systematically investigate intratumoral microbe-host interactions. Associations between key microbes and patient prognosis, ICI response, and response to epidermal growth factor receptor (EGFR)-targeted therapy were assessed across four independent local clinical cohorts. Results: Higher microbial richness, α-diversity, and β-diversity were observed in PT samples than in T samples. Specifically, PT-resident Bradyrhizobium and Prevotella were identified as key bacterial taxa significantly associated with immune cell populations, including CD8+ T cells, natural killer cells, and activated dendritic cells. Among these, PT-resident Prevotella, but not Bradyrhizobium, was independently associated with improved prognosis of patients with NSCLC and ICI response in both local clinical sets and public datasets. Furthermore, a combined diagnostic model integrating PT-resident Prevotella abundance with routine clinical blood indicators demonstrated markedly superior predictive performance for ICI response compared with the conventional biomarker PD-L1. By contrast, PT-resident Prevotella exhibited no association with treatment response in the EGFR-targeted therapy cohort. Conclusion: PT-resident Prevotella is strongly associated with the prognosis and ICI response in patients with NSCLC. Moreover, integration of PT-resident Prevotella with routine clinical blood indicators holds promise as a potential auxiliary diagnostic tool to facilitate personalized immunotherapy in NSCLC.

Hepatocellular carcinoma (HCC) features a tumor immunosuppressive microenvironment (TIME) and limited response to immune checkpoint inhibitors (ICIs). To address this, we develop ultrasound-responsive nanoparticles by encapsulating PD-L1-targeting small interfering RNA (siRNA) and sonodynamic metal-organic frameworks (MOFs) into bacterial membrane vesicles (BMVs) derived from Akkermansia muciniphila. The siRNA-MOF@BMV (SMB) demonstrates HCC-specific accumulation via N-acetylgalactosamine (GalNAc) and induces pyroptosis through NLRP3/Caspase-1/GSDMD pathway activation under ultrasound, releasing tumor antigens. Simultaneously, SMB further induces trained immunity in tumor-associated macrophages (TAMs), promoting CXCL9+ phenotypes that enhance antigen presentation and chemotaxis capacity. This increases cytotoxic CD8+ T cell infiltration and reduces exhausted T cells, reshaping the TIME. Furthermore, SMB exhibits superior tumor suppression compared to clinical ICIs through systematic evaluations in orthotopic HCC mouse models, primary HCC models, patient-derived xenograft (PDX), and organoid models. SMB presents a multifunctional immunotherapeutic strategy integrating targeted pyroptosis induction, innate immune training, and ICI delivery, representing a potent immunotherapeutic agent for HCC.

Serum alpha-fetoprotein (AFP) is one of the most widely used clinical diagnostic and prognostic biomarkers for hepatocellular carcinoma (HCC). However, its potential role in guiding treatment strategies remains limited, largely because the tumor microenvironment of AFP-positive HCC has not been well characterized. We integrated multiple types of public transcriptomic data to systematically delineate the features of AFP-positive HCC and their relevance to immunotherapy. Specifically, we used single-cell RNA-seq datasets, bulk RNA-seq data, and spatial transcriptomic data from several independent public cohorts. We found that STMN1+ and AFP+ malignant cell subsets were enriched in AFP-positive tumor tissues, while CYP3A4+ malignant cells were enriched in AFP-negative HCC. Regarding the immune microenvironment, we focused on two key immune cell types: regulatory CD4+ T cells (Tregs) and dendritic cells (DCs). We found that both Tregs and CXCL10+ DCs (DCs with high CXCL10 expression) were elevated in AFP-positive HCC. Moreover, these two cell types showed a highly significant positive correlation across multiple datasets. Spatial transcriptomic analysis revealed their spatial proximity, suggesting that the interaction between CXCL10+ DCs and Tregs shaped the immunosuppressive environment in AFP-positive HCC. Analysis of single-cell and spatial transcriptome data from patients receiving immunotherapy showed that the increased composition and spatial proximity of these two cell types were associated with non-response to immunotherapy. Our study, based on the computation and analysis of public data, revealed that the interaction between CXCL10+ DCs and Tregs may serve as a crucial factor contributing to the formation of the immunosuppressive microenvironment of AFP-positive HCC. This not only enhances researchers' understanding of the AFP-positive HCC microenvironment but also provides a potential immunotherapy target for AFP-positive HCC.

Colorectal cancer is a heterogeneous disease that develops through a stepwise accumulation, yet the underlying mechanisms at single-cell resolution remain unclear. In this study, we profiled 751,531 single-cell transcriptomes, spatial transcriptomics, and snMultiomes from 142 multistage samples, revealing the cellular and molecular alterations and dynamic intercellular cross-talk during colorectal cancer development. Additionally, we created a colorectal cancer single-cell expression quantitative trait locus (sc-eQTL) map identifying 16,833 significant pairs across 28 cell subtypes, with more than 76% of sc-eQTLs being cell type-specific and fewer than 15% detectable in bulk datasets. A polygenic risk score derived from sc-eQTLs substantially improved colorectal cancer risk prediction. We prioritized rs4794979 that is associated with an increased colorectal cancer risk (OR = 1.11, P = 2.04 × 10-12) by promoting LGALS9 expression mediated by ELK1. Elevated LGALS9 in epithelia interacts with SLC1A5 on fibroblasts, promoting transformation into cancer-associated fibroblasts and simultaneously inducing CD8+ T-cell exhaustion via the LGALS9-TIM3 axis, thereby facilitating colorectal cancer development. Blocking the LGALS9-TIM3 axis enhanced anti-PD-1 therapy to inhibit colorectal cancer progression. SIGNIFICANCE:Our study provides a valuable resource, including a dynamic single-cell landscape and a robust colorectal cancer sc-eQTL atlas, and elucidates the cell type-specific regulation and important cross-talk mechanisms between cell types in the tumor microenvironment, offering deep insights into colorectal cancer tumorigenesis and targeted therapies.

Angiogenic and MHC-II TAM signatures correlate with different patients’ survivals, Related to Figure 1.

Supplementary Figure 23 shows single-cell eQTL colocalization with risk loci of colorectal cancer.

The mutually exclusive pattern of angiogenic and MHC-II also existed in identified TAM subsets, Related to Figure1

Gene expression signatures induced by different combinations of lactic acid, PGE2 and GM-CSF in macrophages, Related to Figure 3.

scRNA-seq datasets for correlation analysis of macrophages' functional programs with effector signature in T cells, Related to Supplementary Figure S12 and Methods

Supplementary Figure 22 shows single-nucleus transcriptomics and chromatin accessibility profiling among multistage tissues.

Early detection and treatment of Streptococcus pneumoniae (SPN) is crucial for patients. However, since nucleic acid testing relies on large-scale equipment and specialized operators, challenges remain for accurate, fast, and low-cost SPN detection. Here, we present a point-of-care testing (POCT) device for rapid and accurate detection of SPN based on low-frequency optical signal enhancement and cluster of regularly interspaced short palindromic repeats (CRISPR). The spotlight tube enables the enhancement of the fluorescence signal, while the combination of an artificial intelligence-assisted autoexposure algorithm and a homomorphic filtering image processing method improves the signal-to-noise ratio of the fluorescence image, thus realizing highly sensitive detection. Nucleic acid identification is performed using CRISPR-based crRNAs, and fluorescent probes were constructed against the IytA gene of SPN. And they showed high specificity and sensitivity for the IytA gene. This device demonstrated excellent sensitivity in detecting the SPN using the developed CRISPR-based nucleic acid detection strategy. The detection threshold of SPN reached 0.1 fM, and the single detection time of the device was only 40 min. Specificity was validated using clinical samples, and the test showed 100% agreement with quantitative polymerase chain reaction results from clinical samples. This method provides a highly sensitive optical and signal processing device, which, in combination with a novel DNA probe for SPN, provides a novel indicator option for POCT of SPN.