Reconfigurable acoustic tweezer for precise tracking and in-situ sensing of trace miRNAs in tumor cells

MicroRNAs (miRNAs) have emerged as critical biomarkers for early cancer diagnosis and monitoring. However, their isolation from clinical samples typically yields only trace amounts, significantly limiting the sensitivity and efficiency of cancer detection. To address this challenge, we present a octangular reconfigurable acoustic tweezer (ORAT) as an integrated platform for precise tumor cell tracking and in-situ detection of trace miRNAs. By simultaneously modulating multidirectional acoustic signals and parameters, the ORAT dynamically reshapes the acoustic field, enabling precise control over manipulation areas, particle spacing, array angles, distribution patterns, and node rotation. This device allows selective particle manipulation across entire regions or specific areas through adaptive adjustments of the microchamber boundary. Notably, the ORAT achieves rapid and accurate localization and labeling of rare tumor cells within a large population of normal cells. Furthermore, it enhances the sensitivity of CRISPR/Cas-based miRNA detection in digital microdroplets by three orders of magnitude, if compared to that of the conventional tube-based method. With its versatile capabilities, the ORAT holds remarkable promise for advancing nucleic acid analysis in a wide range of cancers and related diseases.

Multivalent aptamer-linked tetrahedron DNA assisted catalytic hairpin assembly for accurate SERS assay of cancer-derived exosomes in clinical blood

Exosome-based liquid biopsy plays an increasingly important role in non-invasive cancer diagnosis. However, due to their small size and low abundance, sensitive and accurate detection of cancer-derived exosomes in complex biological samples still faces great challenges. Herein, an ultrasensitive SERS assay based on the multivalent aptamer-linked tetrahedron DNA (MATD) assisted catalytic hairpin assembly (CHA) was developed for accurate detection of cancer-derived exosomes, including MATD-modified SERS sensing chip, identification SERS tags (IS), and assist SERS tags (AS). Taking SGC-7901 cell-derived exosomes as a test model, the exosomes can be captured onto the SERS sensing chip by the specific binding of multivalent aptamers to CD63 proteins, and then the MUC1 aptamers on the IS bind to the highly expressed MUC1 proteins on the SGC-7901 cell-derived exosomes to release the patch strands (P), further triggering the CHA-induced assembly of AuNP network structures between IS and AS with rich hotspots on SERS sensing chip. The proposed SERS assay can achieve ultra-high sensitivity low to 2.98 × 103 particles mL-1 (i.e., approximately 6 exosome particles can be detected from 2 μL of biological sample) within 40 min, high specificity for identifying SGC-7901 cell-derived exosomes, and can accurately distinguish gastric cancer patients from healthy people, which shows the potential applications in clinical diagnosis.

Tumor immune microenvironment in pancreatic ductal adenocarcinoma revisited - Exploring the "Space"

Pancreatic ductal adenocarcinoma (PDAC) remains one of the most deadly malignancies with a highly immunosuppressive tumor immune microenvironment (TIME) that hinders effective therapy. PDAC is characterized by significant heterogeneity in immune cell composition, spatial distribution and activation states, which impacts tumor progression and treatment response. Tumour-infiltrating lymphocytes (TILs), including CD4+ T-helper cells, CD8+ cytotoxic T-cells and FOXP3+ regulatory T-cells, play a key role in immune regulation, yet PDAC is largely an immunologically "cold" tumour with limited effector T-cell infiltration. The surrounding cellular microenvironment, particularly Cancer Associated Fibroblasts (CAFs) and macrophages, contributes to immune evasion by promoting a fibrotic and desmoplastic barrier that limits TIL infiltration. The prognostic significance of TILs is increasingly recognized, with higher densities correlating with improved survival, whereas regulatory T-cell infiltration and immunosuppressive stromal interactions are associated with poor outcomes. Emerging therapeutic strategies targeting the TIME (e.g., CAFs), immune checkpoint inhibitors, and TIL-based therapies offer the potential to overcome resistance. Future research must focus on optimizing immunotherapy strategies and unravelling the complex stromal-immune interactions to improve clinical translation.

The function of microRNA related to cancer-associated fibroblasts in pancreatic ductal adenocarcinoma

Pancreatic ductal adenocarcinoma (PDAC) is a highly lethal malignant tumor characterized by a poor prognosis. A prominent feature of PDAC is the rich and dense stroma present in the tumor microenvironment (TME), which significantly hinders drug penetration. Cancer-associated fibroblasts (CAFs), activated fibroblasts originating from various cell sources, including pancreatic stellate cells (PSCs) and mesenchymal stem cells (MSCs), play a critical role in PDAC progression and TME formation. MicroRNAs (miRNAs) are small, single-stranded non-coding RNA molecules that are frequently involved in tumorigenesis and progression, exhibiting either oncolytic or oncogenic activity. Increasing evidence suggests that aberrant expression of miRNAs can mediate interactions between cancer cells and CAFs, thereby providing novel therapeutic targets for PDAC treatment. In this review, we will focus on the potential roles of miRNAs that target CAFs or CAFs-derived exosomes in PDAC progression, highlighting the feasibility of therapeutic strategies aimed at restoring aberrantly expressed miRNAs associated with CAFs, offering new pathways for the clinical management of PDAC.

Nicotine-driven enhancement of tumor malignancy in triple-negative breast cancer via additive regulation of CHRNA9 and IGF1R

Cigarette smoking is a significant risk factor for cancer development with complex mechanisms. This study aims to investigate the impact of nicotine exposure on the regulation of stemness- and metastasis-related properties via cholinergic receptor nicotinic alpha 9 subunit (CHRNA9) and insulin-like growth factor-1 receptor (IGF1R) and to evaluate their therapeutic potential in triple-negative breast cancer (TNBC). We performed Kaplan-Meier survival analysis of public databases and revealed that high expression of CHRNA9, IGF1R signaling molecules, and stemness genes was significantly associated with poor recurrence-free survival (RFS) and distant metastasis-free survival (DMFS) in TNBC samples. Additionally, we examined two patient cohorts to determine the clinical associations between the expression levels of different genes (n = 67) and proteins (n = 42) and showed a strong positive correlation between the expression levels of CHRNA9, IGF1R signaling molecules, and stemness markers POU5F1/NANOG in tumor tissues. We carried out nicotine treatment and knockdown of CHRNA9 and IGF1R in TNBC cells to identify the effects on stemness-related properties in vitro. Furthermore, primary and secondary metastatic in vivo animal models were examined using micro-computed tomography (μCT) screening and in situ hybridization with a human Alu probe to detect tumor cells. Nicotine was found to upregulate the expression of CHRNA9, POU5F1, and IGF1R, influencing stemness- and metastasis-related properties. Knockdown of CHRNA9 expression attenuated nicotine-induced stemness-related properties in a TNBC cell model. Furthermore, knockdown of IGF1R expression significantly alleviated nicotine/CHRNA9-induced stemness features and cancer cell metastasis in cell cultures and lung metastatic mouse models. These results demonstrate that nicotine triggers IGF1R signaling, thereby enhancing stemness-related properties, cell migration, invasion, and tumor metastasis, resulting in a poorer prognosis for patients with TNBC. These findings highlight IGF1R as a promising therapeutic target for reducing stemness and metastasis in TNBC patients exposed to environmental nicotine. © 2025 The Pathological Society of Great Britain and Ireland.

Sciellin inhibits senescence and promotes pancreatic cancer progress by activating the notch signaling pathway

Pancreatic cancer (PC) incidence is increasing annually globally, and the five-year survival rate of patients with PC is approximately 10%. Cellular senescence is a regulatory mechanism against cancer that prevents tumor development by inhibiting the proliferation of damaged or abnormal cells. However, the mechanisms underlying cellular senescence in PC is unclear. Sciellin (SCEL) is a precursor protein of the cornified envelope predominantly enriched in epithelial cells. Previous studies have discovered potential links between SCEL and cellular senescence through bioinformatics analysis. Therefore, the specific role of SCEL in cellular senescence and the malignant features of PC are unclear. In vivo and in vitro assays were performed to investigate the role of SCEL in PC cell senescence, proliferation, invasion, and metastasis. Gene set enrichment analysis was used to identify the Notch signaling pathways activated by SCEL, and coimmunoprecipitation was used to detect proteins that interact with SCEL. The results revealed that SCEL was significantly upregulated in PC tissues and cell models and was correlated with poor clinical outcomes. Further investigation revealed that the interaction between SCEL and Jagged-1 promotes the activation of the Notch signaling pathway, effectively inhibiting the senescence of PC cells while enhancing their proliferation, invasion, and metastatic capabilities. Therefore, SCEL is a potential therapeutic target for PC.

A tube-based biosensor for DNA and RNA detection

Affordable, sensitive, and simplified DNA/RNA detection is important for disease diagnosis and enables timely medical intervention measures. Usually, high sensitivity depends on expensive instruments and sophisticated procedures, making sensitivity contradict affordability and simplicity. Here, we proposed an ultra-sensitive single-tube biosensor (USTB) where users can visually detect targets by observing the liquid motion state in a glass tube. The developed instrument-free USTB performed low-cost ($0.1), fast (1 min), and ultra-sensitive detection for both the DNA/RNA fragments (≤1 aM) and the clinical positive samples, which commercial reverse transcription polymerase chain reaction (RT-PCR) and PCR kits could not effectively recognize. Furthermore, USTB is promising to be easily applied to detect other-type biomarkers by the designed smart sensing unit.

A competitive aptamer binding-based CRISPR-cas biosensor for sensitive detection of tetracycline residues in biological samples

Tetracycline (TC) is widely used in veterinary medicine and animal feed; however, TC residues in food pose a risk to human health. Thus, the sensitive and selective detection of TC is needed to ensure food safety. Herein, we developed a CRISPR-Cas12a biosensor with competitive aptamer binding to detect TC residues. The aptasensor, formed by hybridizing activator DNA with TC-specific aptamers on streptavidin-modified magnetic beads, releases activator DNA in a TC concentration-dependent manner. This activated the Cas12a-crRNA complex, which cleaved single-strand DNA reporters to generate a detectable fluorescence signal. The TC signal was amplified through a two-step incubation reaction, with a detection limit as low as 9.45 × 10-5 μg L-1. The assay showed high selectivity and good recovery rates in various biological samples (e.g., honey, milk, fish), demonstrating the applicability of the biosensors in pollutant detection.

CRISPR/Cas12a regulated preassembled bulb-shaped G-quadruplex signal unit for FL/CM dual-mode ultrasensitive detection of miRNA-155

High sensitivity and specificity in microRNA detection are of great significance for early cancer screening. This study employed a pre-assembled bulb-shaped G-quadruplex signal unit (G4MB) as a novel and efficient label-free probe. The products amplified by the miRNA-155-targeted exponential amplification reaction (EXPAR) activated the trans-cleavage activity of CRISPR/Cas12a, disrupting the G4MB structure to achieve dual-channel fluorescence/colorimetric (FL/CM) inverse signal output. Due to the strong signal amplification of EXPAR, the highly efficient cleavage by CRISPR/Cas12a, and the ultra-high response signal of the structurally stable G4MB probe, the FL mode achieved a high signal-to-noise ratio (S/N) of approximately 12.5. The CM mode, combined with smart devices for RGB curve adjustment, successfully corrected the background and provided precise and objective image data support while allowing results to be observed with the naked eye. Additionally, the sensor system exhibited high accuracy in complex human serum environments and RNA extracted from three different types of cells. Moreover, the G4MB probe required no complicated labeling, demonstrated structural stability, and had a rapid response. Most importantly, this study analyzed the advantages of the G4MB and applied it to miRNA detection for the first time, providing practical insights for biosensor construction, molecular diagnostics, and clinical applications.

BE-CATCH: Bioamplifier-Equipped CRISPR-Cas12a Transduction System Coupled with Commercial Pregnancy Test Strips to Harness Signal-on Point-of-Care Detection

Repurposing existing commercial diagnostic equipment to enable portable analysis of diverse targets is driving the development of affordable point-of-care testing (POCT). Interestingly, we found that goat antimouse IgG could replace human chorionic gonadotropin (hCG) to make the T line of pregnancy test strips (PTS) appear red color and accordingly synthesized a novel signal output probe, which eliminated the intricate hCG covalent coupling steps, and could meet the multiple needs of expanded POCT. Given this, we introduced a novel separation-free universal POCT strategy termed bioamplifier-equipped CRISPR-Cas12a transduction system coupled with PTS to harness signal-on detection (BE-CATCH). Specifically, target inputs were converted and amplified by the multiplied strand displacement amplification-based bioamplifier, thereby activating Cas12a's trans-cleavage activity. Then, the activated Cas12a would cleave the connector indiscriminately, which ultimately kept the signal output probe in a free state; thus, the inputs could be translated into a colorimetric signal on the PTS. This strategy not only provided boosted sensitivity and specificity but also enhanced user-friendliness by maintaining the signal-on detection mode. We also demonstrated the versatility of the BE-CATCH strategy through selectively detecting miR-155 and flap endonuclease 1. Given its broad adaptability, the BE-CATCH strategy could provide an appealing option to broaden the application of PTS in biomedical diagnostics.

A multi-functional synergistic platform of Cas12a split dsDNA activators

This work comprehensively explores the effects of various positions of Cas12a split activators. Based on this, a multi-functional synergistic platform was constructed. The construction of a structural dynamic network, the sensitive detection of APE1, and a time-controlled photo-activation have been achieved, demonstrating the potential for expanding Cas12a applications.

Tobacco carcinogen NNK promotes pancreatic cancer proliferation via LINC00857/β-catenin

INTRODUCTION

Smoking is a key risk factor for pancreatic cancer (PC). Nicotine-derived nitrosamine ketone (NNK), a major tobacco smoke constituent, has been shown to promote cancer growth, but its specific role in PC progression remains unclear. While long non-coding RNA LINC00857 (lnc RNA) is implicated in cancer progression, its regulation by NNK is unknown. This study aims to investigate whether NNK can drive PC growth and elucidate the underlying mechanisms.

METHODS

Employing an experimental methodology, this investigation treated human pancreatic cancer cell lines (CFPAC-1 and Panc-1) with NNK and utilized various assays (CCK-8, colony formation, and EdU cell proliferation) to assess the effects on cell proliferation. The interplay between LINC00857 expression profiles, PC, and smoking was systematically investigated through cross-database bioinformatic interrogation encompassing public resources and institutional biobank data. Experiments were performed to knock down LINC00857 in PC cells using siRNA technology. We used Western blotting and quantitative real-time PCR (qRT-PCR) to assess β-catenin expression and elucidate the mechanism by which the tobacco carcinogen NNK promotes PC formation.

RESULTS

Some evidence that NNK enhanced the proliferative capacity of PC cells was found. Bioinformatic analysis of public databases, combined with data from our center's database, revealed that LINC00857 was up-regulated in PC and correlated with smoking. Moreover, we discovered that knockdown of LINC00857 inhibited PC cell proliferation, with β-catenin identified as a potential downstream molecule. Importantly, after LINC00857 knockdown, we observed suppression of NNK-induced β-catenin upregulation at both protein and transcriptional levels.

CONCLUSIONS

NNK potentially induces PC progression through the LINC00857/β-catenin axis. These findings provide new perspectives on the mechanisms of PC progression and highlight the clinical relevance of smoking cessation for preventing PC.

CRISPR/Cas12a-based transition state molecular switch for low-background detection of HPV-16 on a microfluidic platform

Human papillomavirus type 16 (HPV-16) is a high-risk oncogenic subtype of HPV, strongly associated with the pathogenesis of multiple cancers. Researchers have developed many detection methods for HPV-16, among which, the detection method based on microfluidic has the characteristics of high efficiency and high sensitivity. However, non-specific adsorption remains a critical challenge, often leading to elevated background signals. Here, we propose an On-Chip assay integrated by transition state molecular switch based on CRISPR-Cas12a (OCTMS-CRISPR) for stable, sensitive, and low-background fluorescence detection of HPV-16. This system leverages a highly integrated molecular switch and Cas12a to perform dual-screening, while the dissociation products of the molecular switch activate trans-cleavage activity. Our data suggest that OCTMS-CRISPR suppresses background signals on microfluidic chip while maintaining the specificity and sensitivity of trans-cleavage. For demonstration, we detected five HPV subtypes and base mismatches at varying positions and quantities. The LOD can reach 7.64 pM (average fluorescence intensity) and 9.91fM (pixel counting), showing great potential in the field of biosensing and DNA chips.

Recent progress on biosensors for detection of circulating miRNA biomarkers

Circulating miRNAs are a class of non-coding endogenous RNAs found in body fluids which typically consist of 19-24 nucleotides in length. The abnormal expression of miRNAs has been demonstrated to be associated with severe human diseases. Aiming to provide valuable insights for the further development of reliable miRNA detectors for disease early diagnosis and treatment, this work systematically summarizes the latest advancements in signal amplification strategies for miRNA analysis, based on nanomaterials, nucleic acids, enzymes, and CRISPR/Cas system. The emerging techniques for detecting circulating miRNAs in human body fluids over the past decade are highlighted, including electrochemical, optical, and dual-mode biosensors. Furthermore, the challenges of trace miRNA detection in complex samples and the development prospects of miRNA biosensors are also discussed.

Programmable spherical nucleic acids integrated with MOF-confined copper nanoclusters facilitate electrochemiluminescence detection of prostate-specific biomarkers

Alpha-methylacyl-CoA racemase (AMACR) is a promising prostate cancer biomarker due to its high specificity in distinguishing prostate cancer from benign prostatic diseases. However, its low abundance in biological environments presents a significant detection challenge. To address this, we developed an innovative all-in-one s̲pherical n̲ucleic a̲cid (SNA) platform for highly sensitive and selective electrochemiluminescence (ECL) detection of AMACR. The SNAs incorporate two types of ice-cream probes (IC probes), each consisting of interlocked hairpins and circular templates. Specifically, the all-in-one SNAs were elaborately designed to achieve key three functions: (i) the arrangement of IC probes on magnetic nanoparticle interfaces creates a spatially confined environment, promoting rapid interactions, and enhances AMACR conversion efficiency; (ii) the integrated templates and primers within the IC probes facilitate rolling circle amplification (RCA), resulting in exponential signal amplification; and (iii) the products generated through RCA serve as activators for the CRISPR/Cas12a system, remarkably improving its activation efficiency. Upon AMACR activation of the aptamer-prelocked DNA walker, the all-in-one SNAs were specifically driven to initiate RCA, generating exponentially amplified activators to effectively activate the CRISPR/Cas12a system. Additionally, we established a novel ECL nano-complex using a zinc-metal-organic framework loaded with Cu nanoclusters for signal output. This platform demonstrates exceptional sensitivity and specificity for detecting low-abundance biomarkers, offering significant potential for advancing clinical diagnostics.

Exploring the potential mechanisms of Da ChaiHu decoction against pancreatic cancer based on network pharmacology prediction and molecular docking approach

Da ChaiHu decoction (DCHD) is used in Chinese medicine to treat pancreatic cancer (PC), but its exact mechanism is not known. The aim of this study was to investigate the main active ingredients and specific mechanisms of DCHD against PC. Firstly, the active ingredients and targets of DCHD and PC-related targets were searched from the TCMSP, DrugBank, NCBI and GeneCards databases, respectively. The intersected targets of both were then taken to construct a PPI network using STRING, and this network was visualized by Cytoscape 3.8.2. GO and KEGG enrichment analyses of the intersected targets were performed using R 4.2.1 "clusterProfiler", "enrichplot", and "ggplot2" packages. Molecular docking was performed utilizing MOE software to detect the binding capacity between compounds and targets. Cell proliferation, apoptosis, invasion and migration were examined through a CCK8 kit, Muse® Cell Analyzer, transwell and wound healing experiment, respectively. The expression levels of five core targets were assessed by RT-qPCR in PANC-1 cells treated with stigmasterol. Molecular dynamic simulations analysis was conducted to analyze the binding affinities and modes of interaction between molecules and stigmasterol using the GROMACS 5.1.4 program package. In this study, 141 common targets of DCHD and PC were obtained. GO-MF items indicated that DCHD exerts its effects on PC primarily by influencing the binding activity of DNA-binding transcription factors. The KEGG analysis revealed that these genes were implicated in various signaling pathways, including the IL-17 signaling pathway and the PI3K/Akt signaling pathway. Stigmasterol was chosen as the final ingredient for subsequent investigation due to its derivation from herb (Da ChaiHu), its encompassment of more common targets, and the scarcity of existing research on its role in PC. The results of molecular docking and Molecular dynamic simulations analysis showed that stigmasterol had good binding activity with BCL2, and ICAM1. In vitro experiments suggested that stigmasterol could effectively inhibit the proliferation, invasion and migration of PANC-1 cells, and promote cell apoptosis. Moreover, stigmasterol treatment led to the reduced expression of AKT1, HIF1A, BCL2, IL1B, and ICAM1. This study is the first to reveal the main active components and potential mechanisms of DCHD against PC, which provides a theoretical basis for studying the role of DCHD in the treatment of PC. Especially, the anti-PC mechanism of active compound stigmasterol might be associated with inhibiting proliferation, invasion and migration and accelerating apoptosis. Furthermore, five targets (AKT1, HIF1A, BCL2, IL1B, and ICAM1) were identified as key targets of stigmasterol, and the mRNA expressions of these genes were down-regulated by stigmasterol through in vitro experiments.

Bacopa monnieri phytochemicals as promising BACE1 inhibitors for Alzheimer's disease therapy

Alzheimer's disease (AD) remains a formidable challenge, necessitating the discovery of effective therapeutic agents targeting β-site amyloid precursor protein cleaving enzyme 1 (BACE1). This study investigates the inhibitory potential of phytochemicals derived from Bacopa monnieri, a plant renowned for its cognitive-enhancing properties, in comparison to established synthetic inhibitors such as Atabecestat, Lanabecestat, and Verubecestat. Utilizing molecular docking and advanced computational simulations, we demonstrate that Bacopaside I exhibits superior binding affinity and a unique interaction profile with BACE1, suggesting a more nuanced inhibitory mechanism. Our findings highlight the promising role of Bacopa monnieri phytochemicals as viable alternatives to synthetic drugs, emphasizing their potential to overcome limitations faced in clinical settings. Furthermore, the development of the SIMANA ( https://simana.streamlit.app/ ) platform enhances the visualization and analysis of protein-ligand interactions, facilitating a deeper understanding of the dynamics involved. This research not only underscores the therapeutic promise of natural compounds in AD treatment but also advocates for a paradigm shift towards integrating traditional medicinal knowledge into contemporary drug discovery efforts.

An ultrasensitive one-pot Cas13a-based microfluidic assay for rapid multiplexed detection of microRNAs

Aberrant microRNA expression is associated with tumor progression in various organs. Detecting microRNAs as clinical cancer biomarkers can facilitate early cancer diagnosis and monitoring. However, the rapid and accurate quantification of microRNAs from biological samples remains a significant challenge. Here we developed a one-pot isothermal assay utilizing a molecular circuit with CRISPR/Cas13a (CRISPR-circuit) to rapidly convert, amplify and report different microRNAs within 15 min at the attomolar (aM) level. Then the full process was performed on an active centrifugal microfluidic chip and its corresponding portable equipment for parallel detection of multiple microRNAs, including miR-21, miR-141, miR-196a, and miR-1246. We also demonstrated its application for identifying cell lines and clinical samples of cancer patients with varying microRNA levels, which showed a strong correlation with the RT-qPCR. The assay can be easily adapted for the detection of any microRNA by simply modifying the converter primer, thereby holding significant potential for accurate disease detection and clinical diagnosis.

Programmable AIESTA: All-in-One Isothermal Enzymatic Signal Transduction Amplifier for Portable Profiling

The Argonaute (Ago) protein exhibits high specificity in nucleic acid recognition and cleavage, making it highly promising for biosensing applications. Its potential is further enhanced by its independence from protospacer adjacent motif (PAM) requirements and the cost-effectiveness of using short DNA guides. Both Ago and CRISPR/Cas systems face challenges in signal amplification, which limit their ability to detect targets at ultralow concentrations. To overcome this limitation, a thermostable quadratic amplification system (T-QAS) was constructed by integrating a thermostable nicking-enzyme-mediated amplification (NEMA) strategy with TtAgo. The system leverages the high stability of T-QAS at elevated temperatures to enhance guide-target interactions and decrease false positives caused by nonspecific amplification. Additionally, nanozyme is integrated with T-QAS to construct the AIESTA platform (all-in-one isothermal enzymatic signal transduction amplifier), which is a single-tube visual sensing platform. Within the AIESTA system, T-QAS improves specificity through high operational temperatures and offers programmable functions, enabling the sensitive detection of miRNA and foodborne toxins. The combination of T-QAS and nanozyme makes AIESTA a candidate of point-of-care testing (POCT) field, showcasing the potential for biosensing in resource-limited and complex environments.

Piezo1-induced durotaxis of pancreatic stellate cells depends on TRPC1 and TRPV4 channels

Pancreatic stellate cells (PSCs) are primarily responsible for producing the stiff tumor tissue in pancreatic ductal adenocarcinoma (PDAC). Thereby, PSCs generate a stiffness gradient between the healthy pancreas and the tumor. This gradient induces durotaxis, a form of directional cell migration driven by differential stiffness. However, the molecular sensors behind durotaxis are still unclear. To investigate the role of mechanosensitive ion channels in PSC durotaxis, we established a two-dimensional stiffness gradient mimicking PDAC. Using pharmacological and genetic methods, we investigated the contribution of the ion channels Piezo1, TRPC1 and TRPV4 in PSC durotaxis. We found that PSC migration towards a stiffer substrate is diminished by altering Piezo1 activity. Moreover, disrupting TRPC1 along with TRPV4 abolishes PSC durotaxis even when Piezo1 is functional. Our results demonstrate that optimal PSC durotaxis requires an intermediary level of ion channel activity, which we simulated via a numerically discretized mathematical model. These findings suggest that mechanosensitive Piezo1 channels detect the differential stiffness microenvironment. The resulting intracellular signals are amplified by TRPV4 and TRPC1 channels to guide efficient PSC durotaxis.

Hydrogel-Based In Situ DNA Extension Assay for Multiplexed and Rapid Detection of MicroRNA

MicroRNAs (miRNAs) are important biomarkers for liquid biopsy, with extensive applicability to diverse diseases. Among diverse miRNA sensing platforms, graphically encoded hydrogel-based miRNA detection technology is a highly promising diagnostic tool, in terms of sensitivity, specificity, and multiplexing capability. However, the conventional hydrogel-based miRNA detection process suffers from a long assay time (more than 3 h) and redundant assay steps, limiting the practical applicability to actual clinical fields. In this study, we develop a hydrogel-based in situ DNA extension assay for rapid, simple, and multiplexed miRNA detection. Unlike typical hydrogel-based assays, the target hybridization and biotinylation for fluorophore labeling are integrated into a single step via target miRNA-primed DNA extension in hydrogel microparticles. Therefore, multiple microRNA targets can be quantitatively detected within 45 min by two assay steps composed of (1) target capture/biotinylation and (2) fluorophore labeling via streptavidin-biotin interaction. We validate robust sensitivities (down to the low picomolar level) and specificities (single-nucleotide level) by conducting singleplex assays for breast cancer-related miRNA markers (miR-16, miR-92a, and let-7a). Furthermore, multiplexed detection of these miRNA markers is conducted to validate robust multiplexing capacity with negligible nonspecific signal expression. Finally, multiple types of miRNAs in the lysate of breast cancer cells (MCF-7) are successfully detected using the developed assay. We expect the developed hydrogel-based assay can contribute to biomedical and omic fields, enabling high-throughput profiling of multiple miRNAs.

A Sensitive and Fast microRNA Detection Platform Based on CRlSPR-Cas12a Coupled with Hybridization Chain Reaction and Photonic Crystal Microarray

Changes in microRNA (miRNA) levels are closely associated with the pathological processes of many diseases. The sensitive and fast detection of miRNAs is critical for diagnosis and prognosis. Here, we report a platform employing CRISPR/Cas12a to recognize and report changes in miRNA levels while avoiding complex multi-thermal cycling procedures. A non-enzyme-dependent hybridization chain reaction (HCR) was used to convert the miRNA signal into double-stranded DNA, which contained a Cas12a activation sequence. The target sequence was amplified simply and isothermally, enabling the test to be executed at a constant temperature of 37 °C. The detection platform had the capacity to measure concentrations down to the picomolar level, and the target miRNA could be distinguished at the nanomolar level. By using photonic crystal microarrays with a stopband-matched emission spectrum of the fluorescent-quencher modified reporter, the fluorescence signal was moderately enhanced to increase the sensitivity. With this enhancement, analyzable fluorescence results were obtained in 15 min. The HCR and Cas12a cleavage processes could be conducted in a single tube by separating the two procedures into the bottom and the cap. We verified the sensitivity and specificity of this one-pot system, and both were comparable to those of the two-step method. Overall, our study produced a fast and sensitive miRNA detection platform based on a CRISPR/Cas12a system and enzyme-free HCR amplification. This platform may serve as a potential solution for miRNA detection in clinical practice.

The role of extracellular matrix viscoelasticity in development and disease

For several decades, research has studied the influence of the extracellular matrix (ECM) mechanical properties in cell response, primarily emphasising its elasticity as the main determinant of cell and tissue behaviour. However, the ECM is not purely elastic; it is viscoelastic. ECM viscoelasticity has now emerged as a major regulator of collective cell dynamics. This review highlights recent findings on the role of ECM viscoelasticity in development and pathology.

Multi-material Volumetric Bioprinting and Plug-and-play Suspension Bath Biofabrication via Bioresin Molecular Weight Tuning and via Multiwavelength Alignment Optics

Volumetric Bioprinting (VBP), enables to rapidly build complex, cell-laden hydrogel constructs for tissue engineering and regenerative medicine. Light-based tomographic manufacturing enables spatial-selective polymerization of a bioresin, resulting in higher throughput and resolution than what is achieved using traditional techniques. However, methods for multi-material printing are needed for broad VBP adoption and applicability. Although converging VBP with extrusion bioprinting in support baths offers a novel, promising solution, further knowledge on the engineering of hydrogels as light-responsive, volumetrically printable baths is needed. Therefore, this study investigates the tuning of gelatin macromers, in particular leveraging the effect of molecular weight and degree of modification, to overcome these challenges, creating a library of materials for VBP and Embedded extrusion Volumetric Printing (EmVP). Bioresins with tunable printability and mechanical properties are produced, and a novel subset of gelatins and GelMA exhibiting stable shear-yielding behavior offers a new, single-component, ready-to-use suspension medium for in-bath printing, which is stable over multiple hours without needing temperature control. As a proof-of-concept biological application, bioprinted gels are tested with insulin-producing pancreatic cell lines for 21 days of culture. Leveraging a multi-color printer, complex multi-material and multi-cellular geometries are produced, enhancing the accessibility of volumetric printing for advanced tissue models.

Prevalence and Risk Factors for Medial Meniscus Ramp Lesions in the Setting of Pediatric Anterior Cruciate Ligament Injuries: A Systematic Review and Meta-analysis

BACKGROUND

Medial meniscus ramp lesions (MMRLs) are commonly associated with anterior cruciate ligament (ACL) injuries and may increase the risk of graft failure after ACL reconstruction (ACLR) if undiagnosed or left untreated. Although MMRLs have been extensively reported in adults, there are limited studies describing them in pediatric patients undergoing ACLR. The purpose of this study was to perform a systematic review and meta-analysis to determine the pooled prevalence of and risk factors for MMRLs in pediatric patients with ACL injuries.

METHODS

PubMed, Scopus, and Cochrane Central Register of Controlled Trials (CENTRAL) databases were queried in December 2023 for studies reporting on MMRLs in pediatric patients (≤21 y old) undergoing ACLR. Articles were only included if they reported on the prevalence and/or risk factors for arthroscopically diagnosed MMRLs. DerSimonian-Laird binary random-effects models were constructed to quantitatively evaluate the association between risk factors and MMRLs by generating effect estimates in the form of odds ratios (OR) with 95% CI.

RESULTS

Seven studies were identified, which included 1362 pediatric patients (mean±SD age, 15.3±1.4 y old) that underwent ACLR. The pooled MMRL prevalence was 16.4% (range, 13.2% to 28%) calculated across 6 studies. Of the 7 studies identified, 5 qualified for the risk factor analysis, which included a total of 536 ACLR patients. Twenty risk factors were identified, of which 8 were amenable to being explored quantitatively. Anterolateral ligament (ALL) injuries on magnetic resonance imaging (MRI) [odds ratio (OR), 4.16; 95% CI, 1.40-12.34; P =0.01], MMRLs on preoperative MRI (OR, 4.09; 95% CI, 2.52-6.64; P <0.00010), posteromedial tibial plateau bone marrow edema (OR, 2.11; 95% CI, 1.16-3.83; P =0.01), and concomitant lateral meniscus tears (OR, 1.70; 95% CI, 1.04-2.76; P =0.03) were important risk factors for pediatric MMRLs. Skeletal maturity (physes open or closed), male sex, or collateral ligament injury was not associated with the presence of pediatric MMRLs.

CONCLUSION

The overall pooled prevalence of MMRLs was 16.4% in pediatric patients undergoing ACLR. Significant risk factors for pediatric MMRLs included the presence of concomitant ALL injuries on MRI, identification of MMRLs on MRI, posteromedial tibia plateau bone marrow edema, and concomitant lateral meniscus tears at the time of surgery. Skeletal maturity, male sex, or collateral ligament injury were not associated with MMRLs in pediatric ACL tears.

LEVEL OF EVIDENCE

Systematic review and meta-analysis; level of evidence: IV.

Development and Validation of the Predictive and Prognostic ChemoResist Signature in Resected Pancreatic Ductal Adenocarcinoma: Multicohort Study

OBJECTIVE

To develop and validate a signature to precisely predict prognosis in pancreatic ductal adenocarcinoma (PDAC) undergoing resection and adjuvant chemotherapy.

BACKGROUND

PDAC is largely heterogeneous and responds discrepantly to treatment.

METHODS

A total of 551 consecutive patients with PDAC from 3 different cohorts of tertiary centers were initially enrolled. Genetic events of the 4 most commonly mutated genes in PDAC and expressions of 12 PI3K/AKT/mammalian target of rapamycin (mTOR) pathway markers were examined. A 9-feature signature for the prediction of chemotherapy benefits was constructed in the training cohort using the least absolute shrinkage and selection operator Cox regression model and validated in 2 independent cohorts.

RESULTS

Utilizing the least absolute shrinkage and selection operator model, a predictive and prognostic signature, named ChemoResist, was established based on KRAS single nucleotide variant (SNV), phosphatase and tensin homologue (PTEN), and mTOR expressions, and 6 clinicopathologic features. Significant differences in survival were observed between high and low-ChemoResist patients receiving chemotherapy in both the training [median overall survival (OS), 17 vs 42 months, P < 0.001; median disease-free survival (DFS), 10 vs 23 months, P < 0.001] and validation cohorts (median OS, 18 vs 35 months, P = 0.034; median DFS, 11 vs 20 months, P = 0.028). The ChemoResist classifier also significantly differentiated patient survival in whole patients regardless of chemotherapy. Multivariable-adjusted analysis substantiated the ChemoResist signature as an independent predictive and prognostic factor. For predicting 2-year OS, the ChemoResist classifier had significantly higher areas under the curve than TNM stage (0.788 vs 0.636, P < 0.001), other clinicopathologic characteristics (0.505-0.668), and single molecular markers (0.507-0.591) in the training cohort. Furthermore, patients with low ChemoResist scores exhibited a more favorable response to adjuvant chemotherapy compared with those with high ChemoResist scores (hazard ratio for OS: training, 0.22 vs 0.57; validation, 0.26 vs 0.50; hazard ratio for DFS: training, 0.35 vs 0.54; validation, 0.18 vs 0.59). The ChemoResist signature was further validated in the total cohort undergoing R0 resection.

CONCLUSIONS

The ChemoResist signature could precisely predict survival in PDAC undergoing resection and chemotherapy, and its predictive value surpassed the TNM stage and other clinicopathologic factors. Moreover, the ChemoResist classifier could assist with identifying patients who would more likely benefit from adjuvant chemotherapy.

RT-RPA-assisted scaffold RNA transcription amplification activation Cas12a trans-cleavage strategy for one-pot miRNA detection

Split crRNA is utilized in the CRISPR system as a highly specific and sensitive tool for nucleic acid identification in molecular diagnostics. Here, we introduce a novel one-pot RT-RPA-assisted Scaffold RNA Transcription Amplification Activation Cas12a Trans-cleavage (ScRNA-TAAT) strategy for miRNA detection. Capable of completing miRNA detection in 50 min with a detection limit of 2.66 aM. The miRNA was amplified into double-stranded DNA amplicons with a T7 promoter using RT-RPA, which is subsequently transcribed into RNA trigger. A split T7 promoter extension sequence with template binds to the RNA trigger, assembly a three-way linker to initiate transcription of the scaffold RNA. The three-way linker with sticky ends joins to its RNA products, assembling a DNA-RNA complex that acts as both a spacer RNA and an activator. Simultaneously, the DNA-RNA hybrid complexes and scaffold RNA could replace the split crRNA and combined with Cas12a, forming an active ribonucleoprotein (RNP) complex with trans-cleavage activity comparable to that of the wild-type Cas12a RNP. Furthermore, we have successfully integrated the ScRNA-TAAT strategy into lateral flow analysis, enabling the visual detection of miRNAs. The assay's exceptional specificity and universality are highlighted by its application to complex biological matrices, including serum and cell lysates. The simplicity, sensitivity, and adaptability of the ScRNA TAAT assay render it a promising candidate for point-of-care testing and high sensitivity in molecular diagnostics.

Highly parallel profiling of the activities and specificities of Cas12a variants in human cells

Several Cas12a variants have been developed to broaden its targeting range, improve the gene editing specificity or the efficiency. However, selecting the appropriate Cas12a among the many orthologs for a given target sequence remains difficult. Here, we perform high-throughput analyses to evaluate the activity and compatibility with specific PAMs of 24 Cas12a variants and develop deep learning models for these Cas12a variants to predict gene editing activities at target sequences of interest. Furthermore, we reveal and enhance the truncation in the integrated tag sequence that may hinder off-targeting detection for Cas12a by GUIDE-seq. This enhanced system, which we term enGUIDE-seq, is used to evaluate and compare the off-targeting and translocations of these Cas12a variants.

Single-cell RNA sequencing reveals an IL1R2+Treg subset driving immunosuppressive microenvironment in HNSCC

Regulatory T cells (Tregs) play an immunosuppressive role in tumor microenvironment (TME) in various of cancer types. However, how different Treg subsets influence and effect on head and neck squamous cell carcinoma (HNSCC) remain unclear. Here, using single-cell RNA sequencing (scRNA-seq), we identified an IL1R2+Treg subset which promoted the progression of HNSCC. Via tissue microassay (TMA) and enzyme-linked immunosorbent assay (ELISA), we verified the clinical diagnostic value of the IL1R2+Treg and soluble IL1R2 (sIL1R2). In addition, we constructed tumor-bearing mouse models to explore the antitumor effects of combined targeting IL1R2 and CTLA4. For mechanism, we found IL-1β promoted the expression of IL1R2 and CTLA4 in Tregs, and upregulated CTLA4 though NR4A1 translocation. These results revealed that IL1R2+Treg and serum IL1R2 level had potential diagnostic and prognostic value of HNSCC and combined targeting of IL1R2 and CTLA4 might be an effective strategy to inhibit tumor progression.

Advances in Spatial Omics Technologies

Rapidly developing spatial omics technologies provide us with new approaches to deeply understanding the diversity and functions of cell types within organisms. Unlike traditional approaches, spatial omics technologies enable researchers to dissect the complex relationships between tissue structure and function at the cellular or even subcellular level. The application of spatial omics technologies provides new perspectives on key biological processes such as nervous system development, organ development, and tumor microenvironment. This review focuses on the advancements and strategies of spatial omics technologies, summarizes their applications in biomedical research, and highlights the power of spatial omics technologies in advancing the understanding of life sciences related to development and disease.

Simple and sensitive SERS platform for Staphylococcus aureus one-pot determination by photoactivated CRISPR/Cas12a cascade system and core-shell DNA tetrahedron@AuNP@Fe3O4 reporter

Staphylococcus aureus (S. aureus) is a widely prevalent Gram-positive bacteria that can cause serious infections and diseases in humans and other organisms. Timely detection and treatment in clinical settings is crucial for patient safety and public health. However, current methods for S. aureus detection still face some limitations, such as time-consuming operation, false positives, and labor-intensive available methodology with low sensitivity. Therefore, it is particularly important to develop a rapid, simple, sensitive, and cost-effective method for detecting S. aureus. We developed a SERS platform based on allosteric aptamer-triggered catalytic hairpin assembly (CHA) and photoactivated CRISPR/Cas12a reactions, combined with a multifunctional core-shell structure as the SERS reporter, enabling highly sensitive one-pot determination of S. aureus. Compared with traditional two-step and one-pot analysis methods, this strategy offers superior sensitivity and can successfully identify real samples contaminated with S. aureus. The platform utilizes light-controlled CHA and CRISPR/Cas12a reactions, effectively preventing interference between different reaction systems. Therefore, the photoactivated one-pot CHA/Cas12a strategy provides a simple, rapid, highly sensitive, specific, and cost-effective method for one-pot determination of S. aureus in clinical samples.

Machine Learning-Aided Identification of Fecal Extracellular Vesicle microRNA Signatures for Noninvasive Detection of Colorectal Cancer

Colorectal cancer (CRC) remains a formidable threat to human health, with considerable challenges persisting in its diagnosis, particularly during the early stages of the malignancy. In this study, we elucidated that fecal extracellular vesicle microRNA signatures (FEVOR) could serve as potent noninvasive CRC biomarkers. FEVOR was first revealed by miRNA sequencing, followed by the construction of a CRISPR/Cas13a-based detection platform to interrogate FEVOR expression across a diverse spectrum of clinical cohorts. Machine learning-driven models were subsequently developed within the realms of CRC diagnostics, prognostics, and early warning systems. In a cohort of 38 CRC patients, our diagnostic model achieved an outstanding accuracy of 97.4% (37/38), successfully identifying 37 of 38 CRC cases. This performance significantly outpaced the diagnostic efficacy of two clinically established biomarkers, CEA and CA19-9, which showed accuracies of mere 26.3% (10/38) and 7.9% (3/38), respectively. We also examined the expression levels of FEVOR in several CRC patients both before and after surgery, as well as in patients with colorectal adenomas (CA). Impressively, the results showed that FEVOR could serve as a robust prognostic indicator for CRC and a potential predictor for CA. This endeavor aimed to harness the predictive power of FEVOR for enhancing the precision and efficacy of CRC management paradigms. We envision that these findings will propel both foundational and preclinical research on CRC, as well as clinical studies.

Analysis of the safety and efficacy of laparoscopic gastrojejunostomy following neoadjuvant chemotherapy for gastric pyloric obstruction

Objective

To explore the safety and feasibility of laparoscopic gastrojejunostomy combined with neoadjuvant chemotherapy (NACT) in patients with locally advanced gastric cancer and pyloric obstruction.

Methods

We included patients with locally advanced gastric cancer who underwent laparoscopic gastrojejunostomy (LGJ) or endoscopic stenting (ES) between May 2017 and October 2022. The prognostic nutritional index (PNI) was used to evaluate the patient nutritional status. Platelet-to-lymphocyte ratio (PLR) and neutrophil-to-lymphocyte ratios were used to evaluate the inflammatory status of patients. The Kaplan-Meier method was used to analyze survival conditions, and the log-rank test was used to compare survival differences. A multivariate logistic regression analysis was performed to identify the factors related that might affect the prognosis.

Results

During the study period, 41 patients received LGJ and 37 patients received endoscopic stenting (ES). Patients in the ES group had higher rates of postoperative complications, particularly bleeding (0 vs. 16.2%, P<0.05). After two cycles NACT, the proportion of PNI≥45 patients in LGJ group was significantly higher than that in ES group (P<0.05). Furthermore, the proportion of patients with PLR<162 in the ES group was significantly higher than that in the LGJ group (P<0.05), and compared to the ES group, patients in the LGJ group were able to tolerate more cycles of NACT (6 vs. 4 cycles). A higher median survival time was observed in the LGJ group, and the multivariate logistic regression analysis confirmed treatment selection as an independent risk factor for overall survival (HR, 6.362; 95% CI:3.285-12.321, P<0.001).

Conclusion

NACT after LGJ shows potential for reducing tumor stage and improving patient prognosis.

IL-1R1 Blockade Boosts CD40 Agonist Immune Responses but Fails to Improve Efficacy or Reduce Hepatotoxicity in Pancreatic Cancer

Pancreatic ductal adenocarcinoma (PDAC) has a poor survival rate and limited treatments. Agonistic CD40 antibodies are promising, but clinical trials have shown only modest efficacy and significant hepatotoxicity. We previously reported that IL-1 pathway blockade enhances agonistic CD40 antibody efficacy against melanoma by depleting polymorphonuclear myeloid-derived suppressor cells (PMN-MDSCs; CD11b+Ly6C+Ly6G+). Because PMN-MDSCs also cause liver toxicity, we investigated the impact of IL-1R1 blockade on the efficacy and toxicity of agonistic CD40 antibody therapy in PDAC. Agonistic CD40 antibody therapy induced immune activation and significantly prolonged survival in orthotopic PDAC-bearing mice. IL-1R1 blockade monotherapy downregulated innate and adaptive immune response and exacerbated tumor growth. Although combination therapy upregulated several immune-related pathways and boosted innate and adaptive immune responses. IL-1R1 blockade failed to improve the overall antitumor efficacy of agonistic CD40 antibody therapy and exacerbated liver toxicity. Ly6G+ cell depletion in mice reduced the efficacy of agonistic CD40 antibody therapy, suggesting that Ly6G+ immune cells (PMN-MDSCs or neutrophils) exhibit an antitumor rather than immunosuppressive role in PDAC. Our findings underscore the complex role of IL-1 signaling in modulating immune responses in PDAC and caution against pursuing IL-1R1 blockade, either as monotherapy or combined with agonistic CD40 antibodies, in clinical trials for PDAC.

Ligation-recognition triggered RPA-Cas12a cis-cleavage fluorogenic RNA aptamer for one-pot and label-free detection of MicroRNA in breast cancer

"One-pot" assays which combine amplification with CRISPR/Cas12a system are in constant attracted for biosensors development. Herein, we present a one-pot isothermal assay that Ligation-recognition triggered Recombinase Polymerase Amplification (RPA)-CRISPR/Cas12a cis-cleavage (LRPA-CRISPR) fluorescent biosensor for sensitive, specific, and label-free miRNA detection. Firstly, we reveal the programmed double-stranded DNA amplicons, which utilized the ligation-recognition and polymerization to form and amplified by the RPA system. Meanwhile, we enabled exponential ligation-recognition triggered recombinase polymerase amplification of miRNA-21 sequences and exploited the cis-cleavage mechanism of Cas12a with transcription to generate functional Mango RNA for signal output. This assay can be completed within 40 min and can allow a limit of detection of 3.43 aM for miRNA-21 detection, owing to the RPA with transcription amplification and enables to product the functional Mango RNA aptamer by in vitro transcription that binds to the TO1-Biotin fluorogenic dye. Moreover, our method exhibits the advantages of self-supply crRNA, label-free, excellent specificity, and universal detection platform via the design of one-pot detection in serum and cell samples, showing tremendous potential in biomarkers diagnostics of breast cancer.

Identification and validation of prognostic biomarkers related to tumor immune invasion in pancreatic cancer

Background

The diagnosis and treatment of pancreatic adenocarcinoma (PAAD) remain clinically challenging, and new molecular markers for prognostic assessment and targeted therapy are urgently needed. The tumor microenvironment (TME) and immune invasion play an important role in pancreatic cancer development and progression. Therefore, immunotherapeutic strategies based on the TME and immune invasion may have important clinical value.

Methods

In this study, we extracted transcriptome and clinicopathological data for 179 PAAD samples from the TCGA database and evaluated the immune composition, stromal composition, and infiltrating immune cell landscape in the tumor samples. Then, we identified relevant differentially expressed genes (DEGs) and performed functional annotation and prognostic correlation analysis to identify prognostic biomarkers for pancreatic cancer, the correlation between biomarkers and tumor immune invasion was analyzed to reveal the molecular immune mechanism of pancreatic cancer. Finally, GEO databases (GES71729), GEPIA, TISIDB, TIMER databases and RT-PCR were used for further analysis.

Results

CXCL10 and CXCL11 were highly expressed in pancreatic cancer and associated with poor prognosis of patients through cell adhesion molecules chemokine signaling, cytokine-cytokine receptor interaction, natural killer cell-mediated cytotoxicity, and Toll-like receptor signaling pathways. Finally, the correlation between CXCL10 and CXCL11 and tumor immune invasion was analyzed. The results confirmed that the expression levels of CXCL10 and CXCL11 were positively correlated with the contents of CD8+ T cells. Activated memory CD4+ T cells, M1 macrophages and resting mast cells. The levels of CXCL10 and CXCL11 were related to but negatively correlated with the contents of memory B cells, Tregs and M0 macrophages.

Conclusion

Our study demonstrates that CXCL10 and CXCL11 are novel biomarkers of TME and immune cell infiltration in pancreatic cancer by affecting the distribution of immune cells. CXCL10 and CXCL11 may be new targets for molecular targeted therapy and immunotherapy of pancreatic cancer.

Electric Field-Resistant Bubble-Enhanced Wash-Free Profiling of Extracellular Vesicle Surface Markers

Efficient profiling of circulating extracellular vesicles (EVs) benefits noninvasive cancer diagnosis and therapeutic monitoring, but is technically hampered by tedious isolation, multistep washing, and poor sensitivity. Here, we report multifunctional bubbles that enable self-separation, wash-free, single-step, and ultrasensitive profiling of EV surface markers in plasma samples for early diagnosis and treatment monitoring of lung cancer. In this assay, the buoyancy-dominated bubble is electric field-resistant, allowing EV-responsive release of electroactive probes for electrohydrodynamic nanoshearing force-enhanced hybridization, self-separation from the electrode interface for minimizing noise in electrochemical measurements, and one-step wash-free EV profiling. This assay achieves sensitivity near a single-EV level, shows high specificity against nontarget EVs, and tracks EV phenotypic changes induced by drugs. We further show that this technology can classify plasma samples (n = 111) between cancer patients and noncancer controls with accuracies >95%, enable accurate early diagnosis via machine learning, and monitor pre/post-surgery efficacy with higher accuracy over routine clinical serum markers. This bubble-driven one-step EV assay provides a promising wash-free quantitative tool to enable clinical precision liquid biopsies.

Precise amplification-free detection of highly structured RNA with an enhanced SCas12a assay

The CRISPR/Cas12a system has revolutionized molecular diagnostics, yet the direct detection of RNA, particularly those with complex structures, remains a significant challenge. Here, we present an updated SCas12a system, termed SCas12aV2, which enables precise, amplification-free detection of highly structured RNA molecules. By optimizing the length of scaffold RNA, targeting asymmetric structures, and utilizing dsDNA-ssDNA hybrid activators, we have significantly reduced steric hindrance in the detection system, thereby markedly enhancing both sensitivity and kinetics compared to traditional DNA activators. The SCas12aV2 assay achieves a detection limit of 246 aM for pooled activators and 10 pM for single-site targeting, demonstrating high specificity for single nucleotide polymorphisms (SNPs). It successfully identifies viable bacteria and SARS-CoV-2 infections in clinical samples. The assay is versatile and can be applied to various Cas12a orthologs, including thermostable CtCas12a. This work advances molecular diagnostics by improving the accuracy and efficiency of RNA detection.

Nutrients Lowering Obesity-Linked Chemokines Blamable for Metastasis

Food intake is an essential contributor to both health and disease. Nutrients contribute to a beneficial metabolic equilibrium at the cellular level, preventing or delaying disease onset. Dietary intake contributes to obesity, and obesity supports further cancer and metastasis. Metastasis, a multifactorial and multistep process, is supported by the systemic inflammation of obesity. Spreading of the cancer cells requires the presence of a plethora of recruiter and regulator molecules. Molecules such as chemokines are provided at high levels by obesity-associated fat depots. Chemokine up-regulation in adipose tissue of obese individuals has been associated with different types of cancers such as breast, prostate, colon, liver, and stomach. Chemokines support all metastasis steps from invasion/migration to intravasation, circulation, extravasation, and ending with colonization. The obesity pool of chemokines supporting these processes includes CCL2, CCL3, CCL4, CCL5, CCL7, CCL8, CCL11, CCL18, CCL19, CCL20, CXCL1, CXCL5, CXCL 8, CXCL10, and CXCL12. Keeping obesity under control can be beneficial in reducing the levels of pro-inflammatory chemokines and the risk of poor cancer outcome. Nutrients can help, support, and boost cancer treatment effects or jeopardize the treatment. Constituents with anti-inflammatory and anti-obesity properties such as polyphenols, organosulfur components, fatty acids, curcumin, and vitamin E have a proven beneficial effect in lowering obesity and its contribution to metastasis.

From morphology to single-cell molecules: high-resolution 3D histology in biomedicine

High-resolution three-dimensional (3D) tissue analysis has emerged as a transformative innovation in the life sciences, providing detailed insights into the spatial organization and molecular composition of biological tissues. This review begins by tracing the historical milestones that have shaped the development of high-resolution 3D histology, highlighting key breakthroughs that have facilitated the advancement of current technologies. We then systematically categorize the various families of high-resolution 3D histology techniques, discussing their core principles, capabilities, and inherent limitations. These 3D histology techniques include microscopy imaging, tomographic approaches, single-cell and spatial omics, computational methods and 3D tissue reconstruction (e.g. 3D cultures and spheroids). Additionally, we explore a wide range of applications for single-cell 3D histology, demonstrating how single-cell and spatial technologies are being utilized in the fields such as oncology, cardiology, neuroscience, immunology, developmental biology and regenerative medicine. Despite the remarkable progress made in recent years, the field still faces significant challenges, including high barriers to entry, issues with data robustness, ambiguous best practices for experimental design, and a lack of standardization across methodologies. This review offers a thorough analysis of these challenges and presents recommendations to surmount them, with the overarching goal of nurturing ongoing innovation and broader integration of cellular 3D tissue analysis in both biology research and clinical practice.

Engineering a DNA polymerase for modifying large RNA at specific positions

The synthesis of large RNA with precise modifications at specific positions is in high demand for both basic research and therapeutic applications, but efficient methods are limited. Engineered DNA polymerases have recently emerged as attractive tools for RNA labelling, offering distinct advantages over conventional RNA polymerases. Here, through semi-rational designs, we engineered a DNA polymerase variant and used it to precisely incorporate a diverse range of modifications, including base modifications, 2'-ribose modifications and backbone modifications, into desired positions within RNA. We achieved efficiencies exceeding 85% in the majority of modification cases, demonstrating success in introducing 2'-O-methyl, phosphorothioate, N4-acetylcytidine and a fluorophore to specific sites in eGFP and Firefly luciferase messenger RNA. Our mRNA products with N4-acetylcytidine, 2'-O-methyl and/or phosphorothioate have demonstrated the ability to enhance stability and affect protein production. This method presents a promising tool for the comprehensive functionalization of RNA, enabling the introduction of plentiful modifications irrespective of RNA lengths and sequences.

Subtype-associated complexity and prognostic significance of the NLRP3 inflammasome landscape in pancreatic neoplasms

Intraductal papillary mucinous neoplasm (IPMN) can progress into malignant pancreatic cancer, posing challenges in accurately assessing the risk of malignancy. While the nucleotide-binding oligomerization domain (NOD)-like receptor pyrin domain containing 3 (NLRP3) inflammasome pathway's role in pancreatic ductal adenocarcinoma (PDAC) has been extensively studied, its implications in IPMN remain unexplored. This study aimed to investigate the prognostic significance of NLRP3 inflammasome-related proteins across IPMN subtypes and their associations with tumor characteristics, with a secondary focus on comparing expression patterns in IPMN and PDAC. A cohort of 187 patients (100 IPMN and 87 PDAC) underwent high-dimensional histopathological imaging using the multiplexed immunohistochemical consecutive staining on single slide method and a semi-automated image analysis workflow. Expression levels of NLRP3, apoptosis-associated speck-like protein containing a caspase-recruitment domain (ASC), caspase-1, interleukin-1 beta, interleukin-18 (IL-18), interleukin-1 receptor antagonist, and interleukin-18 binding protein (IL-18BP) were evaluated and compared between IPMN and PDAC samples. The relationships between protein expression and tumor characteristics were examined. Principal component analysis distinguished between intestinal and nonintestinal clusters based on NLRP3-associated proteins. Lower IL-18 expression was linked to the intestinal subtype, while higher caspase-1 was linked to the pancreatobiliary subtype. Elevated caspase-1 and ASC expression were associated with invasiveness in IPMN. No significant correlation was found between the examined proteins and later-stage tumor characteristics in invasive cases. The IL-18/IL-18BP ratio was an independent prognostic factor in invasive IPMN. Our findings highlight the prognostic significance of IL-18 and the IL-18/IL-18BP ratio in invasive IPMNs. These results point to a complex regulation of NLRP3 inflammasome proteins, especially effector cytokines, in pancreatic neoplasms, which are strongly linked to subtype and prognosis.

TE-RPA: One-tube telomerase extension recombinase polymerase amplification-based electrochemical biosensor for precise diagnosis of urothelial carcinoma

Telomerase demonstrates potential as a non-invasive urinary biomarker for urothelial carcinoma (UC); however, current detection methods are either labor-intensive or exhibit suboptimal performance. There is a need for alternative approaches to enable rapid and early diagnosis of UC. In this study, we propose TE-RPA, which combines telomerase extension (TE) with recombinase polymerase amplification (RPA) for one-tube isothermal amplification. The GC content and length of the telomerase substrate were first considered during the screening process. TE-RPA exponential amplification was initiated by the addition of MgOAc along with a forward primer derived from the products of telomerase-mediated extension and a corresponding reverse primer. The amplification product from TE-RPA was subsequently detected using CRISPR-Cas12a system for trans-cleavage of signal probes on the surface of screen-printed electrode in an electrochemical biosensor, resulting in a current change that reflects the corresponding concentration of telomerase. The TE-RPA/CRISPR-Cas12a/electrochemical sensing platform achieves a limit of detection (LOD) for telomerase activity as low as a single-cell level. In addition, the platform attained an area under the curve (AUC) value of 0.9589 in a clinical evaluation involving urine samples from 43 suspected UC patients. Overall, our proposed platform not only offers an efficient method for telomerase isothermal amplification but also provides a portable and precise diagnostic tool for UC.

Human placental extract improves liver cirrhosis in mice with regulation of macrophages and senescent cells

INTRODUCTION

Cirrhosis is a disease with poor prognosis that requires the development of a novel therapeutic approach alternative to liver transplantation. In this study, we focused on the placenta and aimed to clarify the effects of human placental extract (HPE) on cirrhosis.

METHODS

A mouse model of carbon tetrachloride-induced cirrhosis was used to evaluate the effect of HPE administration subcutaneously and compared with the control group (n = 8 for each group). In vitro and in vivo, real time-PCR and immunostaining were performed for HPE mechanistic analysis. Spatial transcriptomics was also performed for detailed analysis of the effect of HPE on cirrhosis.

RESULTS

HPE administration improved serum ALT levels compared to control mice. Furthermore, there was a decrease in the number of senescent cells in the liver and the mRNA levels of secrete senescence-associated secretory phenotype factors and Cdkn2a (p16). In vitro, HPE induced macrophage polarization to the anti-inflammatory M2 phenotype. Spatial transcriptomics was also performed to analyze the underlying anti-inflammatory mechanism. The results showed that HPE strongly polarized macrophages to the M2 phenotype, especially in macrophage-rich regions in the liver. Gene expression pathway analysis using spatial transcriptomics also revealed the possibility of improving senescent cell-derived inflammation via mitochondrial function.

CONCLUSIONS

HPE improves serum ALT levels via anti-inflammatory mechanisms in macrophages and senescent cells. HPE serves as a novel agent for cirrhosis treatment.

Alkaline Phosphatase-Regulated DNAzyme Cleavage Coupled with CRISPR/Cas12a for Quantitative Detection of Deoxynivalenol in Agricultural Crops

Sensitive and simplified detection of a mycotoxin such as deoxynivalenol (DON) is crucial for food safety. In recent years, the CRISPR/Cas technology has demonstrated significant potential in detecting non-nucleic acids. Herein, we present a triple enzyme-assisted fluorescence immunoassay (TEFIA) that integrates alkaline phosphatase (ALP)-regulated DNAzyme cleavage with the CRISPR/Cas12a assay for the accurate detection of mycotoxin. By employing this method for detecting DON, we exhibit a low detection limit of 0.05 ng/mL and a satisfactory linear response between 0.1 and 10 ng/mL. This performance exceeds the conventional sensitivity levels found in traditional methods. TEFIA also demonstrates a good correlation with ic-ELISA for testing DON in real samples. Thus, it offers a robust and efficient detection platform for DON in complex matrices. Furthermore, TEFIA can be employed to identify various targets of interest by merely altering the antibody-antigen pairs, indicating its great potential in a wide range of applications.

N-Deficient B-Doped g-C3N4/CdS Heterojunction-Based PEC-FL Biosensor Assisted by CRISPR-Cas12a System for Ultrasensitive Determination of microRNA

Near-infrared light (NIR)-driven photoelectrochemical (PEC) processes are mainly faced with the limitation of weak photocurrents. Here, N-deficient B-doped g-C3N4/CdS (NB-g-C3N4/CdS) is proposed to construct a NIR-driven PEC biosensor assisted by CRISPR-Cas12a system for the determination of microRNA-21 (miRNA-21). To promote the optical absorption as well as the separation of photogenerated electrons and holes of g-C3N4, NB-g-C3N4/CdS is constructed via engineering the electronic and band structure in terms of N defect, B doping, and heterojunction, achieving high PEC performance. To obtain the high luminescence efficiency for exciting NB-g-C3N4/CdS under NIR, the core-shell NaYF4:Yb3+, Tm3+@NaYF4 upconversion nanoparticles (UCNPs) with repaired defects are prepared. Furthermore, the rolling circle amplification (RCA)-assisted CRISPR-Cas12a system is integrated to fragment the DNA on UCNPs, achieving sensitive detection of miRNA-21. On the one hand, the uncleavaged signal probes on UCNPs combined with NB-g-C3N4/CdS through π-π stacking interaction, generating photocurrents under the irradiation of NIR. On the other hand, the cleavaged signal probes which cannot link with NB-g-C3N4/CdS exhibited the fluorescence (FL) signals. The proposed PEC-FL dual-mode biosensor provides a mutual authentication of testing results and demonstrates ultrasensitivity (the detection limit of 1.1 fM for PEC mode and 7.0 fM for FL mode) and excellent specificity, which is promising in the clinical analysis of miRNA.

Harnessing crRNA Transformer for Facile and Specific Nucleic Acid Detection

CRISPR/Cas systems have emerged as promising tools for nucleic acid detection. However, their practical applications have been limited by poor specificity and the need for additional preprocessing steps. Inspired by the concept of transformers, we found that changing the forms of crRNA with spatial arrangement may endow CRISPR/Cas with an enhanced performance for nucleic acid detection. Specifically, we rationally designed two crRNA transformers─swap crRNA and split crRNA─and found that they direct the CRISPR/Cas system for cis- and trans- cleavage with enhanced specificity and decreased Cas binding affinity and possess both DNA and RNA detection abilities. Based on these findings, our strategy enabled the identification of clinical prostatic cancer in a one-step reaction, with a remarkable sensitivity of 90.0% and specificity of 96.0%. Our study deepens the understanding of CRISPR/Cas systems and introduces a promising strategy for simple nucleic acid detection with enhanced specificity, sensitivity, and functionality in clinical molecular diagnosis.

Primer Exchange Reaction with Cascade RNA Transcription for Highly Specific Detection of Exosomal miRNA and Liver Cancer Diagnosis

Exosomal microRNAs (miRNAs) serve as dependable and noninvasive biomarkers for early cancer diagnosis. However, the accurate and feasible detection of exosomal miRNAs is often hindered by their low abundance and the requirement of specialized equipment for miRNA detection. In this study, we present a novel approach, termed primer exchange reaction-based fluorescence emission with cascade RNA aptamers transcription (PERFECT) for the highly sensitive detection of exosomal miRNA. The design of this method involves the selective interaction of a DNA probe with the target miRNA, leading to its activation. Once activated, isothermal signal amplification and RNA aptamer transcription are initiated, resulting in an amplified fluorescent signal within 90 min. This method achieves a detection limit of 2.2 fM at 37 °C and 2.7 fM at room temperature (25 °C). We used the PERFECT technology to analyze miR-21 expression levels in cell extracts, cell-derived exosomes, and human plasma-derived exosomes, achieving a diagnostic accuracy of 93.6% in distinguishing hepatocellular carcinoma (HCC) patients. Overall, this study highlights its broad range of detection temperature, simplicity of the detection process, and strong potential for clinical application, rendering it a promising tool for early cancer diagnosis.

Inflammation, microbiota, and pancreatic cancer

Pancreatic cancer (PC) is a malignancy of gastrointestinal tract threatening the life of people around the world. In spite of the advances in the treatment of PC, the overall survival of this disease in advanced stage is less than 12%. Moreover, PC cells have aggressive behaviour in proliferation and metastasis as well as capable of developing therapy resistance. Therefore, highlighting the underlying molecular mechanisms in PC pathogenesis can provide new insights for its treatment. In the present review, inflammation and related pathways as well as role of gut microbiome in the regulation of PC pathogenesis are highlighted. The various kinds of interleukins and chemokines are able to regulate angiogenesis, metastasis, proliferation, inflammation and therapy resistance in PC cells. Furthermore, a number of molecular pathways including NF-κB, TLRs and TGF-β demonstrate dysregulation in PC aggravating inflammation and tumorigenesis. Therapeutic regulation of these pathways can reverse inflammation and progression of PC. Both chronic and acute pancreatitis have been shown to be risk factors in the development of PC, further highlighting the role of inflammation. Finally, the composition of gut microbiota can be a risk factor for PC development through affecting pathways such as NF-κB to mediate inflammation.

SPEAR: CRISPR-mediated ultrasensitive, specific and rapid one-pot detection strategy for cancer-related SNPs

Rationale: The ultrasensitive and accurate detection of driver mutations is critical for early cancer screening and precision medicine. Current methods face challenges in balancing sensitivity, specificity, and speed, which limits their clinical utility. Therefore, a rapid, sensitive, and specific method is essential for detecting cancer-related SNPs. Methods: This study introduces SPEAR (Specific Point mutation Evaluation via CRISPR-Cas Assisted Recognition), a novel methodology combining NEAR (Nicking Enzyme Amplification Reaction) isothermal amplification with SNP-specific recognition by Cas12b RNP in a one-pot configuration to detect cancer-related single nucleotide polymorphisms (SNPs). SPEAR leverages the power of NEAR isothermal amplification to efficiently amplify target DNA, followed by Cas12b RNP for SNP-specific recognition. This integrated approach ensures a rapid and precise mutation detection system in a single reaction. Results: The method was applied to blood samples for the detection of cancer-related mutations, with results obtained in approximately 30 min. The SPEAR enables detection of gene mutations at the single-molecule level and it can detect targets at a 0.1% ratio despite strong background interference. The method exhibits single-base resolution specificity, allowing for the detection of multiple SNPs in a single reaction. It outperforms first-generation sequencing (FGS) in both convenience and sensitivity, while remaining compatible with next-generation sequencing (NGS). Conclusion: SPEAR offers a rapid, sensitive, and convenient approach to detect cancer-related SNPs, with significant potential for clinical applications, including real-time detection and molecular diagnostics in precision medicine.