Immuno-SABER enables highly multiplexed and amplified protein imaging in tissues

Glass Fiber Interfaced Special Rolling Circle Amplification for Multiplexed Protein Detection with Paper Strip Digital Readouts

Point-of-care testing (POCT) for proteins faces challenges, including limited sensitivity and multiplexing capabilities. The recently developed minimum secondary structured rolling circle amplification (MSS-RCA) promised POCT with desirable sensitivity in nucleic acid detection under isothermal conditions, but with a long assay time. This study integrates the 5' specific enzymatic activity of T7 exonuclease with the high-speed template elongation ability of MSS-RCA in a one-pot system to establish the dual amplification T7-MSSRCA detection platform. T7-MSSRCA employed a specialized reporter modified with human chorionic gonadotrophin (hCG) molecules for signal output on hCG test strips, which could be measured by a lateral flow assay (LFA) analyzer. The integration of T7-MSSRCA with glass fiber interfaced immunoassays enabled multiplexed detection of low-abundance protein targets (α-synuclein, IL-6, TNF-α, and IFN-γ) at subpicogram levels in serum samples of Parkinson's disease with high specificity and accuracy, promising its application in biomarker identification of chronic diseases.

Erasable Fluorescence Imaging Technology Enables Continuous Tracking for Identical Living Cells

Subtle molecular events may trigger a cascade of "butterfly effects" to reverse cell fate, so dynamic tracking of relevant markers can provide crucial clues to decipher the unknown. However, existing analytical techniques are still at static-analysis level, and cutting-edge fluorescence imaging is limited by signal interference at adjacent time, failing to realize continuous observation for identical live cells. Herein, we develop a new temperature-controlled imaging technology, where melamine-mediated reversible DNA self-assembly drives the fluorescence illuminating and extinguishing at any time, achieving repeated erasable imaging for identical living cells. This method can track cell behaviors by taking dynamic monitoring of cell differentiation as an example, and timely fluorescence erasing guarantees authenticity for imaging results and minimizes interference with cellular activities. Thanks to high feasibility in fundamental experimental scenarios, this method hopefully provides a powerful preliminary screening tool for exploring new biological mechanisms in cell interactions, developmental transformations, downstream response inquiry, and so forth.

Imaging 3D cell cultures with optical microscopy

Three-dimensional (3D) cell cultures have gained popularity in recent years due to their ability to represent complex tissues or organs more faithfully than conventional two-dimensional (2D) cell culture. This article reviews the application of both 2D and 3D microscopy approaches for monitoring and studying 3D cell cultures. We first summarize the most popular optical microscopy methods that have been used with 3D cell cultures. We then discuss the general advantages and disadvantages of various microscopy techniques for several broad categories of investigation involving 3D cell cultures. Finally, we provide perspectives on key areas of technical need in which there are clear opportunities for innovation. Our goal is to guide microscope engineers and biomedical end users toward optimal imaging methods for specific investigational scenarios and to identify use cases in which additional innovations in high-resolution imaging could be helpful.

Sensitive and reliable gastric ulcer related MicroRNA detection by bridge catalytic hairpin assembly (bCHA) mediated primer exchange reaction

MicroRNAs (miRNA) have a significant role in the progression of gastric ulcer, and the sensitive and reliable detection of miRNAs is pivotal for the early diagnosis and treatment of gastrointestinal diseases. In this study, we developed a novel and efficient method for detecting miRNA-122, a crucial biomarker used to assess the prognosis of gastric ulcers. This method combines the bridge catalytic hairpin assembly (bCHA)-based target sequence recycling with the primer exchange reaction (PER), resulting in a highly sensitive and label-free approach. Specifically, the bridge CHA technique, which offers superior target recognition accuracy and increased signal amplification efficiency compared to the classic CHA procedure, can selectively identify the target miRNA and release the complementary sequence to serve as a primer to facilitate the PER. This PER process produces a large number of G-quadruplex sequences, which then bind with thioflavin T to significantly increase its fluorescence. This enhanced fluorescence is used to detect miRNA-122, with a detection limit as low as 3.12 fM. The proposed approach can achieve exact discrimination of the target miRNA-122. Due to its label-free character, high selectivity, and sensitivity, this technology can serve as a practical and universal approach for detecting different biomarkers in the early stages of gastrointestinal diseases.

A Validation Workflow for Novel Oligonucleotide Sequences to Expand the Multiplexing Capacity of the CO-Detection by indEXing (CODEX) Platform

Antibody-based multiplexed tissue imaging has the potential to provide critical advances in biological discoveries and their translation for clinical applications. With the increasing introduction of markers and modalities for spatial analysis, there is an according demand for the expansion of multiplexing capacities of such imaging platforms. CO-Detection by indEXing (CODEX) is a widely used multiplexed tissue imaging platform that utilizes DNA-conjugated antibodies for imaging. The multiplexing capacity of CODEX is limited by the availability of unique DNA-oligonucleotide sequences for antibody barcoding. In this study, we demonstrate a workflow for the validation and the introduction of novel sets of candidate DNA-oligonucleotide sequences for CODEX. Through cross-validation multicycle experiments with the already published library of DNA barcodes, we here present a set of 27 novel oligonucleotide sequences for CODEX, increasing the potential multiplexing capacity to 85+ markers. We confirmed the utility of the new barcodes using a 74-plex antibody panel on a multitumor tissue microarray of paraffin-embedded tissues. The workflow presented here provides a reproducible method for extending the plexity of the CODEX platform, facilitating a deeper understanding of tissue microenvironments.

AND logic gate-based alternating PER-Cas12a signal amplification system for ultrasensitive detection of sEVs

Protein biomarkers on breast cancer-derived small extracellular vesicles (BC-sEVs) hold great promise in liquid biopsy. However, it remains challenging due to their inherent heterogeneity and low abundance. Herein, we developed an AND logic gate-based DNA cascade signal amplification strategy, termed Alternating Primer Exchange Reaction-activated Cas12a (Alt-PER-Cas12a), for the ultrasensitive detection of BC-sEVs in clinic samples. This dual-protein recognition system employs EpCAM/MUC1-specific capture probes to release two DNA hairpins (Hep and Hmu) as AND gate inputs in Alt-PER. The corresponding Hep and Hmu hairpins can initiate the Alt-PER with a large amount of primers to generate long single-stranded DNA products with alternating repeat units. Each repeating unit serves as a CRISPR activator, inducing the trans-cleavage activity of Cas12a and enabling cascade signal amplification. The as-constructed strategy exhibits excellent sensitivity with LOD of 2.6 × 103 particles/mL. It has been successfully used to discriminate breast cancer patients from healthy donors (AUC = 0.992) in clinical validation, and shows great potential for liquid biopsy.

DNA-PAINT Imaging with Hydrogel Imprinting and Clearing

Hydrogel-embedding is a versatile technique in fluorescence microscopy, offering stabilization, optical clearing, and the physical expansion of biological specimens. DNA-PAINT is a super-resolution microscopy approach based on the diffusion and transient binding of fluorescently labeled oligos, but its feasibility in hydrogels has not yet been explored. In this study, we demonstrate that polyacrylamide hydrogels support sufficient diffusion for effective DNA-PAINT imaging. Using acrydite-anchored oligonucleotides imprinted from patterned DNA origami nanostructures and microtubule filaments in fixed cells, we find that hydrogel embedding preserves docking strand positioning at the nanoscale. Sample clearing via protease treatment had minor structural effects on the microtubule structure and enhanced diffusion and accessibility to hydrogel-imprinted docking strands. Our work demonstrates promising potential for diffusion and binding-based fluorescence imaging applications in hydrogel-embedded samples.

Extended Linear Confined Zipper Cascaded Reaction for Highly Efficient Intracellular Imaging and Assisting Diagnosis of Thyroid Cancer

Highly sensitive detection and in situ tracing analysis of small-molecule biomarkers are particularly indispensable to deciphering the pathogenesis and pathological process. Despite DNA assembly-based barcoding and amplification strategies across the breadth of molecular in situ analysis, an easy-to-design, nonenzymatic, highly efficient, background leakage-avoided, highly specific, and sensitive system is highly required yet is still in its infancy. Spatial confinement nano-assembly can increase the reaction efficiency in a localized isothermal autonomous manner. Here in this work, the DNA assembly that originally relies on random collisions between freely diffusing probes is constructed between two extended linear confined probes, by which a novel confined reaction model named as extended linear confined zipper hybridization chain reaction (ZHCR) is proposed. ZHCR can significantly improve the efficiency of probe assembly and enable stable assembly within live cells, providing precise in situ target information. ZHCR system is employed to analyze two thyroid cancer-specific miRNAs, achieving in situ tracing and serum content detection. By integrating machine learning algorithms, ZHCR demonstrates significant potential in thyroid cancer auxiliary diagnosis, establishing a versatile platform that enables both highly sensitive homogeneous detection and in situ analysis of low-abundance nucleic acid fragments.

Spatial analysis identifies DC niches as predictors of pembrolizumab therapy in head and neck squamous cell cancer

Head and neck squamous cell carcinoma (HNSCC) shows variable response to anti-programmed cell death protein 1 (PD-1) therapy, which can be partially explained by a combined positive score (CPS) of tumor and immune cell expression of programmed death-ligand 1 (PD-L1) within the local tumor microenvironment (TME). To better define TME immune determinants associated with treatment efficacy, we conduct a study of n = 48 HNSCC tumors from patients prior to pembrolizumab therapy. Our investigation combines a rapid bioorthogonal multiplex staining method with computational analysis of whole-slide imaging to capture the single-cell spatial heterogeneity and complexity of the TME. Analyzing 6,316 fields of view (FOVs), we provide comprehensive PD-L1 phenotyping and cell proximity assays across the entirety of tissue sections. While none of the PD-L1 metrics adequately predict response, we find that the spatial organization of CCR7+ dendritic cells (DCs) in niches better predicts overall patient survival than CPS alone. This study highlights the importance of understanding the spatial context of immune networks for immunotherapy.

Nicking endonuclease-mediated primer exchange reaction for rapid and sensitive miRNA detection

Primer exchange reaction (PER) is a novel and simple nucleic acid-templated extension technique that has recently attracted much attention in the field of biosensing. However, current PER reactions have shown relatively slow rates and low amplification performances, resulting in long assay times and limited detection sensitivities. Here we report a nicking endonuclease-mediated PER reaction (named NEPER) that rapidly releases amplified DNA products by adding a nicking endonuclease to hydrolyze the hybridized double-stranded DNA (dsDNA), and consequently has a maximum speed that is thirty orders of magnitude greater than the maximum for conventional PER. We further combined a CRISPR/Cas12a signal readout technique and developed a cascade NEPER-CRISPR/Cas12a method that can detect miRNA-155 with a limit of detection (LOD) down to 3.1 fM. We also show that the NEPER-CRISPR/Cas12a can be used to detect targets in serum samples.

Orthogonal DNA self-assembly technology enables rapid and accurate analysis of circulating tumor cells in breast cancer

BACKGROUND

As a non-invasive liquid biopsy technology, the detection of circulating tumor cells (CTCs) overcomes the limitations of traditional tissue biopsy methods, enabling continuous sample collection and long-term dynamic monitoring. However, current CTCs analysis methods typically rely on cell size to separate and identify tumor cells, which fails to effectively distinguish tumor cells from different sources. In addition, existing methods are often constrained by limited antibody species, typically detecting only 2-3 molecular phenotypes. This narrow detection scope does not fully capture the heterogeneity of CTCs at the single-cell level, thus limiting its utility in precision diagnosis and personalized treatment. To address these challenges, it is urgent to develop CTCs detection methods that can simultaneously integrate comprehensive target and cell morphology information.

RESULTS

Using breast cancer as a research model, we developed a computer-aided design-based hybridization chain reaction (CAD-HCR) by combining DNA encoding and antibody coupling technologies with orthogonal DNA self-assembly to achieve multiple detection and heterogeneity analysis of breast cancer mimic samples. This technology overcomes the limitation of antibody species in traditional CTCs detection and utilizes antibody-trigger strand coupling to convert target protein signals into DNA signals, thereby circumventing throughput limitation of existing detection methods. By utilizing the signal amplification effect of DNA self-assembly, this technology enhances sensitivity significantly, allowing for accurate single-cell level detection of CTCs.

SIGNIFICANCE

This technology provides spatial positioning and cell morphological characteristics information for CTCs analysis of breast cancer, which is expected to provide a more accurate basis for diagnosis and treatment decision-making for in-depth understanding of tumor heterogeneity and clinical applications.

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.

Signal amplification by cyclic extension enables high-sensitivity single-cell mass cytometry

Mass cytometry uses metal-isotope-tagged antibodies to label targets of interest, which enables simultaneous measurements of ~50 proteins or protein modifications in millions of single cells, but its sensitivity is limited. Here, we present a signal amplification technology, termed Amplification by Cyclic Extension (ACE), implementing thermal-cycling-based DNA in situ concatenation in combination with 3-cyanovinylcarbazole phosphoramidite-based DNA crosslinking to enable signal amplification simultaneously on >30 protein epitopes. We demonstrate the utility of ACE in low-abundance protein quantification with suspension mass cytometry to characterize molecular reprogramming during the epithelial-to-mesenchymal transition as well as the mesenchymal-to-epithelial transition. We show the capability of ACE to quantify the dynamics of signaling network responses in human T lymphocytes. We further present the application of ACE in imaging mass cytometry-based multiparametric tissue imaging to identify tissue compartments and profile spatial aspects related to pathological states in polycystic kidney tissues.

Locked Nucleic Acid-Enhanced Entropy-Driven Amplifier Combined with Catalytic Hybridization Reaction-Based DNA Circuit for Dual Amplified Detection of Single Nucleotide Polymorphisms and Asymmetric Encryption of Gene Information

Single-nucleotide polymorphisms (SNPs) play a pivotal role in investigations of disease-associated genes and in the genetic analysis of animal and plant varieties. Therefore, the detection of SNPs is essential for advancing biomedical diagnostics and therapeutics. Here, we report a locked nucleic acid (LNA)-enhanced dual signal amplification strategy for high-contrast detecting single-nucleotide polymorphisms (SNPs) in the KRAS_G12C gene. By integrating entropy-driven amplification with catalytic hybridization reaction, the proposed method achieves significant amplification of fluorescence and resonance Rayleigh scattering signals. The incorporation of LNA modification enhances the thermodynamic stability and reaction kinetics of the DNA computing circuit, resulting in superior sensitivity and specificity for SNPs detection. The method exhibits a low detection limit of 0.19 fM and a wide dynamic range from 1 fM to 0.1 nM for the KRAS_G12C gene. Compared to traditional DNA-based circuits, the LNA-modified system demonstrates enhanced discrimination of single-base mismatches and improved signal gain. Moreover, the proposed method was further demonstrated for its potential application in human serum samples. Impressively, this research not only presents a highly sensitive and selective platform for SNPs detection but also demonstrates its potential for molecular-level information encryption. The incorporation of LNA in dual signal amplification significantly elevates the intricacy and robustness of information encryption. Therefore, this study underscores the potential of DNA-based technologies to serve as a bridge between the era of biomedical research and the emerging Internet of things.

SPECTREPlex: an automated, fast, high-resolution enabled approach for multiplexed cyclic imaging and tissue spatial analysis

Mapping the spatial organization of tissues is critical to understanding organ biology in health and disease. Developments in multiplexed antibody-based, fluorescence labelling methods have provided unique insights into tissue microenvironments. However, many current methods have a variety of limitations that reduce their practical utilization including cost, time and technical complexity. To address these drawbacks, we developed Spatial Photo-inactivation Enhanced Cyclic Target REsolved multiPlexing (SPECTRE-Plex). SPECTRE-Plex is a relatively low cost, end-to-end technique based on a series of methods that significantly improve speed, automation, and resolution of cyclic multiplex immunofluorescence imaging. We describe a representative example of the application of the method by investigating spatial cellular and neighborhood changes in the proximal small intestine between healthy tissue and active celiac disease.

DNA Origami Scaffold-Based Peptide-Major Histocompatibility Complex Multimers for Spatial Imaging of T Cells

Visualizing the spatial distribution of antigen-specific T cells is essential for understanding immune responses and improving therapeutic strategies. However, detecting low-affinity antigen-specific T cells and enhancing signals from low-abundance populations remain challenging due to limitations in sensitivity. Here, we report DNA origami scaffold-based peptide-major histocompatibility complex multimers (DOS-pMHCs) with precise spatial organization of pMHC and signaling molecules on the nanoscale for enhanced in situ visualization of antigen-specific T cells. The two-dimensional triangular DNA origami precisely organizes pMHCs and signaling molecules with high valency, significantly improving binding to antigen-specific T cells and signal amplification. These DOS-pMHCs facilitate enhanced visualization of antigen-specific T cells in lymphoid tissues compared to traditional tetramers. Moreover, we show that DOS-pMHCs enable the in situ detection of autoimmune T cells with lower affinity T cell receptors (TCRs), which are difficult to identify using traditional tetramers. This in situ detection strategy provides a powerful tool for mapping the spatial distribution of antigen-specific T cells, thus holding great potential for advancing our understanding of immune responses and guiding personalized immunotherapy.

High-dimensional imaging using combinatorial channel multiplexing and deep learning

Understanding tissue structure and function requires tools that quantify the expression of multiple proteins at single-cell resolution while preserving spatial information. Current imaging technologies use a separate channel for each protein, limiting throughput and scalability. Here, we present combinatorial multiplexing (CombPlex), a combinatorial staining platform coupled with an algorithmic framework to exponentially increase the number of measured proteins. Every protein can be imaged in several channels and every channel contains agglomerated images of several proteins. These combinatorically compressed images are then decompressed to individual protein images using deep learning. We achieve accurate reconstruction when compressing the stains of 22 proteins to five imaging channels. We demonstrate the approach both in fluorescence microscopy and in mass-based imaging and show successful application across multiple tissues and cancer types. CombPlex can escalate the number of proteins measured by any imaging modality, without the need for specialized instrumentation.

Single-Cell Multi-Omics: Insights into Therapeutic Innovations to Advance Treatment in Cancer

Advances in single-cell multi-omics technologies have deepened our understanding of cancer biology by integrating genomic, transcriptomic, epigenomic, and proteomic data at single-cell resolution. These single-cell multi-omics technologies provide unprecedented insights into tumour heterogeneity, tumour microenvironment, and mechanisms of therapeutic resistance, enabling the development of precision medicine strategies. The emerging field of single-cell multi-omics in genomic medicine has improved patient outcomes. However, most clinical applications still depend on bulk genomic approaches, which fail to directly capture the genomic variations driving cellular heterogeneity. In this review, we explore the common single-cell multi-omics platforms and discuss key analytical steps for data integration. Furthermore, we highlight emerging knowledge in therapeutic resistance and immune evasion, and the potential of new therapeutic innovations informed by single-cell multi-omics. Finally, we discuss the future directions of the application of single-cell multi-omics technologies. By bridging the gap between technological advancements and clinical implementation, this review provides a roadmap for leveraging single-cell multi-omics to improve cancer treatment and patient outcomes.

POSA for fast, amplified and multiplexed protein imaging

Fluorescent π-conjugated polymers (FCPs) are known for their superior brightness but are still unavailable for highly multiplexed molecular imaging in single cells as they are hydrophobic and lack targeting capability toward biomolecules. Herein, we develop a π-conjugated polymer-based amplification (POSA) method to achieve highly multiplexed signal amplification. Optical amplification by virtue of the high brightness of FCPs makes POSA a simple and quick signal amplification technique that can spatially resolve the distribution of multiplexed proteins in single cells, with a 28- to 126-fold signal amplification effect. By this POSA method, we demonstrate that the high brightness of FCPs can be used to strengthen the images of subcellular biomolecules and showcase the phenomenon of optical amplification of FCPs at the cellular level. Additionally, with its sensitivity, ease of use, and quick imaging features, the POSA technique proves to be a valuable tool for advanced biological research.

Comparative prospects of imaging methods for whole-brain mammalian connectomics

Mammalian whole-brain connectomes are a foundational ingredient for a holistic understanding of brains. Indeed, imaging connectomes at sufficient resolution to densely reconstruct cellular morphology and synapses represents a long-standing goal in neuroscience. Mouse connectomes could soon come within reach, while human connectomes remain a more distant yet still worthy goal. Though the technologies needed to reconstruct whole-brain connectomes have not yet reached full maturity, they are advancing rapidly. Close examination of these technologies may help plan connectomics projects. Here, we quantitatively compare imaging technologies that have the potential to enable whole-brain mammalian connectomics. We perform calculations on electron microscopy (EM) techniques and expansion light-sheet fluorescence microscopy (ExLSFM) methods. We consider techniques that have sufficient resolution to identify all synapses and sufficient speed to be relevant for whole mammalian brains. We offer this analysis as a resource for those considering how to organize efforts toward imaging whole-brain mammalian connectomes.

Emerging Trends in DNA Nanotechnology-Enabled Cell Surface Engineering

Cell surface engineering is a rapidly advancing field, pivotal for understanding cellular physiology and driving innovations in biomedical applications. In this regard, DNA nanotechnology offers unprecedented potential for precisely manipulating and functionalizing cell surfaces by virtue of its inherent programmability and versatile functionalities. Herein, this Perspective provides a comprehensive overview of emerging trends in DNA nanotechnology for cell surface engineering, focusing on key DNA nanostructure-based tools, their roles in regulating cellular physiological processes, and their biomedical applications. We first discuss the strategies for integrating DNA molecules onto cell surfaces, including the attachment of oligonucleotides and the higher-order DNA nanostructure. Second, we summarize the impact of DNA-based surface engineering on various cellular processes, such as membrane protein degradation, signaling transduction, intercellular communication, and the construction of artificial cell membrane components. Third, we highlight the biomedical applications of DNA-engineered cell surfaces, including targeted therapies for cancer and inflammation, as well as applications in cell capture/protection and diagnostic detection. Finally, we address the challenges and future directions in DNA nanotechnology-based cell surface engineering. This Perspective aims to provide valuable insights for the rational design of DNA nanotechnology in cell surface engineering, contributing to the development of precise and personalized medicine.

High Dimensional Proteomic Multiplex Imaging of the Central Nervous System Using the COMET™ System

Sequential multiplex methodologies such as Akoya CODEX, Miltenyi MACSima, Rarecyte Orion, and others require modification of the antibodies by conjugation to an oligo or a specific fluorophore which means the use of off-the-shelf reagents is not possible. Modifications of these antibodies are typically performed via reduction chemistry and thus require verification and validation post-modification. Fixed panels are therefore developed due to various limitations including spectral overlap that creates spectral unmixing issues, steric hindrance, harsh antibody removal, and tissue degradation throughout the labeling. As such, a complex interrogation evaluating multiple study hypotheses and/or endpoints requires the development of sequential panels, reconstruction, and realignment of the tissue that necessitate a z-stack strategy. Standardized antibody panels are typically fixed and require substantial validation efforts to modify a single target and thus do not evolve with the pace of research interests. To increase the throughput of profiling cells within the human central nervous system (CNS), we developed and validated a CNS-specific library with an associated analysis platform using the newly developed Lunaphore COMET TM platform. The COMET TM is an automated staining/imaging instrument integrating a reagent deck for staining buffers and off-the-shelf label-free primary antibodies and fluorophore-labeled secondary antibodies, which feed into a circular plate holding up to 4 slides that are automatically imaged in microscope-operated control software. For this study, standard formalin fixed paraffin embedded histology slides are used. However, the COMET is capable of imaging fresh-frozen samples using specialized settings. Our methodologies address an unmet need in the neuroscience field while leveraging prior developmental efforts in the domain of immunology spatial profiling. Cataloging and validating a large series of antibodies on the COMET™ along with developing CNS autofluorescence management strategies while optimizing standard operating procedures have allowed for the visualization at the subcellular level. Forty analytes can be used to analyze one specimen which has clinical utility in cases in which the CNS can only be sampled by biopsy. CNS biopsies, depending on the anatomical location, can have limited available volume to a degree that requires prioritization and restriction to select analysis. In-depth bioinformatic imaging analysis can be done using standard bioinformatic tools and software such as Visiopharm®. These results establish a general framework for imaging and quantifying cell populations and networks within the CNS while providing the scientific community with standard operating procedures.

Derivative Technologies of Expansion Microscopy and Applications in Biomedicine

Expansion microscopy (ExM) is an innovative super-resolution imaging technique that utilizes physical expansion to magnify biological samples, facilitating the visualization of cellular structures that are challenging to observe using traditional optical microscopes. The fundamental principle of ExM revolves around employing a specialized hydrogel to uniformly expand biological samples, thereby achieving super-resolution imaging under conventional optical imaging conditions. This technology finds application not only in various biological samples such as cells and tissue sections, but also enables super-resolution imaging of large biological molecules including proteins, nucleic acids, and metabolite molecules. In recent years, numerous researchers have delved into ExM, resulting in the continuous development of a range of derivative technologies that optimize experimental protocols and broaden practical application fields. This article presents a comprehensive review of these derivative technologies, highlighting the utilization of ExM for anchoring nucleic acids, proteins, and other biological molecules, as well as its applications in biomedicine. Furthermore, this review offers insights into the future development prospects of ExM technology.

High-throughput multiplexed serology via the mass-spectrometric analysis of isotopically barcoded beads

In serology, each sample is typically tested individually, one antigen at a time. This is costly and time consuming. Serology techniques should ideally allow recurrent measurements in parallel in small sample volumes and be inexpensive and fast. Here we show that mass cytometry can be used to scale up multiplexed serology testing by leveraging polystyrene beads uniformly loaded with combinations of stable isotopes. We generated 18,480 unique isotopically barcoded beads to simultaneously detect, in a single tube with 924 serum samples, the levels of immunoglobulins G and M against 19 proteins from SARS-CoV-2 (a total of 36,960 tests in 400 nl of sample volume and 30 μl of reaction volume). As a rapid, high-throughput and cost-effective technique, serology by mass cytometry may contribute to the effective management of public health emergencies originating from infectious diseases.

Nucleic Acid Covalent Tags

The selective and site-specific chemical labeling of proteins has emerged as a pivotal research area in chemical biology and cell biology. An effective protein labeling typically meets several criteria, including high specificity, rapid and robust conjugation under physiological conditions, operation at low concentrations with biocompatibility, and minimal perturbation of the protein function and activity. The conjugation of nucleic acids with proteins has garnered significant attention recently due to the rapid advancements in nucleic acid probe technologies, leveraging the programmable nature of nucleic acids alongside the multifaceted functionalities of proteins. It helps to convert protein-specific information into nucleic acid signals, facilitating upstream versatile recognition and downstream signal amplification for the target protein. This review critically evaluates the recent progress in nucleic acid-based protein labeling methodologies, with a specific focus on covalent labeling using aptamer tags, protein fusion tags or the technique of metabolic oligosaccharide engineering. The tags establish covalent linkages with target proteins through various modalities such as small molecules or metabolic glycan engineering. The insights presented in the review highlight promising avenues for the development of highly specific and versatile protein labeling techniques, which is essential for the improvement of protein-targeted detection and imaging across diverse biological contexts.

A magnetic separation-assisted auto-cyclic primer extension for OSCC-associated salivary miRNA detection

It has attracted considerable attention in the detection of salivary miRNAs for the non-invasive diagnosis of oral squamous cell carcinoma (OSCC). Herein, we report an innovative magnetic separation-assisted auto-cyclic primer extension (MS-ACPE) for label-free and sensitive detection of miRNA-31 in human saliva. In this work, low-abundance miRNA-31 is initially transduced into primers that can be selectively separated and concentrated using a simple magnetic separation technology. By leveraging the high local concentration, the recognition and capture events between the primers and the hairpin can be greatly enhanced. Consequently, a "bind-copy-release" cycle can be effectively initiated, generating a user-prescribed, ultra-long single-stranded DNA with numerous repetitive quadruplex sequences. This allows for directly lighting up the fluorescence of thioflavin T, enabling amplified detection of miRNA-31. We experimentally demonstrate that MS-ACPE exhibits high specificity and sensitivity for miRNA-31, with a limit of detection as low as 0.31 pM. Furthermore, its reliability and applicability for the detection of miRNA-31 in saliva samples have been explored. More importantly, this novel MS-ACPE can effectively discriminate cancer patients from clinical samples with high accuracy (AUC = 1), potentially opening new avenues for the non-invasive diagnosis of OSCC in clinical applications.

CRISPR/Cas13a-Enhanced Porous Hydrogel Encapsulated Photonic Barcodes for Multiplexed Detection of Virus

In this study, we present an ultrasensitive and specific multiplexed detection method for SARS-CoV-2 and influenza (Flu) utilizing CRISPR/Cas13a technology combined with a hydrogel-encapsulated photonic crystal (PhC) barcode integrated with hybridization chain reaction (HCR). The barcodes, characterized by core-shell structures, are fabricated through partial replication of periodically ordered hexagonally close-packed silicon dioxide beads. Consequently, the opal hydrogel shell of these barcodes features abundant interconnected pores that provide a substantial surface area for probe immobilization. Furthermore, the inherent structural colors remain stable during detection events due to the robust mechanical strength of the barcode cores. This integration of CRISPR/Cas13a and HCR leverages both the highly specific RNA recognition capabilities and trans-cleavage activity of Cas13a while employing HCR to enhance sensitivity. Upon encountering target RNA, Cas13a cleaves a hairpin probe, thereby initiating subsequent HCR amplification for enhanced detection sensitivity. Our method demonstrates high accuracy and sensitivity in multiplexed detection of SARS-CoV-2, Flu A and Flu B RNA with a limit-of-detection as low as 200 aM. Importantly, this assay also exhibits acceptable accuracy in repeated clinical sample testing. Thus, our platform represents a promising strategy for highly sensitive multiplexed virus detection in clinical.

The spatial biology of HIV infection

HIV infection implicates a spectrum of tissues in the human body starting with viral transmission in the anogenital tract and subsequently persisting in lymphoid tissues and brain. Though studies using isolated cells have contributed significantly towards our understanding of HIV infection, the tissue microenvironment is characterised by a complex interplay of a range of factors, all of which can influence the course of infection but are otherwise missed in ex vivo studies. To address this knowledge gap, it is necessary to investigate the dynamics of infection and the host immune response in situ using imaging-based approaches. Over the last decade, emerging imaging techniques have continually redefined the limits of detection, both in terms of the scope and the scale of the targets. In doing so, this has opened up new questions that can be answered by in situ studies. This review discusses the high-dimensional imaging modalities that are now available and their application towards understanding the spatial biology of HIV infection.

Ultrasensitive detection of cancer-associated nucleic acids and mutations by primer exchange reaction-based signal amplification and flow cytometry

The detection of cancer-associated nucleic acids and mutations through liquid biopsy has emerged as a highly promising non-invasive approach for early cancer detection and monitoring. In this study, we report the development of primer exchange reaction (PER) based signal amplification strategy that enables the rapid, sensitive and specific detection of nucleic acids bearing cancer specific single nucleotide mutations using flow cytometry. Using micrometer size beads as support for immobilizing oligonucleotides and programmable PER assembly for target oligonucleotide recognition and fluorescence signal amplification, we demonstrated the versatile detection of target nucleic acids including KRAS oligonucleotide, fragmented mRNAs, and miR-21. Moreover, our detection system can discriminate single base mutations frequently occurred in cancer-associated genes including KRAS, PIK3CA and P53 from cell extracts and circulating tumor DNAs (ctDNAs). The detection is highly sensitive, with a limit of detection down to 27 fM without pre-amplification. In view of a clinical application, we demonstrate the detection of single mutations after extraction and pre-amplification of ctDNAs from the plasma of breast cancer patients. Importantly, our detection strategy enabled the detection of single KRAS mutation even in the presence of 1000-fold excess of wild type (WT) DNA using multi-color flow cytometry detection approach. Overall, our strategy holds immense potential for clinical applications, offering significant improvements for early cancer detection and monitoring.

Highly Tunable, Nanomaterial-Functionalized Structural Templating of Intracellular Protein Structures Within Biological Species

Inside living organisms, proteins are self-assembled into diverse 3D structures optimized for specific functions. This structure-function relationship can be exploited to synthesize functional materials through biotemplating and depositing functional materials onto protein structures. However, conventional biotemplating faces limitations due to the predominantly intracellular existence of proteins and associated challenges in achieving tunability while preserving functionality. In this study, Conversion to Advanced Materials via labeled Biostructures (CamBio), an integrated biotemplating platform that involves labeling target protein structures with antibodies followed by the growth of functional materials, ensuring outstanding nanostructure tunability is proposed. Protein-derived plasmonic nanostructures created by CamBio can serve as precise quantitative tools for assessing target species is demonstrated. The assessment is achieved through highly tunable and efficient surface-enhanced Raman spectroscopy (SERS). CamBio enables the formation of dense nanogap hot spots among metal nanoparticles, templated by diverse fibrous proteins comprising densely repeated monomers. Furthermore, iterative antibody labeling strategies to adjust the antibody density surrounding targets, amplifying the number of nanogaps and consequently improving SERS performance are employed. Finally, cell-patterned substrates and whole meat sections as SERS substrates, confirming their easily accessible, cost-effective, scalable preparation capabilities and dimensional tunability are incorporated.

Advancements in Single-Cell Proteomics and Mass Spectrometry-Based Techniques for Unmasking Cellular Diversity in Triple Negative Breast Cancer

BACKGROUND

Triple-negative breast cancer (TNBC) is an aggressive and complex subtype of breast cancer characterized by a lack of targeted treatment options. Intratumoral heterogeneity significantly drives disease progression and complicates therapeutic responses, necessitating advanced analytical approaches to understand its underlying biology. This review aims to explore the advancements in single-cell proteomics and their application in uncovering cellular diversity in TNBC. It highlights innovations in sample preparation, mass spectrometry-based techniques, and the potential for integrating proteomics into multi-omics platforms.

METHODS

The review discusses the combination of improved sample preparation methods and cutting-edge mass spectrometry techniques in single-cell proteomics. It emphasizes the challenges associated with protein analysis, such as the inability to amplify proteins akin to transcripts, and examines strategies to overcome these limitations.

RESULTS

Single-cell proteomics provides a direct link to phenotype and cell behavior, complementing transcriptomic approaches and offering new insights into the mechanisms driving TNBC. The integration of advanced techniques has enabled deeper exploration of cellular heterogeneity and disease mechanisms.

CONCLUSION

Despite the challenges, single-cell proteomics holds immense potential to evolve into a high-throughput and scalable multi-omics platform. Addressing existing hurdles will enable deeper biological insights, ultimately enhancing the diagnosis and treatment of TNBC.

Multiplexed Immunophenotyping of Lymphoma Tissue Samples

High-plex imaging techniques enable the detection and quantification of a multitude of markers in tissue biopsies at single-cell or near-single-cell resolution. In lymphoma, this can facilitate the detection and characterization of cellular phenotypes and interactions, describing both tumor and microenvironmental cells. In combination with other techniques, high-plex imaging allows the investigation of biological mechanisms and clinically relevant biomarkers. CO-Detection by IndEXing (CODEX), one of such techniques, is based on antibodies labeled with unique DNA oligonucleotides that can be visualized by complementary reporter oligonucleotides coupled to a fluorophore. Here, we provide an overview of the key steps of a CODEX-based project, including (1) antibody panel design, (2) cohort selection, (3) staining and imaging, (4) data analysis. By sharing our CODEX protocol and our experience with FFPE tissue samples, we aim to encourage wider use of this powerful technique in lymphoma research and improve insight into cellular composition and spatial dynamics for improved diagnostics and therapy.

Programmable DNA Reactions for Advanced Fluorescence Microscopy in Bioimaging

Biological organisms are composed of billions of molecules organized across various length scales. Direct visualization of these biomolecules in situ enables the retrieval of vast molecular information, including their location, species, and quantities, which is essential for understanding biological processes. The programmability of DNA interactions has made DNA-based reactions a major driving force in extending the limits of fluorescence microscopy, allowing for the study of biological complexity at different scales. This review article provides an overview of recent technological advancements in DNA-based fluorescence microscopy, highlighting how these innovations have expanded the technique's capabilities in terms of target multiplexity, signal amplification, super-resolution, and mechanical properties. These advanced DNA-based fluorescence microscopy techniques have been widely used to uncover new biological insights at the molecular level.

Highly multiplexed fluorescence microscopy with spectrally tunable semiconducting polymer dots

Current studies of biological tissues require visualizing diverse cell types and molecular interactions, creating a growing need for versatile techniques to simultaneously probe numerous targets. Traditional multiplexed imaging is limited to around five targets at once. Emerging methods using sequential rounds of staining, imaging, and signal removal can probe tens of targets but require specialized hardware and time-consuming workflows and face challenges with sample distortion and artifacts. We present a highly multiplexed fluorescence microscopy method using semiconducting polymer dots (Pdots) in a single round of staining and imaging. Pdots are small, bright, and photostable fluorescent probes with a wide range of tunable Stokes shifts (20 to 450 nanometers). Multiple series of Pdots with varying excitation wavelengths allow for fast (<1 minute) and single-round imaging of up to 21 targets in the brain and kidney. This method is based on a simple immunofluorescence workflow, efficient use of spectral space, standard hardware, and straightforward analysis, making it widely applicable for bioimaging laboratories.

Constructions, Purifications and Applications of DNA-Antibody Conjugates: A Review

A DNA-antibody conjugate is a synthetic molecule that combines the unique functions of both an antibody and DNA. With the increased accessibility of commercialized kits, the procedure for constructing conjugates is simplified and the requirement for chemistry background is reduced. As a result, the difficulty of preparing a DNA-antibody conjugate has been significantly lowered. Therefore, the application of DNA-antibody conjugates has attracted more interest in recent years. The most common application of DNA-antibody conjugates is based on the amplifiable property of DNA through PCR. This includes single-conjugate-based immuno-PCR, paired-conjugates-based proximity ligation assay, and proximity extension assay. These methods achieve highly sensitive or specific detection of target proteins. The conjugated single stranded DNA molecules can also specifically hybridize with another strand containing its complementary sequence. This property can be used to selectively bind fluorophore labeled DNA strands, which plays an important role in tissue imaging and spatial omics. All these factors make DNA-antibody conjugates have a broad range of applications in research, diagnosis, and potentially therapy.

Transcription-coupled changes in genomic region proximities during transcriptional bursting

The orchestration of our genes heavily relies on coordinated communication between enhancers and promoters, yet the mechanisms behind this dynamic interplay during active transcription remain unclear. Here, we investigated enhancer-promoter (E-P) interactions in relation to transcriptional bursting in mouse embryonic stem cells using sequential DNA/RNA/immunofluorescence-fluorescence in situ hybridization analyses. Our data reveal that the active state of specific genes is characterized by specific proximities between different genomic regions and the accumulation of transcriptional regulatory factors. Mathematical simulations suggest that an increase in local viscosity could potentially contribute to stabilizing the duration of these E-P proximities. Our study provides insights into the association among E-P proximity, protein accumulation, and transcriptional dynamics, paving the way for a more nuanced understanding of gene-specific regulatory mechanisms.

Orthogonal DNA Self-Assembly-Based Expansion Microscopy Platform for Amplified, Multiplexed Biomarker Imaging

Expansion microscopy (ExM) facilitates nanoscale imaging under conventional microscopes, but it frequently encounters challenges such as fluorescence losses, low signal-to-noise ratio (SNR), and limited detection throughput. To address these issues, a method of orthogonal DNA self-assembly-based ExM (o-DAExM) platform is developed, which employs hybridization chain reaction instead of conventional fluorescence labeling units, showcasing signal amplification efficacy, enhancement of SNR, and expandable multiplexing capability at any stage of the ExM process. In this work, o-DAExM has been applied to compare with immunofluorescence-based ExM for cellular cytoskeleton imaging, and the resolved nanoscale spatial distributions of cytoskeleton show outstanding performance and reliability of o-DAExM. Furthermore, the study demonstrates the utility of o-DAExM in accurately revealing exosome heterogeneous information and multiplexed analysis of protein targets in single cells, which provides infinite possibilities in super-resolution imaging of cells and other samples. Therefore, o-DAExM offers a straightforward expansion and signal labeling method, highlighting future prospects to study nanoscale structures and functional networks in biological systems.

Multiplexed expansion revealing for imaging multiprotein nanostructures in healthy and diseased brain

Proteins work together in nanostructures in many physiological contexts and disease states. We recently developed expansion revealing (ExR), which expands proteins away from each other, in order to support better labeling with antibody tags and nanoscale imaging on conventional microscopes. Here, we report multiplexed expansion revealing (multiExR), which enables high-fidelity antibody visualization of >20 proteins in the same specimen, over serial rounds of staining and imaging. Across all datasets examined, multiExR exhibits a median round-to-round registration error of 39 nm, with a median registration error of 25 nm when the most stringent form of the protocol is used. We precisely map 23 proteins in the brain of 5xFAD Alzheimer's model mice, and find reductions in synaptic protein cluster volume, and co-localization of specific AMPA receptor subunits with amyloid-beta nanoclusters. We visualize 20 synaptic proteins in specimens of mouse primary somatosensory cortex. multiExR may be of broad use in analyzing how different kinds of protein are organized amidst normal and pathological processes in biology.

Visualizing highly bright and uniform cellular ultrastructure by expansion-microscopy with tetrahedral DNA nanostructures

Expansion Microscopy (ExM) is a widely used super-resolution technique that enables imaging of structures beyond the diffraction limit of light. However, ExM suffers from weak labeling signals and expansion distortions, limiting its applicability. Here, we present an innovative approach called Tetrahedral DNA nanostructure Expansion Microscopy (TDN-ExM), addressing these limitations by using tetrahedral DNA nanostructures (TDNs) for fluorescence labeling. Our approach demonstrates a 3- to 10-fold signal amplification due to the multivertex nature of TDNs, allowing the modification of multiple dyes. Previous studies have confirmed minimal distortion on a large scale, and our strategy can reduce the distortion at the ultrastructural level in samples because it does not rely on anchoring agents and is not affected by digestion. This results in a brighter fluorescence, better uniformity, and compatibility with different labeling strategies and optical super-resolution technologies. We validated the utility of TDN-ExM by imaging various biological structures with improved resolutions and signal-to-noise ratios.

Programming Fast DNA Amplifier Circuits with Versatile Toehold Exchange Pathway

DNA amplifier circuits establish powerful tools to dynamically control molecular assembly for computation, sensing, and biological applications. However, the slow reaction speed remains a major barrier to their practical utility. Here, diverse fast DNA amplifier circuits termed toehold exchange polymerization (TEP) and toehold exchange catalysis (TEC) using toehold exchange-mediated assembly as a fundamental mechanism are built. Both TEP and TEC with a duplex and a hairpin can respond within minutes to diverse nucleic acid inputs with high fidelity. In addition, the circuits can amplify live-cell signals for fluorescence imaging target RNA dynamics and discriminating different cell lines. Compared with existing DNA circuits that involve time scales of hours for transducing small signals, TEP and TEC exhibit much faster dynamics, simpler design, and comparable sensitivity. These features make TEP and TEC promising platforms to develop programmable nucleic acid tools and devices and to create fast sensing and processing systems, amenable to wide practical applications.

Highly Multiplexed Tissue Imaging in Precision Oncology and Translational Cancer Research

Precision oncology tailors treatment strategies to a patient's molecular and health data. Despite the essential clinical value of current diagnostic methods, hematoxylin and eosin morphology, immunohistochemistry, and gene panel sequencing offer an incomplete characterization. In contrast, highly multiplexed tissue imaging allows spatial analysis of dozens of markers at single-cell resolution enabling analysis of complex tumor ecosystems; thereby it has the potential to advance our understanding of cancer biology and supports drug development, biomarker discovery, and patient stratification. We describe available highly multiplexed imaging modalities, discuss their advantages and disadvantages for clinical use, and potential paths to implement these into clinical practice. Significance: This review provides guidance on how high-resolution, multiplexed tissue imaging of patient samples can be integrated into clinical workflows. It systematically compares existing and emerging technologies and outlines potential applications in the field of precision oncology, thereby bridging the ever-evolving landscape of cancer research with practical implementation possibilities of highly multiplexed tissue imaging into routine clinical practice.

Single-shot 20-fold expansion microscopy

Expansion microscopy (ExM) is in increasingly widespread use throughout biology because its isotropic physical magnification enables nanoimaging on conventional microscopes. To date, ExM methods either expand specimens to a limited range (~4-10× linearly) or achieve larger expansion factors through iterating the expansion process a second time (~15-20× linearly). Here, we present an ExM protocol that achieves ~20× expansion (yielding <20-nm resolution on a conventional microscope) in a single expansion step, achieving the performance of iterative expansion with the simplicity of a single-shot protocol. This protocol, which we call 20ExM, supports postexpansion staining for brain tissue, which can facilitate biomolecular labeling. 20ExM may find utility in many areas of biological investigation requiring high-resolution imaging.

Multiplexed Assay for Small-Molecule Quantification via Photo-cross-linking of Structure Switching Aptamers

There is an unmet need for molecular detection assays that enable the multiplexed quantification of small-molecule analytes. We present xPlex, an assay that combines aptamer switches with ultraviolet-cross-linkable complementary strands to record target-binding events. When the aptamer's small-molecule target is present, the cross-linkable strand is displaced, enabling PCR amplification and detection of the relevant aptamer. In the absence of that target, the aptamer is readily cross-linked to the strand, preventing amplification from happening. The resulting aptamer-specific amplicons can be detected and quantified in a multiplexed fashion using high-throughput sequencing. We demonstrate quantitative performance for a pair of small-molecule analytes, dopamine and glucose, and show that this assay retains good specificity with mixtures of the two molecules at various concentrations. We further show that xPlex can effectively evaluate the specificity of cross-reactive aptamers to a range of different small-molecule analytes. We believe that the xPlex assay format could offer a useful strategy for achieving multiplexed analysis of small-molecule targets in a variety of scenarios.

GlycoSS: A DNA Glycosignal Sieve for Deciphering Spatially Resolved EpCAM-Specific Glycoforms

Malignant transformation of cancer is often accompanied by aberrant glycopatterns. Epithelial-mesenchymal transition (EMT) is a crucial biological process in cancer migration and invasion, accelerating cancer deterioration. High-precision analysis of protein-glycan spatial profiling in the EMT process is essential for elucidating glycosylation functions and cancer progression. However, the diversity of glycans in composition and conformation complicates their spatial analysis. Here, we develop a DNA glycosignal sieve (GlycoSS) visualization platform for screening glycoform expression with a protein spatial dimension. GlycoSS utilizes protein-anchored DNA nanoscanners of distinct lengths to control glycosignal readout, enabling protein-glycan distance modulations, and simultaneously orthogonally amplify glycoform output through signal amplification by an exchange reaction. Using GlycoSS, we screened EpCAM-specific hypoglycosylated glycoform signals in different breast cancer cell subtypes, especially characterizing the spatial distribution of glycans on the MCF-7 cell surface. Considering that the EpCAM-specific N-glycan dysregulation in EMT is pivotal, GlycoSS revealed dynamic glycan fluctuations during IGF-1-induced EMT, revealing that the N-glycans were positively associated with tumor malignancy and metastasis. GlycoSS is anticipated to accelerate the identification of aberrant N-glycosylation in tumor progression, advancing systemic glycobiology insights. Notably, GlycoSS is capable of analyzing diverse glycoprotein profiles, offering additional dimensions into the role of glycoprotein nanoenvironments in regulating membrane protein function.

NanoPlex: a universal strategy for fluorescence microscopy multiplexing using nanobodies with erasable signals

Fluorescence microscopy has long been a transformative technique in biological sciences. Nevertheless, most implementations are limited to a few targets, which have been revealed using primary antibodies and fluorescently conjugated secondary antibodies. Super-resolution techniques such as Exchange-PAINT and, more recently, SUM-PAINT have increased multiplexing capabilities, but they require specialized equipment, software, and knowledge. To enable multiplexing for any imaging technique in any laboratory, we developed NanoPlex, a streamlined method based on conventional antibodies revealed by engineered secondary nanobodies that allow the selective removal of fluorescence signals. We develop three complementary signal removal strategies: OptoPlex (light-induced), EnzyPlex (enzymatic), and ChemiPlex (chemical). We showcase NanoPlex reaching 21 targets for 3D confocal analyses and 5-8 targets for dSTORM and STED super-resolution imaging. NanoPlex has the potential to revolutionize multi-target fluorescent imaging methods, potentially redefining the multiplexing capabilities of antibody-based assays.

Multiplexed In Situ Imaging of Site-Specific m6A Methylation with Proximity Hybridization Followed by Primer Exchange Amplification (m6A-PHPEA)

Post-transcriptional modification of N6-methyladenosine (m6A) is crucial for ribonucleic acid (RNA) metabolism and cellular function. The ability to visualize site-specific m6A methylation at the single-cell level would markedly enhance our understanding of its pivotal regulatory functions in the field of epitranscriptomics. Despite this, current in situ imaging techniques for site-specific m6A are constrained, posing a significant barrier to epitranscriptomic studies and pathological diagnostics. Capitalizing on the precise targeting capability of deoxyribonucleic acid (DNA) hybridization and the high specificity of the m6A antibody, we present a method, termed proximity hybridization followed by primer exchange amplification (m6A-PHPEA), for the site-specific imaging of m6A methylation within cells. This approach enables high-resolution, single-cell imaging of m6A methylation across various RNA molecules coupled with efficient signal amplification. We successfully imaged three distinct m6A methylation sites concurrently in multiple cell types, revealing cell-to-cell variability in expression levels. This method promises to illuminate the dynamics of m6A-modified RNAs, potentially revolutionizing epitranscriptomic research and the development of advanced pathological diagnosis for chemical modifications.

Application of spatial omics in gastric cancer

Gastric cancer (GC), a globally prevalent and lethal malignancy, continues to be a key research focus. However, due to its considerable heterogeneity and complex pathogenesis, the treatment and diagnosis of gastric cancer still face significant challenges. With the rapid development of spatial omics technology, which provides insights into the spatial information within tumor tissues, it has emerged as a significant tool in gastric cancer research. This technology affords new insights into the pathology and molecular biology of gastric cancer for scientists. This review discusses recent advances in spatial omics technology for gastric cancer research, highlighting its applications in the tumor microenvironment (TME), tumor heterogeneity, tumor genesis and development mechanisms, and the identification of potential biomarkers and therapeutic targets. Moreover, this article highlights spatial omics' potential in precision medicine and summarizes existing challenges and future directions. It anticipates spatial omics' continuing impact on gastric cancer research, aiming to improve diagnostic and therapeutic approaches for patients. With this review, we aim to offer a comprehensive overview to scientists and clinicians in gastric cancer research, motivating further exploration and utilization of spatial omics technology. Our goal is to improve patient outcomes, including survival rates and quality of life.

Highly sensitive detection platform-based diagnosis of oesophageal squamous cell carcinoma in China: a multicentre, case-control, diagnostic study

BACKGROUND

Early detection and screening of oesophageal squamous cell carcinoma rely on upper gastrointestinal endoscopy, which is not feasible for population-wide implementation. Tumour marker-based blood tests offer a potential alternative. However, the sensitivity of current clinical protein detection technologies is inadequate for identifying low-abundance circulating tumour biomarkers, leading to poor discrimination between individuals with and without cancer. We aimed to develop a highly sensitive blood test tool to improve detection of oesophageal squamous cell carcinoma.

METHODS

We designed a detection platform named SENSORS and validated its effectiveness by comparing its performance in detecting the selected serological biomarkers MMP13 and SCC against ELISA and electrochemiluminescence immunoassay (ECLIA). We then developed a SENSORS-based oesophageal squamous cell carcinoma adjunct diagnostic system (with potential applications in screening and triage under clinical supervision) to classify individuals with oesophageal squamous cell carcinoma and healthy controls in a retrospective study including participants (cohort I) from Sun Yat-sen University Cancer Center (SYSUCC; Guangzhou, China), Henan Cancer Hospital (HNCH; Zhengzhou, China), and Cancer Hospital of Shantou University Medical College (CHSUMC; Shantou, China). The inclusion criteria were age 18 years or older, pathologically confirmed primary oesophageal squamous cell carcinoma, and no cancer treatments before serum sample collection. Participants without oesophageal-related diseases were recruited from the health examination department as the control group. The SENSORS-based diagnostic system is based on a multivariable logistic regression model that uses the detection values of SENSORS as the input and outputs a risk score for the predicted likelihood of oesophageal squamous cell carcinoma. We further evaluated the clinical utility of the system in an independent prospective multicentre study with different participants selected from the same three institutions. Patients with newly diagnosed oesophageal-related diseases without previous cancer treatment were enrolled. The inclusion criteria for healthy controls were no obvious abnormalities in routine blood and tumour marker tests, no oesophageal-associated diseases, and no history of cancer. Finally, we assessed whether classification could be improved by integrating machine-learning algorithms with the system, which combined baseline clinical characteristics, epidemiological risk factors, and serological tumour marker concentrations. Retrospective SYSUCC cohort I (randomly assigned [7:3] to a training set and an internal validation set) and three prospective validation sets (SYSUCC cohort II [internal validation], HNCH cohort II [external validation], and CHSUMC cohort II [external validation]) were used in this step. Six machine-learning algorithms were compared (the least absolute shrinkage and selector operator regression, ridge regression, random forest, logistic regression, support vector machine, and neural network), and the best-performing algorithm was chosen as the final prediction model. Performance of SENSORS and the SENSORS-based diagnostic system was primarily assessed using accuracy, sensitivity, specificity, and area under the receiver operating characteristic curve (AUC).

FINDINGS

Between Oct 1, 2017, and April 30, 2020, 1051 participants were included in the retrospective study. In the prospective diagnostic study, 924 participants were included from April 2, 2022, to Feb 2, 2023. Compared with ELISA (108·90 pg/mL) and ECLIA (41·79 pg/mL), SENSORS (243·03 fg/mL) showed 448 times and 172 times improvements, respectively. In the three retrospective validation sets, the SENSORS-based diagnostic system achieved AUCs of 0·95 (95% CI 0·90-0·99) in the SYSUCC internal validation set, 0·93 (0·89-0·97) in the HNCH external validation set, and 0·98 (0·97-1·00) in the CHSUMC external validation set, sensitivities of 87·1% (79·3-92·3), 98·6% (94·4-99·8), and 93·5% (88·1-96·7), and specificities of 88·9% (75·2-95·8), 74·6% (61·3-84·6), and 92·1% (81·7-97·0), respectively, successfully distinguishing between patients with oesophageal squamous cell carcinoma and healthy controls. Additionally, in three prospective validation cohorts, it yielded sensitivities of 90·9% (95% CI 86·1-94·2) for SYSUCC, 84·8% (76·1-90·8) for HNCH, and 95·2% (85·6-98·7) for CHSUMC. Of the six machine-learning algorithms compared, the random forest model showed the best performance. A feature selection step identified five features to have the highest performance to predictions (SCC, age, MMP13, CEA, and NSE) and a simplified random forest model using these five features further improved classification, achieving sensitivities of 98·2% (95% CI 93·2-99·7) in the internal validation set from retrospective SYSUCC cohort I, 94·1% (89·9-96·7) in SYSUCC prospective cohort II, 88·6% (80·5-93·7) in HNCH prospective cohort II, and 98·4% (90·2-99·9) in CHSUMC prospective cohort II.

INTERPRETATION

The SENSORS system facilitates highly sensitive detection of oesophageal squamous cell carcinoma tumour biomarkers, overcoming the limitations of detecting low-abundance circulating proteins, and could substantially improve oesophageal squamous cell carcinoma diagnostics. This method could act as a minimally invasive screening tool, potentially reducing the need for unnecessary endoscopies.

FUNDING

The National Key R&D Program of China, the National Natural Science Foundation of China, and the Enterprises Joint Fund-Key Program of Guangdong Province.

TRANSLATION

For the Chinese translation of the abstract see Supplementary Materials section.

Single-cell and spatial omics unravel the spatiotemporal biology of tumour border invasion and haematogenous metastasis

Solid tumours exhibit a well-defined architecture, comprising a differentiated core and a dynamic border that interfaces with the surrounding tissue. This border, characterised by distinct cellular morphology and molecular composition, serves as a critical determinant of the tumour's invasive behaviour. Notably, the invasive border of the primary tumour represents the principal site for intravasation of metastatic cells. These cells, known as circulating tumour cells (CTCs), function as 'seeds' for distant dissemination and display remarkable heterogeneity. Advancements in spatial sequencing technology are progressively unveiling the spatial biological features of tumours. However, systematic investigations specifically targeting the characteristics of the tumour border remain scarce. In this comprehensive review, we illuminate key biological insights along the tumour body-border-haematogenous metastasis axis over the past five years. We delineate the distinctive landscape of tumour invasion boundaries and delve into the intricate heterogeneity and phenotype of CTCs, which orchestrate haematogenous metastasis. These insights have the potential to explain the basis of tumour invasion and distant metastasis, offering new perspectives for the development of more complex and precise clinical interventions and treatments.

Multiplexed and Quantitative Imaging of Live-Cell Membrane Proteins by a Precise and Controllable DNA-Encoded Amplification Reaction

Amplifying DNA conjugated affinity ligands can improve the sensitivity and multiplicity of cell imaging and play a crucial role in comprehensively deciphering cellular heterogeneity and dynamic changes during development and disease. However, the development of one-step, controllable, and quantitative DNA amplification methods for multiplexed imaging of live-cell membrane proteins is challenging. Here, we introduce the template adhesion reaction (TAR) method for assembling amplifiable DNA sequences with different affinity ligands, such as aptamers or antibodies, for amplified and multiplexed imaging of live-cell membrane proteins with high quantitative fidelity. The precisely controllable TAR enables proportional amplification of membrane protein targets with variable abundances by modulating the concentration ratios of hairpin templates and primers, thus allowing sensitive visualization of multiple membrane proteins with enhanced signal-to-noise ratios (SNRs) without disturbing their original ratios. Using TAR, we achieved signal-enhanced imaging of six proteins on the same live-cell within 1-2 h. TAR represents an innovative and programmable molecular toolkit for multiplexed profiling of membrane proteins in live-cells.