Novel SERCA2 inhibitor Diphyllin displays anti-tumor effect in non-small cell lung cancer by promoting endoplasmic reticulum stress and mitochondrial dysfunction.

Abnormal calcium signaling is associated with non-small cell lung cancer (NSCLC) malignant progression, poor survival and chemotherapy resistance. Targeting endoplasmic reticulum (ER) Ca2+ channels or pumps to block calcium uptake in the ER induces ER stress and concomitantly promotes mitochondrial calcium uptake, leading to mitochondrial dysfunction and ultimately inducing cell death. Here, we identified Diphyllin was a potential specific inhibitor of endoplasmic reticulum (ER) calcium-importing protein sarco/endoplasmic-reticulum Ca2+ ATPase 2 (SERCA2). In vitro and in vivo studies showed that Diphyllin increased NSCLC cell apoptosis, along with inhibition of cell proliferation and migration. Mechanistically, Diphyllin promoted ER stress by directly inhibiting SERCA2 activity and decreasing ER Ca2+ levels. At the same time, the accumulated Ca2+ in cytoplasm flowed into mitochondria to increase reactive oxygen species (ROS) and decrease mitochondrial membrane potential (MMP), leading to cytochrome C (Cyto C) release and mitochondrial dysfunction. In addition, we found that Diphyllin combined with cisplatin could have a synergistic anti-tumor effect in vitro and in vivo. Taken together, our results suggested that Diphyllin, as a potential novel inhibitor of SERCA2, exerts anti-tumor effects by blocking ER Ca2+ uptake and thereby promoting ER stress and mitochondrial dysfunction.

DNA response element-based smart drug delivery systems for precise drug release.

Smart drug delivery systems (DDSs) that respond to, interact with, or are actuated by biological signals or pathological abnormalities (e.g., the tumor microenvironment) for controllable drug release are appealing therapeutic platforms for cancer treatment. Owing to their inherent self-assembled nature, nucleic acids have emerged as programmable materials for the development of multifunctional structures. In response to external environmental stimuli, DNA response elements can serve as switches to trigger conformational changes in DNA structures. Their stimulus-responsive properties make them promising candidates for constructing smart DDSs, and advancements in DNA response element-based DDSs in the field of biomedicine have been made. This review summarizes different types of DNA response elements, including DNA aptamers, DNAzymes, disulfide bond-modified DNA, pH-responsive DNA motifs, and photocleavable DNA building blocks, and highlights the advancements in DNA response element-based smart DDSs for precise drug release. Finally, future challenges and perspectives in this field are discussed.

MoS2-Based Sensor Array for Accurate Identification of Cancer Cells with Ensemble-Modified Aptamers.

In this work, we present an array-based chemical nose sensor that utilizes a set of ensemble-modified aptamer (EMAmer) probes to sense subtle physicochemical changes on the cell surface for cancer cell identification. The EMAmer probes are engineered by domain-selective incorporation of different types and/or copies of positively charged functional groups into DNA scaffolds, and their differential interactions with cancer cells can be transduced through competitive adsorption of fluorophore-labeled EMAmer probes loaded on MoS2 nanosheets. We demonstrate that this MoS2-EMAmer-based sensor array enables rapid and effective discrimination among six types of cancer cells and their mixtures with a concentration of 104 cells within 60 min, achieving a 94.4% accuracy in identifying blinded unknown cell samples. The established MoS2-EMAmer sensing platform is anticipated to show significant promise in the advancement of cancer diagnostics.

PDZ and LIM Domain-Encoding Genes: Their Role in Cancer Development.

PDZ-LIM family proteins (PDLIMs) are a kind of scaffolding proteins that contain PDZ and LIM interaction domains. As protein-protein interacting molecules, PDZ and LIM domains function as scaffolds to bind to a variety of proteins. The PDLIMs are composed of evolutionarily conserved proteins found throughout different species. They can participate in cell signal transduction by mediating the interaction of signal molecules. They are involved in many important physiological processes, such as cell differentiation, proliferation, migration, and the maintenance of cellular structural integrity. Studies have shown that dysregulation of the PDLIMs leads to tumor formation and development. In this paper, we review and integrate the current knowledge on PDLIMs. The structure and function of the PDZ and LIM structural domains and the role of the PDLIMs in tumor development are described.

Identification of m7G-Related miRNA Signatures Associated with Prognosis, Oxidative Stress, and Immune Landscape in Lung Adenocarcinoma.

The role of N7-methylguanosine(m7G)-related miRNAs in lung adenocarcinoma (LUAD) remains unclear. We used LUAD data from The Cancer Genome Atlas (TCGA) to establish a risk model based on the m7G-related miRNAs, and divided patients into high-risk or low-risk subgroups. A nomogram for predicting overall survival (OS) was then constructed based on the independent risk factors. In addition, we performed a functional enrichment analysis and defined the oxidative stress-related genes, immune landscape as well as a drug response profile in the high-risk and low-risk subgroups. This study incorporated 28 m7G-related miRNAs into the risk model. The data showed a significant difference in the OS between the high-risk and low-risk subgroups. The receiver operating characteristic curve (ROC) predicted that the area under the curve (AUC) of one-year, three-year and five-year OS was 0.781, 0.804 and 0.853, respectively. The C-index of the prognostic nomogram for predicting OS was 0.739. We then analyzed the oxidative stress-related genes and immune landscape in the high-risk and low-risk subgroups. The data demonstrated significant differences in the expression of albumin (ALB), estimated score, immune score, stromal score, immune cell infiltration and functions between the high-risk and low-risk subgroups. In addition, the drug response analysis showed that low-risk subgroups may be more sensitive to tyrosine kinase inhibitor (TKI) and histone deacetylase (HDAC) inhibitors. We successfully developed a novel risk model based on m7G-related miRNAs in this study. The model can predict clinical prognosis and guide therapeutic regimens in patients with LUAD. Our data also provided new insights into the molecular mechanisms of m7G in LUAD.

Circulating insulin-like growth factor-1 and risk of lung diseases: A Mendelian randomization analysis.

Background: Insulin-like growth factor-1 (IGF-1) display a vital role in in the pathogenesis of lung diseases, however, the relationship between circulating IGF-1 and lung disease remains unclear. Methods: Single nucleotide polymorphisms (SNPs) associated with the serum levels of IGF-1 and the outcomes data of lung diseases including asthma, chronic obstructive pulmonary disease (COPD), lung cancer and idiopathic pulmonary fibrosis (IPF) were screened from the public genome-wide association studies (GWAS). Two-sample Mendelian randomization (MR) analysis was then performed to assess the independent impact of IGF-1 exposure on these lung diseases. Results: Totally, 416 SNPs related to circulating IGF-1 levels among 358,072 participants in UK Biobank. According to a primary casual effects model with MR analyses by the inverse variance weighted (IVW) method, the circulating IGF-1 was demonstrated a significantly related with the risk of asthma (OR, 0.992; 95% CI, 0.985-0.999, P=0.0324), while circulating IGF-1 showed no significant correlation with CODP (OR, 1.000; 95% CI, 0.999-1.001, P=0.758), lung cancer (OR, 0.979, 95% CI, 0.849-1.129, P=0.773), as well as IPIGFF (OR, 1.100, 95% CI, 0.794-1.525, P=0.568). Conclusion: The present study demonstrated that circulating IGF-1 may be causally related to lower risk of asthma.

DNA origami-based artificial antigen-presenting cells for adoptive T cell therapy.

Nanosized artificial antigen-presenting cells (aAPCs) with efficient signal presentation hold great promise for in vivo adoptive cell therapy. Here, we used DNA origami nanostructures as two-dimensional scaffolds to regulate the spatial presentation of activating ligands at nanoscale to construct high-effective aAPCs. The DNA origami-based aAPC comprises costimulatory ligands anti-CD28 antibody anchored at three vertices and T cell receptor (TCR) ligands peptide-major histocompatibility complex (pMHC) anchored at three edges with varying density. The DNA origami scaffold enables quantitative analysis of ligand-receptor interactions in T cell activation at the single-particle, single-molecule resolution. The pMHC-TCR-binding dwell time is increased from 9.9 to 12.1 s with increasing pMHC density, driving functional T cell responses. In addition, both in vitro and in vivo assays demonstrate that the optimized DNA origami-based aAPCs show effective tumor growth inhibiting capability in adoptive immunotherapy. These results provide important insights into the rational design of molecular vaccines for cancer immunotherapy.

Recent advances of nanomaterial-based anti-angiogenic therapy in tumor vascular normalization and immunotherapy.

Anti-angiogenesis therapy and immunotherapy are the first-line therapeutic strategies for various tumor treatments in the clinic, bringing significant advantages for tumor patients. Recent studies have shown that anti-angiogenic therapy can potentiate immunotherapy, with many clinical trials conducted based on the combination of anti-angiogenic agents and immune checkpoint inhibitors (ICIs). However, currently available clinical dosing strategies and tools are limited, emphasizing the need for more improvements. Although significant progress has been achieved, several big questions remained, such as how to achieve cell-specific targeting in the tumor microenvironment? How to improve drug delivery efficiency in tumors? Can nanotechnology be used to potentiate existing clinical drugs and achieve synergistic sensitization effects? Over the recent few years, nanomedicines have shown unique advantages in antitumor research, including cell-specific targeting, improved delivery potentiation, and photothermal effects. Given that the applications of nanomaterials in tumor immunotherapy have been widely reported, this review provides a comprehensive overview of research advances on nanomaterials in anti-angiogenesis therapy, mainly focusing on the immunosuppressive effects of abnormal tumor vessels in the tumor immune microenvironment, the targets and strategies of anti-angiogenesis nanomedicines, and the potential synergistic effects and molecular mechanisms of anti-angiogenic nanomedicines in combination with immunotherapy, ultimately providing new perspectives on the nanomedicine-based synergy between anti-angiogenic and immunotherapy.

Ensemble Modified Aptamer Based Pattern Recognition for Adaptive Target Identification.

The difficulty of the molecular design and chemical synthesis of artificial sensing receptors restricts their diagnostic and proteomic applications. Herein, we report a concept of "ensemble modified aptamers" (EMAmers) that exploits the collective recognition abilities of a small set of protein-like side-chain-modified nucleic acid ligands for discriminative identification of molecular or cellular targets. Different types and numbers of hydrophobic functional groups were incorporated at designated positions on nucleic acid scaffolds to mimic amino acid side chains. We successfully assayed 18 EMAmer probes with differential binding affinities to seven proteins. We constructed an EMAmer-based chemical nose sensor and demonstrated its application in blinded unknown protein identification, giving a 92.9% accuracy. Additionally, the sensor is generalizable to the detection of blinded unknown bacterial and cellular samples, which enabled identification accuracies of 96.3% and 94.8%, respectively. This sensing platform offers a discriminative means for adaptive target identification and holds great potential for diverse applications.

Multiple-Aptamer-Integrated DNA-Origami-Based Chemical Nose Sensors for Accurate Identification of Cancer Cells.

Developing simple, rapid, and accurate methods for cancer cell identification could facilitate early cancer diagnosis and tumor metastasis research. Herein, we develop a novel chemical nose sensor that employs the collective recognition abilities of a set of multiple-aptamer-integrated DNA origami (MADO) probes for discriminative identification of cancer cells. By controlling the types and/or copies of aptamers assembled on the DNA origami nanostructure, we constructed five MADO probes with differential binding affinities (ranging from 3.08 to 78.92 nM) to five types of cells (HeLa, MDA-MB-468, MCF-7, HepG2, and MCF-10A). We demonstrate the utility of the MADO-based chemical nose sensor in the identification of blinded unknown cell samples with a 95% accuracy. This sensing platform holds great potential for applications in medical diagnostics.

Nanoscale organization of two-dimensional multimeric pMHC reagents with DNA origami for CD8+ T cell detection.

Peptide-MHC (pMHC) multimers have excelled in the detection of antigen-specific T cells and have allowed phenotypic analysis using other reagents, but their use for detection of low-affinity T cells remains a challenge. Here we develop a multimeric T cell identifying reagent platform using two-dimensional DNA origami scaffolds to spatially organize pMHCs (termed as dorimers) with nanoscale control. We show that these dorimers enhance the binding avidity for low-affinity antigen-specific T cell receptors (TCRs). The dorimers are able to detect more antigen-specific T cells in mouse CD8+ T cells and early-stage CD4+CD8+ double-positive thymocytes that express less dense TCRs, compared with the equivalent tetramers and dextramers. Moreover, we demonstrate dorimer function in the analysis of autoimmune CD8+ T cells that express low-affinity TCRs, which are difficult to detect using tetramers. We anticipate that dorimers could contribute to the investigation of antigen-specific T cells in immune T cell function or immunotherapy applications.

Programming Receptor Clustering with DNA Probabilistic Circuits for Enhanced Natural Killer Cell Recognition.

Developing strategies to enhance the recognition ability of immune cells is important to the success of cell-based cancer immunotherapy. Herein, we report programming receptor clustering on membrane with DNA probabilistic circuits for enhanced immune cell recognition. By designing the circuit output to activate receptors for binding to adjacent receptors, we can engineer DNA probabilistic circuits for programmable regulation of receptor clustering. The generated receptor clusters show higher binding affinity to target cancer cells and improved membrane-anchoring stability compared with monomers. We demonstrate that programming receptor clustering could allow to modulate the recognition capability of natural killer cells and control natural killer cell-cancer cell interactions to promote efficient cancer cell killing. This work provides insights for precise control over cellular recognition and opens new opportunities for the development of cell-based immunotherapy.

Nucleic Acid-Based Cell Surface Engineering Strategies and Their Applications.

The cell membrane is a biological interface regulating the communications between cells and their environment. The ability to functionalize the cell membrane with molecules or nanomaterials allows us to manipulate cellular behaviors and to expand cellular functions. Due to their unique merits of synthetic accessibility, flexible design, and precise programmability, nucleic acids provide an emerging and promising molecular toolkit for cell surface engineering. In this review, the recent progress in nucleic acid-based cell surface engineering are summarized. We first introduce approaches to nucleic acid-based cell surface engineering, including monovalent and polyvalent surface engineering strategies. Then, the biological applications of nucleic acid-based cell surface engineering in biosensing of extracellular microenvironment, programming cell-cell interactions, and mimicking cellular behaviors are reviewed. Finally, we analyze the current challenges existing in this area and discuss the prospects for the future development.

Aptamer-Functionalized Fractal Nanoplasmonics-Assisted Laser Desorption/Ionization Mass Spectrometry for Metabolite Detection.

Accurate profiling of metabolites in biofluids provides a feasible approach to disease diagnosis and therapeutic evaluation in clinics. However, current material-based analytical platforms for in vitro metabolite detection often requires tedious sample pretreatment. To address this issue, herein, we report an aptamer-functionalized fractal gold nanoflower (Apt-AuNF)-based sensing platform for metabolite analysis. A series of fractal AuNFs with tunable nanoshell structures was synthesized using DNA-engineered strategy, and optimized Apt-AuNFs were demonstrated to enable efficient trap of target analytes with ∼5-fold enhanced enrichment, thus achieving selective analysis of metabolites in complex biofluids without requirement of pre-enrichment and purification. We applied Apt-AuNF-assisted laser desorption/ionization mass spectrometry for disease diagnosis, identifying diabetic patients through daily monitoring and glucose quantification in serum. This work provides a guideline to design materials for high-performance metabolic analysis and precise disease diagnosis.

Multi-Mode Reconfigurable DNA-Based Chemical Reaction Circuits for Soft Matter Computing and Control.

Developing smart material systems for performing different tasks in diverse environments remains challenging. Here, we show that by integrating stimuli-responsive soft materials with multi-mode reconfigurable DNA-based chemical reaction circuits (D-CRCs), it can control size change of microgels with multiple reaction pathways and adapt expansion behaviors to meet diverse environments. We first use pH-responsive intramolecular conformational switches for regulating DNA strand displacement reactions (SDRs). The ability to regulate SDRs with tunable pH-dependence allows to build dynamic chemical reaction networks with diverse reaction pathways. We confirm that the designed DNA switching circuits are reconfigurable at different pH and perform different logic operations, and the swelling of DNA switching circuit-integrated microgel systems can be programmably directed by D-CRCs. Our approach provides insight into building smart responsive materials and fabricating autonomous soft robots.

DNA-Scaffolded Disulfide Redox Network for Programming Drug-Delivery Kinetics.

In response to specific stimuli, dynamic covalent materials enable the generation of new structures by reversibly forming/breaking chemical bonds, thus showing great potential for application in controlled drug release. However, using dynamic covalent chemistry to program drug-delivery kinetics remains challenging. Herein, an in situ polymerization-generated DNA-scaffolded disulfide redox network (DdiSRN) is reported in which nucleic acids are used as a scaffold for dynamic disulfide bonds. The constructed DdiSRN allows selective release of loading cargos inside cancer cells in response to redox stimuli. Moreover, the density of disulfide bonds in network can be tuned by precise control over their position and number on DNA scaffolds. As a result, drug-delivery kinetics can be programmed with a half-life, t1/2 , decreasing from 8.3 to 4.4 h, thus facilitating keeping an adequate drug concentration within the therapeutic window. Both in vitro and in vivo studies confirm that co-delivery of DOX and siRNA in combination with fast drug release inside cells using this DdiSRN enhances the therapeutic effect on multidrug-resistant cancer. This nontrivial therapeutic platform enabling kinetic control provides a good paradigm for precision cancer medicine.

Assembly Pathway Selection with DNA Reaction Circuits for Programming Multiple Cell-Cell Interactions.

The manipulation of cell-cell interactions promotes the study of multicellular behavior, but it remains a great challenge for programming multicellular assembly in complex reaction pathways with multiple cell types. Here we report a DNA reaction circuit-based approach to cell-surface engineering for the programmable regulation of multiple cell-cell interactions. The DNA circuits are designed on the basis of a stem-loop-integrated DNA hairpin motif, which has the capability of programming diverse molecular self-assembly and disassembly pathways by sequential allosteric activation. Modifying the cell surface with such DNA reaction circuits allows for performing programmable chemical functions on cell membranes and the control of multicellular self-assembly with selectivity. We demonstrate the selective control of targeting the capability of natural killer (NK) cells to two types of tumor cells, which show selectively enhanced cell-specific adaptive immunotherapy efficacy. We hope that our method provides new ideas for the programmable control of multiple cell-cell interactions in complex reaction pathways and potentially promotes the development of cell immunotherapy.

Optochemical Control of DNA-Switching Circuits for Logic and Probabilistic Computation.

Precise control of DNA-circuit functions facilitates the construction of complex DNA networks to perform sophisticated functions. Inspired by optochemical genetics with high precision for controlling and studying neural networks by photoregulation of membrane receptors, we herein report optochemically controlled DNA switching circuits for regulating computation functions. The DNA-switching circuits involve a CG-C+ triplex-based DNA switch that undergoes structural transition from triplex to duplex states after exposure to UV irradiation due to proton transfer, showing optochemical control. We demonstrate that the DNA-switching circuits enable the regulation of computation functions by optochemical control of the state of the DNA switch, including multiple logic computations and probabilistic computation. We hope this work will broaden DNA-circuit functions and facilitate the construction of complex DNA networks.

Circularized blocker-displacement amplification for multiplex detection of rare DNA variants.

A superselective isothermal amplification technique, termed circularized blocker-displacement amplification, was developed for multiplex analysis of rare DNA variants.

Fractal SERS nanoprobes for multiplexed quantitative gene profiling.

Quantitative analysis is critical for biological and chemical sensing applications, yet still remains a great challenge in surface-enhanced Raman spectroscopy (SERS). Here we report the development of a novel fractal SERS nanoprobe with robust internal calibration standard and high multiplexing capability for ultrasensitive detection of DNA and microRNA. This fractal SERS nanoprobe consists of a solid Au core of ~13 nm, an inner hollow gap of ~1 nm, and a stellate outer shell. The inner hollow gap enables the embedding of Raman tags that can serve as a self-calibrating internal standard to effectively correct the fluctuations of samples and measuring conditions. The outer shell morphology is highly tunable, which provides distinct SERS enhancement and enables a reproducible quantitative measurement of nucleic acids down to femtomolar level. In addition, the flexibility of encoding crosstalk-free Raman tag molecules makes such SERS sensor particularly attractive for multiplexed bioassays. This technique is simple, reliable, and of wide applicability to various genomic screening and diagnostic applications.