Multiplexed sequential imaging in living cells with orthogonal fluorogenic RNA aptamer/dye pairs.

Detecting multiple targets in living cells is important in cell biology. However, multiplexed fluorescence imaging beyond two-to-three targets remains a technical challenge. Herein, we introduce a multiplexed imaging strategy, 'sequential Fluorogenic RNA Imaging-Enabled Sensor' (seqFRIES), which enables live-cell target detection via sequential rounds of imaging-and-stripping. In seqFRIES, multiple orthogonal fluorogenic RNA aptamers are genetically encoded inside cells, and then the corresponding cell membrane permeable dye molecules are added, imaged, and rapidly removed in consecutive detection cycles. As a proof-of-concept, we have identified in this study four fluorogenic RNA aptamer/dye pairs that can be used for highly orthogonal and multiplexed imaging in living bacterial and mammalian cells. After further optimizing the cellular fluorescence activation and deactivation kinetics of these RNA/dye pairs, the whole four-color semi-quantitative seqFRIES process can be completed in ∼20 min. Meanwhile, seqFRIES-mediated simultaneous detection of critical signalling molecules and mRNA targets was also achieved within individual living cells. We expect our validation of this new seqFRIES concept here will facilitate the further development and potential broad usage of these orthogonal fluorogenic RNA/dye pairs for multiplexed and dynamic live-cell imaging and cell biology studies.

Targeted RNA condensation in living cells via genetically encodable triplet repeat tags.

Living systems contain various membraneless organelles that segregate proteins and RNAs via liquid-liquid phase separation. Inspired by nature, many protein-based synthetic compartments have been engineered in vitro and in living cells. Here, we introduce a genetically encoded CAG-repeat RNA tag to reprogram cellular condensate formation and recruit various non-phase-transition RNAs for cellular modulation. With the help of fluorogenic RNA aptamers, we have systematically studied the formation dynamics, spatial distributions, sizes and densities of these cellular RNA condensates. The cis- and trans-regulation functions of these CAG-repeat tags in cellular RNA localization, life time, RNA-protein interactions and gene expression have also been investigated. Considering the importance of RNA condensation in health and disease, we expect that these genetically encodable modular and self-assembled tags can be widely used for chemical biology and synthetic biology studies.

RNA Condensate as a Versatile Platform for Improving Fluorogenic RNA Aptamer Properties and Cell Imaging.

Fluorogenic RNA aptamers are valuable tools for cell imaging, but they still suffer from shortcomings such as easy degradation, limited photostability, and low fluorescence enhancement. Molecular crowding conditions enable the stabilization of the structure, promotion of folding, and improvement of activity of functional RNA. Based on artificial RNA condensates, here we present a versatile platform to improve fluorogenic RNA aptamer properties and develop sensors for target analyte imaging in living cells. Using the CUG repeat as a general tag to drive phase separation, various fluorogenic aptamer-based RNA condensates (FLARE) were prepared. We show that the molecular crowding of FLARE can improve the enzymatic resistance, thermostability, photostability, and binding affinity of fluorogenic RNA aptamers. Moreover, the FLARE systems can be modularly engineered into sensors (FLARES), which demonstrate enhanced brightness and sensitivity compared to free sensors dispersed in homogeneous solution. This scalable design principle provides new insights into RNA aptamer property regulation and cellular imaging.

Covalent Organic Frameworks-Based Fluorescence Sensor Array and QSAR Study for Identification of Energetic Heterocyclic Compounds.

The accurate identification of energetic heterocyclic compounds (EHCs) is of great significance in munition assessment, environmental monitoring, and biosafety but remains largely underexplored. Herein, a covalent organic frameworks-based fluorescence sensor array (COFx sensor array) for efficient screening of EHCs is reported. The topologies of the COFs were rationally designed by modulating the pore sizes and linkage strategies to achieve the simplified sensor array. Eighteen EHC representatives, including single-, dual-, and three-ring EHCs with multivariate substructures, were successfully discriminated ranging from 10 µM to 1 mM. The sensor array showed robust selectivity against a wide range of interferences. The quantitative structure-activity relationship (QSAR) analysis has been conducted for the mechanistic study of the sensor array. Three multiple linear regression models have been established using molecular descriptors to evaluate and predict Stern-Volmer coefficient values, achieving explicit correlation between EHC structures and the signal outputs of the sensor array. Five molecular descriptors are retained to reveal the governing factors of the sensor array resolution. The QSAR analysis facilitates the design and development of the COFx sensor array, offering a new approach for customized multivariate analysis.

Synergistic Mitochondrial Genotoxicity of Carbon Dots and Arsenate in Earthworms Eisenia fetida across Generations: The Critical Role of Binding.

The escalating utilization of carbon dots (CDs) in agriculture raises ecological concerns. However, their combined toxicity with arsenic remains poorly understood. Herein, we investigated the combined mitochondrial genotoxicity of CDs and arsenate at environmentally relevant concentrations across successive earthworm generations. Iron-doped CDs (CDs-Fe) strongly bound to arsenate and arsenite, while nitrogen-doped CDs (CDs-N) exhibited weaker binding. Both CDs enhanced arsenate bioaccumulation without affecting its biotransformation, with most arsenate being reduced to arsenite. CDs-Fe generated significantly more reactive oxygen species than did CDs-N, causing stronger mitochondrial DNA (mtDNA) damage. Arsenate further exacerbated the oxidative mtDNA damage induced by CDs-N, as evidenced by increased reactive oxygen species, elevated 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-OHdG) levels, and a higher correlation between 8-OHdG and mtDNA damage. This was due to arsenic inhibiting the antioxidant enzyme catalase. This exacerbation was negligible with CDs-Fe because their strong binding with arsenic prevented catalase inhibition. Maternal mitochondrial DNA damage was inherited by filial earthworms, which experienced significant weight loss in coexposure groups coupled with mtDNA toxicity. This study reveals the synergistic genotoxicity of CDs and arsenate, suggesting that CDs could disrupt the arsenic biogeochemical cycle, increase arsenate risk to terrestrial animals, and influence ecosystem stability and health through multigenerational impacts.

Photocatalytic Multisite Functionalization of Unactivated Terminal Alkenes by Merging Polar Cycloaddition and Radical Ring-Opening Process.

Although highly appealing for rapid access of molecular complexity, multi-functionalization of alkenes that allows incorporation of more than two functional groups remains a prominent challenge. Herein, we report a novel strategy that merges dipolar cycloaddition with photoredox promoted radical ring-opening remote C(sp3)-H functionalization, thus enabling a smooth 1,2,5-trifunctionalization of unactivated alkenes. A highly regioselective [3+2] cycloaddition anchors a reaction trigger onto alkene substrates. The subsequent halogen atom transfer (XAT) selectively initiates ring-opening process, which is followed by a series of 1,5-hydrogen atom transfer (1,5-HAT) and intermolecular fluorine atom transfer (FAT) events. With this method, site-selective introduction of three different functional groups is accomplished and a broad spectrum of valuable ß-hydroxyl-ϵ-fluoro-nitrile products are synthesized from readily available terminal alkenes.

Amplification of an Electrochemiluminescence-Emissive Aptamer into DNA Nanotags for Sensitive Fecal Calprotectin Determination.

The precision additive manufacturing and tessellated multitasking out of the structural DNA nanotechnology enable a configurable expression of densified electrochemiluminescent (ECL) complexes, which would streamline the bioconjugation while multiplying signals. Herein, a completely DNA-scaffold ECL "polyploid" was replicated out via the living course of rolling circle amplification. The amplicon carried the aptameric sequences of ZnPPIX/TSPP porphyrin as photoreactive centers that rallied at periodical intervals of the persistent extension into a close-packed nanoflower, ZnPDFI/II. Both microscopies and electrophoresis proved the robust nesting of guests at their deployed gene loci, while multispectral comparisons among cofactor substituents pinpointed the pivotal roles of singlet seclusion and Zn2+-chelation for the sake of intensive ECL irradiation. The adversity-resilient hydrogel texture made lipoidal filmogens as porphyrinic ECL prerequisites to be of no need at all, thus not only simplifying assay flows but also inspiring an in situ labeling plan. Upon bioprocessing optimization, an enriched probe ZnPDFIII was further derived that interpolated the binding motif related to calprotectin as validated by molecular docking and affinity titration. With it being a strongly indicative marker of inflammatory bowel disease (IBD), a competitive ECL aptasensing strategy was contrived, managing a signal-on and sensitive detection in mild conditions with a subnanogram-per-milliliter limit of detection by 2 orders of magnitude lower than the standard method as well as a comparable accuracy in clinical stool sample testing. Distinct from those conventional chemophysical rebuilding routes, this de novo biosynthetic fusion demonstrated a promising alternative toward ECL-source bioengineering, which may intrigue vibrant explorations of other ECL-shedding fabrics and, accordingly, a new bioanalytic mode downstream.

Covered SEMS failed to cure airway fistula closed by an amplatzer device.

BACKGROUND: Airway fistula is a rare but threatening complication associated with high rates of morbidity and mortality. We report the experience of Amplatzer device application in airway fistulae that failed to be cured with a covered self-expandable metallic stent (SEMS). MATERIALS AND METHODS: Patients who failed occlusion with a covered self-expandable metallic stent and received Amplatzer device placement from Jan 2015 to Jan 2020 were retrospectively enrolled. A total of 14 patients aged 42 to 66 years (55.14 ± 7.87) were enrolled in this study. The primary diseases, types of fistula, types of stents, duration, size of fistula, and follow-up were recorded. RESULTS: All 14 patients with airway fistula failed to be occluded with a covered metallic stent and received Amplatzer device placement. Among the 14 patients, 6 had BPF, 3 had TEF and 5 had GBF. The average stent time was 141.93 ± 65.83 days. The sizes of the fistulae ranged from 3 to 6 mm. After Amplatzer device placement, the KPS score improved from 62.14 ± 4.26 to 75.71 ± 5.13 (P < 0.05). No procedure-related complications occurred. During the 1-month, 3-month and 6-month follow-ups, all the Amplatzer devices were partially surrounded with granulation. Only 1 patient with BPF failed with Amplatzer device occlusion due to the recurrence of lung cancer. CONCLUSION: In conclusion, the application of the Amplatzer device is a safe and effective option in the treatment of airway fistula that failed to be occluded with SEMSs.

Cobalt Metal-Organic Frameworks with Aggregation-Induced Emission Characteristics for Fluorometric/Colorimetric Dual Channel Detection of Nitrogen-Rich Heterocyclic Compounds.

Nitrogen-rich heterocyclic compounds (NRHCs) are an emerging type of explosive, and their quantification is important in national security inspection and environmental monitoring. Up until now, designing an efficient NRHCs sensing strategy was still in the early stages. Herein, a new metal-organic framework (MOF) with aggregation-induced emission (AIE) characteristics is synthesized with fluorometric/colorimetric responses for rapid and selective detection of NRHCs. The nonemissive probe is designed with tetraphenylethylene derivative as the linker and Co as the node, quencher, and color-changing agent. Cobalt AIE-MOF exhibits a turn-on emission enhancement due to the competitive coordination substitution between NRHCs and the scaffold as well as the following AIE process of the liberative linkers. Meanwhile, the color appearance of the probe changes from blue to yellow based on the dissociation of the original Co coordinating system. Using this dual-mode probe, single- and dual-ring NRHCs are successfully detected from 5 µM to 7.5 mM within 25 s. The cobalt AIE-MOF exhibits excellent selectivity of NRHCs against a variety of interferences, providing a promising tool for designing a multichannel detection strategy.

α-Iminyl Cation-Involved Indole Construction via Brønsted Acid-Promoted Reaction of Isoxazol-5-ones.

Herein, we report a strategically novel method for the efficient construction of indole skeletons using 2-phenylisoxazol-5-ones as the starting material. This reaction proceeds via Brønsted acid-promoted α-iminyl cation generation by N-O bond cleavage and a subsequent intramolecular cyclization to afford 1H-indole-3-carboxylic acid, which further undergoes decarboxylation to yield the final product. Control experiments show that N-O bond cleavage and intramolecular cyclization proceed so fast that the 1H-indole-3-carboxylic acid could be isolated in high yields even after 5-10 min. The substrate scope of this transformation is broad, and the desired products are obtained in moderate to good yields. The transition-metal-free reaction condition, CO2 as the sole byproduct, and good practicability add to the synthetic potential of this transformation in the pharmaceutical and flavor industries.

The application of Caprini Risk Assessment Model in evaluation of deep vein thrombosis for patients with end-stage osteoarthritis before arthroplasty.

BACKGROUND: Deep vein thrombosis (DVT) was a fatal complication of knee arthroplasty. We had neglected the risk factors of preoperative DVT although patients undergoing knee arthroplasty were at high risk for VTE. This study was to determine the risk factors for preoperative DVT and application of Caprini Risk Assessment Model (RAM) in patients with end-stage knee osteoarthritis (OA). METHODS: We retrospectively analyzed 1808 cases with end-stage knee OA undergoing primary knee arthroplasty from May 2015 to December 2020. Based on the results of ultrasonography in lower extremities, all patients were divided into non-DVT group and DVT group. Distribution of risk factors and risk levels were compared using χ2 test between two groups. Binary logistic regression analysis was used to determine the risk factors and relationship of risk levels and preoperative DVT. RESULTS: The incidence of preoperative DVT was 5.53% (n = 100). Distribution of the study population by risk level was low, 4.09%; moderate, 23.95%; high, 66.98%; and highest 4.98%. Female (P = 0.002), age (P = 0.012), swollen legs (P = 0.035) and history of blood clots (P < 0.001) was correlated with preoperative DVT. Difference among four risk levels was significant (P = 0.007). Patients with highest risk level had statistically significant association with preoperative DVT (P = 0.005, OR = 2.93, 95%CI [1.375-6.246]). CONCLUSION: The incidence of preoperative DVT was 5.53% in end-stage knee OA patients. The gender (female) and age were independent risk factors for preoperative DVT. The risk group classification by Caprini RAM was significantly associated with preoperative DVT. The usage of Caprini RAM before knee arthroplasty may be beneficial for prophylaxis of DVT.

Metformin attenuates synergic effect of diabetes mellitus and Helicobacter pylori infection on gastric cancer cells proliferation by suppressing PTEN expression.

It has been reported that CagA of Helicobacter pylori reduced PTEN expression by enhancing its promoter methylation. Furthermore, diabetes mellitus (DM) may also promote the methylation status of PTEN, a tumour suppressor gene in gastric cancer (GC). It is intriguing to explore whether DM may strengthen the tumorigenic effect of H pylori (HP) by promoting the methylation of PTEN promoter and whether the administration of metformin may reduce the risk of GC by suppressing the methylation of PTEN promoter. In this study, we enrolled 107 GC patients and grouped them as HP(-)DM(-) group, HP(+)DM(-) group and HP(+)DM(+) group. Bisulphite sequencing PCR evaluated methylation of PTEN promoter. Quantitative real-time PCR, immunohistochemistry and Western blot, immunofluorescence, flow cytometry and MTT assay were performed accordingly. DNA methylation of PTEN promoter was synergistically enhanced in HP(+)DM(+) patients, and the expression of PTEN was suppressed in HP(+)DM(+) patients. Cell apoptosis was decreased in HP(+)DM(+) group. Metformin showed an apparent effect on restoring CagA-induced elevation of PTEN promoter methylation, thus attenuating the PTEN expression. The reduced PTEN level led to increased proliferation and inhibited apoptosis of HGC-27 cells. In this study, we collected GC tumour tissues from GC patients with or without DM/HP to compare their PTEN methylation and expression while testing the effect of metformin on the methylation of PTEN promoter. In summary, our study suggested that DM could strengthen the tumorigenic effect of HP by promoting the PTEN promoter methylation, while metformin reduces GC risk by suppressing PTEN promoter methylation.

In Situ Genetically Cascaded Amplification for Imaging RNA Subcellular Locations.

In situ amplification methods, such as hybridization chain reaction, are valuable tools for mapping the spatial distribution and subcellular location of target analytes. However, the live-cell applications of these methods are still limited due to challenges in the probe delivery, degradation, and cytotoxicity. Herein, we report a novel genetically encoded in situ amplification method to noninvasively image the subcellular location of RNA targets in living cells. In our system, a fluorogenic RNA reporter, Broccoli, was split into two nonfluorescent fragments and conjugated to the end of two RNA hairpin strands. The binding of one target RNA can then trigger a cascaded hybridization between these hairpin pairs and thus activate multiple Broccoli fluorescence signals. We have shown that such an in situ amplified strategy can be used for the sensitive detection and location imaging of various RNA targets in living bacterial and mammalian cells. This new design principle provides an effective and versatile platform for tracking various intracellular analytes.

"Second-generation" fluorogenic RNA-based sensors.

A fluorogenic aptamer can specifically interact with a fluorophore to activate its fluorescence. These nucleic acid-based fluorogenic modules have been dramatically developed over the past decade, and have been used as versatile reporters in the sensor development and for intracellular imaging. In this review, we summarize the design principles, applications, and challenges of the first-generation fluorogenic RNA-based sensors. Moreover, we discuss some strategies to develop next-generation biosensors with improved sensitivity, selectivity, quantification property, and eukaryotic robustness. Using genetically encoded catalytic hairpin assembly strategy as an example, we further introduce a standard protocol to design, characterize, and apply these fluorogenic RNA-based sensors for in vitro detection and cellular imaging of target biomolecules. By incorporating natural RNA machineries, nucleic acid nanotechnology, and systematic evolution approaches, next-generation fluorogenic RNA-based devices can be potentially engineered to be widely applied in cell biology and biomedicine.

Evaluation of the Physiological Changes in the Central Airway on Multi-Detector Computed Tomography.

BACKGROUND: Most data about the trachea are collected during deep inspiration breath holding (DIBH) using multi-detector computed tomography (MDCT). Images of the physiological changes in the central airway are lacking. OBJECTIVE: The aim of this study was to explore the physiological changes in the central airway on MDCT during DIBH and deep expiration breath holding (DEBH). METHOD: The data from 62 patients (38 men and 24 women) who underwent enhanced computed tomography in our hospital were collected. Patients were grouped according to sex and age (18-45, 46-60, and >61 years). Anteroposterior diameter (APD) and transverse diameter (TD) at 3 levels (cricoid, intrathoracic inlet, and 2 cm above the carina), tracheal length, bronchial length, and subcarina angle (SCA) were measured. RESULTS: The average length of the trachea from the cricoid cartilage to the carina was 103.91 ± 10.37 mm at DEBH and 108.63 ± 11.31 mm at DIBH (p < 0.001). The APD of the trachea at the level of the cricoid, intrathoracic inlet, and 2 cm above the carina showed no differences between DEBH and DIBH. The TD of the trachea at the level of the cricoid, intrathoracic inlet, and 2 cm above the carina showed no differences between DEBH and DIBH. The average length of the right main bronchus during DEBH and DIBH was measured as 13.21 ± 3.60 and 13.24 ± 3.49 mm, respectively (p = 0.956). The average length of the left main bronchus at DEBH and DIBH was measured as 44.19 ± 5.50 and 44.27 ± 5.11 mm, respectively (p = 0.929). The average SCA was 81.74 ± 14.56 at DIBH, while it was 80.53 ± 14.38 at DEBH. The change in SCA between DIBH and DEBH showed no significant difference (p = 0.642). CONCLUSIONS: The APD at the level of the intrathoracic inlet is larger than that at the cricoid and 2 cm above the carina, while the TD is the opposite. These findings about the trachea and bronchus in our study may contribute to bronchoscopy examinations, tube applications, stent design, and stenting.

A Genetically Encoded RNA Photosensitizer for Targeted Cell Regulation.

Genetically encoded RNA devices have emerged for various cellular applications in imaging and biosensing, but their functions as precise regulators in living systems are still limited. Inspired by protein photosensitizers, we propose here a genetically encoded RNA aptamer based photosensitizer (GRAP). Upon illumination, the RNA photosensitizer can controllably generate reactive oxygen species for targeted cell regulation. The GRAP system can be selectively activated by endogenous stimuli and light of different wavelengths. Compared with their protein analogues, GRAP is highly programmable and exhibits reduced off-target effects. These results indicate that GRAP enables efficient noninvasive target cell ablation with high temporal and spatial precision. This new RNA regulator system will be widely used for optogenetics, targeted cell ablation, subcellular manipulation, and imaging.

VEGF gene rs3025039C/T and rs833052C/A variants are associated with bladder cancer risk in Asian descendants.

INTRODUCTION: Polymorphisms of vascular endothelial growth factor (VEGF) gene were evaluated in a number of studies to evaluate bladder cancer (BCa) susceptibility but with controversial conclusions. MATERIAL AND METHODS: We performed a pooled analysis and used odds ratios (ORs) with corresponding 95% confidence intervals (95% CIs) to investigate the correlation between VEGF gene rs3025039C/T and rs833052C/A variants and risk of BCa. Furthermore, we utilized in silico tools to demonstrate the relationship of VEGF expression correlated with BCa susceptibility and survival time. RESULTS: A total of eight studies including 4359 BCa patients and 5417 control subjects were enrolled in our study. For VEGF rs3025039C/T, a significant association was indicated between this variant and BCa risk in homozygote comparison (OR = 1.51; 95% CI = 1.13-2.02; P heterogeneity = 0.815) and recessive genetic model (OR = 1.49; 95% CI = 1.12-1.99; P heterogeneity = 0.874), in particular in an Asian population subgroup. For VEGF rs833052C/A, we observed a positive association between this variant and BCa susceptibility in Asian descendants. Results from in silico tool showed evidence that VEGF expression in bladder carcinoma tissue is higher than that in normal counterpart (transcripts per kilobase million = 7.21 vs 6.85; P < 0.05). CONCLUSIONS: The VEGF gene rs3025039C/T and rs833052C/A variants may contribute to the risk of developing BCa, especially in Asian descendants. Future larger sample studies should be continued to focus on this issue in more detail.

Knockdown of LncRNA PVT1 inhibits tumorigenesis in non-small-cell lung cancer by regulating miR-497 expression.

Plasmacytoma variant translocation1 (PVT1) was reported to be upregulated in non-small-cell lung cancer (NSCLC) tissues, serve as a promising biomarker for diagnosis and prognosis of NSCLC, and promoted NSCLC cell proliferation. However, the detailed molecular mechanism of PVT1 involved in the pathogenesis and development of NSCLC remains largely unknown. In this study, the expression levels of PVT1 and miR-497 in NSCLC cells were determined by qRT-PCR. Cell viability, invasion and apoptosis were detected by MTT assay, cell invasion assay and flow cytometry analysis, respectively. RNA immunoprecipitation (RIP) and luciferase reporter assay were performed to confirm whether PVT1 directly interacts with miR-497. A xenograft mouse model was established to confirm the effect of PVT1 on tumor growth in vivo and the underlying molecular mechanism. Our findings indicated that PVT1 was significantly upregulated and miR-497 was markedly downregulated in NSCLC cell lines. si-PVT1 effectively decreased the expression of PVT1 and increased the expression of miR-497. PVT1 knockdown remarkably inhibited cell viability, invasion and promoted apoptosis in NSCLC cells. RIP and luciferase reporter assay demonstrated that PVT1 could directly interact with miR-497. Moreover, PVT1 overexpression reversed the inhibitory effect of miR-497 on cell viability, invasion and promotion effect on apoptosis of NSCLC cells. Furthermore, in vivo experiment showed that knockdown of PVT1 inhibited tumor growth in vivo and promoted miR-497 expression. In conclusion, knockdown of PVT1 inhibited cell viability, invasion and induced apoptosis in NSCLC by regulating miR-497 expression, elucidating the molecular mechanism of the oncogenic role of PVT1 in NSCLC and providing an lncRNA-directed target for NSCLC.

Genetically Encoded Ratiometric RNA-Based Sensors for Quantitative Imaging of Small Molecules in Living Cells.

Precisely determining the intracellular concentrations of metabolites and signaling molecules is critical in studying cell biology. Fluorogenic RNA-based sensors have emerged to detect various targets in living cells. However, it is still challenging to apply these genetically encoded sensors to quantify the cellular concentrations and distributions of targets. Herein, using a pair of orthogonal fluorogenic RNA aptamers, DNB and Broccoli, we engineered a modular sensor system to apply the DNB-to-Broccoli fluorescence ratio to quantify the cell-to-cell variations of target concentrations. These ratiometric sensors can be broadly applied for live-cell imaging and quantification of metabolites, signaling molecules, and other synthetic compounds.