Absolute quantification and analysis of extracellular vesicle lncRNAs from the peripheral blood of patients with lung cancer based on multi-colour fluorescence chip-based digital PCR

Chip-based digital PCR with large-field one-shot imaging for high-sensitivity nucleic acid quantification

To enhance the absolute detection limit of digital polymerase chain reaction (dPCR) by accommodating more templates in a single loading, we developed a chip-based dPCR (cdPCR) device with dimensions of 26 mm × 16 mm, incorporating 21,384 microreaction chambers. Traditional fluorescence imaging systems cannot capture the entire chip in a one-shot, necessitating image stitching, which slows detection and introduces the risk of stitching errors. To overcome this limitation, we designed a large-field fluorescence imaging system with an effective imaging area of 28 mm × 20 mm, enabling one-shot acquisition of the entire cdPCR fluorescence image in 1 s. A Köhler illumination system was employed to achieve 90 % illumination uniformity, enhancing image quality. Additionally, image processing modules, including rotation and brightness correction, were employed to ensure precise detection. Validation experiments using lung cancer DNA demonstrated a strong correlation (R2 > 0.9997) between measured and theoretical values. This system provides an automated, rapid, and accurate platform for cdPCR fluorescence image processing, eliminating stitching errors and advancing absolute quantification in dPCR analysis.

Opto-digital molecular analytics

In contrast to conventional ensemble-average-based methods, opto-digital molecular analytic approaches digitize detection by physically partitioning individual detection events into discrete compartments or directly locating and analyzing the signals from single molecules. The sensitivity can be enhanced by signal amplification reactions, signal enhancement interactions, labelling by strong signal emitters, advanced optics, image processing, and machine learning, while specificity can be improved by designing target-selective probes and profiling molecular dynamics. With the capabilities to attain a limit of detection several orders lower than the conventional methods, reveal intrinsic molecular information, and achieve multiplexed analysis using a small-volume sample, the emerging opto-digital molecular analytics may be revolutionarily instrumental to clinical diagnosis, molecular chemistry and science, drug discovery, and environment monitoring. In this article, we provide a comprehensive review of the recent advances, offer insights into the underlying mechanisms, give comparative discussions on different strategies, and discuss the current challenges and future possibilities.

Influence of the lncRNA SLC9A3-AS1 on colon cancer and the biological activities of colon cancer cells

BACKGROUND

Circulating long non-coding RNAs expression was associated with diagnosis and therapies of various diseases. The current study investigated the expression of lncRNA SLC9A3-AS1 in the serum samples from colon cancer patients and explored its potential functions in colon cancer cells.

METHODS

Serum expression levels of SLC9A3-AS1 and miR-486 were measured in 130 patients with colon cancer and 96 healthy individuals using RT-qPCR. The influence of SLC9A3-AS1 expression and miR-486 expression on colon cancer cellular behaviors was detected by MTT assay and Transwell chamber assays. Pearson correlation analysis was used to analyze the association between SLC9A3-AS1 and miR-486.

RESULTS

We found serum expression levels of SLC9A3-AS1 were overexpressed in sera of colon cancer patients. ROC curve analysis showed that SLC9A3-AS1 had a high area under the ROC curve value for early detection of colon cancer patients from a healthy control. The proliferation potential, migration, and invasion behaviors were weakened by si-SLC9A3-AS1 and reversed by the miR-486 inhibitor.

CONCLUSION

Serum SLC9A3-AS1 may be used as a non-invasive diagnostic predictor for the early screening of colon cancer. LncRNA SLC9A3-AS1 affects colon cancer cellular activities by negatively modulating miR-486. A major limitation of this study is the small sample size, and in addition, the lack of longitudinal data prevented us from conducting an in-depth analysis of long-term changes in variables.

Demystifying EV heterogeneity: emerging microfluidic technologies for isolation and multiplexed profiling of extracellular vesicles

Extracellular vesicles (EVs) are heterogeneous lipid containers carrying complex molecular cargoes, including proteins, nucleic acids, glycans, etc. These vesicles are closely associated with specific physiological characteristics, which makes them invaluable in the detection and monitoring of various diseases. However, traditional isolation methods are often labour-intensive, inefficient, and time-consuming. In addition, single biomarker analyses are no longer accurate enough to meet diagnostic needs. Routine isolation and molecular analysis of high-purity EVs in clinical applications is even more challenging. In this review, we discuss a promising solution, microfluidic-based techniques, that combine efficient isolation and multiplex detection of EVs, to further demystify EV heterogeneity. These microfluidic-based EV multiplexing platforms will hopefully facilitate development of liquid biopsies and offer promising opportunities for personalised therapy.

A Pioneer Review on Lactoferrin-Conjugated Extracellular Nanovesicles for Targeting Cellular Melanoma: Recent Advancements and Future Prospects

Melanoma, a highly aggressive form of skin cancer, presents a formidable challenge in terms of treatment due to its propensity for metastasis and resistance to conventional therapies. The development of innovative nanocarriers for targeted drug delivery has opened new avenues in cancer therapy. Lactoferrin-conjugated extracellular nanovesicles (LF-EVs) have emerged as a promising vehicle in the targeted treatment of cellular melanoma, owing to their natural biocompatibility, enhanced bioavailability, and ability to traverse biological barriers effectively. This review synthesizes recent advancements in the use of LF-EVs as a novel drug delivery system for melanoma, emphasizing their unique capacity to enhance cellular uptake through LF's receptor-mediated endocytosis pathways. Key studies demonstrate that LF conjugation significantly increases the specificity of extracellular nanovesicles for melanoma cells, minimizes off-target effects, and promotes efficient intracellular drug release. Furthermore, we explore how LF-EVs interact with the tumor microenvironment, potentially inhibiting melanoma progression and metastasis while supporting antitumor immune responses. Future prospects in this field include optimizing LF conjugation techniques, improving the scalability of LF-EV production, and integrating multifunctional payloads to target drug resistance mechanisms. This review highlights the potential of LF-EVs to transform melanoma treatment strategies, bridging current gaps in therapeutic delivery and paving the way for personalized and less invasive melanoma therapies.

Digital recombinase polymerase amplification chip based on asymmetric contact angle composite interface

BACKGROUND

Digital recombinase polymerase amplification (dRPA) is an effective tool for the absolute quantification of nucleic acids and the detection of rare mutations. Due to the high viscosity or other physical properties of the reagent, this can compromise the accuracy and reproducibility of detection results, which limits the broader adoption and practical application of this technology. In this study, we developed an asymmetric contact angle digital isothermal detection (ACA-DID) chip and optimized the ACA-DID chip structure to achieve rapid digital recombinase polymerase amplification.

RESULT

We designed with a pressure-driven and highly asymmetric contact angle composite interface to enable robust digital RPA. The addition of surfactants to the PDMS creates an asymmetric contact angle between the upper and lower surfaces of the fluid channel, improving reagent flow and facilitating entry into microwells. This design addresses the challenges posed by high-viscosity reagents, which typically complicate effective digital discretization and lead to fluorescence signal aggregation. By diluting specific components of the RPA reagent, we improved the uniformity of amplification and effectively reduced signal aggregation. The hydrophobic surface of results strong adsorption to biological macromolecules, such as nucleic acids and proteins, which will decrease the efficiency of dRPA amplification. To achieve efficient amplification of reagents in the microchamber, this work uses a surface modification strategy of PDMS doped surfactant, which eliminates the issue of PDMS materials hindering dRPA amplification efficiency.

SIGNIFICANCE AND NOVELTY

The ACA-DID chip demonstrated excellent analytical accuracy in the quantification of African swine fever DNA samples, highlighting its potential to enhance the accessibility and effectiveness of dRPA technology. This innovation promises to overcome key limitations in current digital RPA amplification platforms, driving broader adoption and application, especially in cost-sensitive or resource-limited settings.

Functional Immunoaffinity 3D Magnetic Core-Shell Nanometallic Structure for High-Efficiency Separation and Label-Free SERS Detection of Exosomes

Tumor exosomes, known as maternal cell messengers, play an important role in cancer occurrence, proliferation, metastasis, immune escape, drug resistance, and other processes and are an entry point for cancer research. However, there is still a lack of an efficient detection technology for exosomes. In this study, the ultrahigh sensitivity SERS nanoprobe with a three dimensional (3D) magnetic core/Au nanocolumn/Au nanoparticles shell strongly coupling multistage structure (Fe3O4@NR-NPs) was constructed by crystal growth of nanocrystals in the confined space of a central radiating single particle mesoporous molecular sieve channel and strong coupling secondary growth of gold particles. The exosomes were confined onto the "hot spot" of plasmonic nanoparticles and rapidly enriched by CD63 antibody functional-Fe3O4@NR-NPs to achieve high sensitivity detection, with the limit of detection of 1 × 103 particles/mL (S/N = 3). The spectral data set of different exosomes is applied to train for multivariate classification of cell types and to estimate how the normal exosome data resemble cancer cell exosomes by principal component analysis (PCA). Finally, this detection method has also been successfully employed for the detection of exosomes in complex samples; this proves that the proposed SERS-based method is a promising tool for clinical cancer screening.

The new advance of exosome-based liquid biopsy for cancer diagnosis

Liquid biopsy is a minimally invasive method that uses biofluid samples instead of tissue samples for cancer diagnosis. Exosomes are small extracellular vesicles secreted by donor cells and act as mediators of intercellular communication in human health and disease. Due to their important roles, exosomes have been considered as promising biomarkers for liquid biopsy. However, traditional methods for exosome isolation and cargo detection methods are time-consuming and inefficient, limiting their practical application. In the past decades, many new strategies, such as microfluidic chips, nanowire arrays and electrochemical biosensors, have been proposed to achieve rapid, accurate and high-throughput detection and analysis of exosomes. In this review, we discussed about the new advance in exosome-based liquid biopsy technology, including isolation, enrichment, cargo detection and analysis approaches. The comparison of currently available methods is also included. Finally, we summarized the advantages and limitations of the present strategies and further gave a perspective to their future translational use.

LncRNA SLC9A3-AS1 knockdown increases the sensitivity of liver cancer cell to triptolide by regulating miR-449b-5p-mediated glycolysis

Triptolide (TP) is involved in the progression of liver cancer. However, the detailed molecular network regulated through TP is still unclear. Long non-coding RNA (LncRNA) SLC9A3 exerts roles in various pathological progresses. Nevertheless, whether SLC9A3 affects the sensitivity of liver cancer cells to TP have not been uncovered. The content of SLC9A3-AS1 and miR-449b-5p was estimated by utilizing quantitative real-time polymerase-chain reaction (qRT-PCR). Cell counting kit 8 (CCK-8) assay was introduced to assess cell viability. Additionally, cell viability as well as invasion was tested via transwell assay. The direct binding between miR-449b-5p and SLC9A3-AS1 or LDHA was confirmed through luciferase reporter gene assay. Moreover, glycolysis rate was tested by calculating the uptake of glucose in addition to the production of lactate in Huh7 cells. LncRNA SLC9A3-AS1 was up-regulated in liver cancer tissue samples and cells. Knockdown of SLC9A3-AS1 notably further inhibited viability, migration as well as invasion in Huh7 cells. MiR-449b-5p was the direct downstream miRNA of SLC9A3-AS1 and was down-regulated by SLC9A3-AS1 in Huh7 cells. In addition, miR-449b-5p was reduced in liver cancer tissues and cells. Overexpressed miR-449b-5p increased the sensitivity of Huh7 cells to TP remarkably. Moreover, miR-449b-5p negatively regulated LDHA expression in Huh7 cells. This work proved that SLC9A3-AS1 increased the sensitivity of liver cancer cells to TP by regulating glycolysis rate mediated via miR-449b-5p/LDHA axis. These findings implied that TP is likely to be a potent agent for treating patients diagnosed with liver cancer.

Enhancing CRISPR/Cas-mediated electrochemical detection of nucleic acid using nanoparticle-labeled covalent organic frameworks reporters

Molecular detection of nucleic acid plays an important role in early diagnosis and therapy of disease. Herein, a novel and enhanced electrochemical biosensor was exploited based on target-activated CRISPR/Cas12a system coupling with nanoparticle-labeled covalent organic frameworks (COFs) as signal reporters. Hollow spherical COFs (HCOFs) not only served as the nanocarriers of silver nanoparticles (AgNPs)-DNA conjugates for enhanced signal output but also acted as three-dimensional tracks of CRISPR/Cas12a system to improve the cleavage accessibility and efficiency. The presence of target DNA triggered the trans-cleavage activity of the CRISPR/Cas12a system, which rapidly cleaved the AgNPs-DNA conjugates on HCOFs, resulting in a remarkable decrease of the electrochemical signal. As a proof of concept, the fabricated biosensing platform realized highly sensitive and selective detection of human papillomavirus type 16 (HPV-16) DNA ranging from 100 fM to 1 nM with the detection limit of 57.2 fM. Furthermore, the proposed strategy provided a versatile and high-performance biosensor for the detection of different targets by simple modification of the crRNA protospacer, holding promising applications in disease diagnosis.

Exosomal mRNA in plasma serves as a predictive marker for microvascular invasion in hepatocellular carcinoma

BACKGROUND AND AIM

There is a pressing need for non-invasive preoperative prediction of microvascular invasion (MVI) in hepatocellular carcinoma (HCC). This study investigates the potential of exosome-derived mRNA in plasma as a biomarker for diagnosing MVI.

METHODS

Patients with suspected HCC undergoing hepatectomy were prospectively recruited for preoperative peripheral blood collection. Exosomal RNA profiling was conducted using RNA sequencing in the discovery cohort, followed by differential expression analysis to identify candidate targets. We employed multiplexed droplet digital PCR technology to efficiently validate them in a larger sample size cohort.

RESULTS

A total of 131 HCC patients were ultimately enrolled, with 37 in the discovery cohort and 94 in the validation cohort. In the validation cohort, the expression levels of RSAD2, PRPSAP1, and HOXA2 were slightly elevated while CHMP4A showed a slight decrease in patients with MVI compared with those without MVI. These trends were consistent with the findings in the discovery cohort, although they did not reach statistical significance (P > 0.05). Notably, the expression level of exosomal PRPSAP1 in plasma was significantly higher in patients with more than 5 MVI than in those without MVI (0.147 vs 0.070, P = 0.035).

CONCLUSION

This study unveils the potential of exosome-derived PRPSAP1 in plasma as a promising indicator for predicting MVI status preoperatively.

Current Evidence for a Lung Cancer Screening Program

Background

Lung cancer screening is still in an early phase compared to other cancer screening programs, despite its high lethality particularly when diagnosed late. Achieving early diagnosis is crucial to obtain optimal outcomes.

Summary

In this review, we will address the current evidence on lung cancer screening through low-dose computed tomography (LDCT) and its impact on mortality reduction, existing screening recommendations, patient eligibility criteria, screening frequency and duration, benefits and harms, cost-effectiveness and some insights on lung cancer screening implementation and adoption. Additionally, new non-imaging, noninvasive biomarkers with high diagnostic potential are also briefly highlighted.

Key Messages

LDCT screening in a prespecified population based on age and smoking history proved to reduce lung cancer mortality. Optimization of the target population and management of LDCT pitfalls can further improve lung cancer screening efficiency and cost-effectiveness. Novel screening technologies and biomarkers being studied can potentially be game-changers in lung cancer screening and diagnosis.

Recent progress of exosomal lncRNA/circRNA-miRNA-mRNA axis in lung cancer: implication for clinical application

Lung cancer is the leading cause of death among malignant tumors in the world. High lung cancer mortality rate is due to most of patients diagnosed at advanced stage. The Liquid biopsy of lung cancer have received recent interest for early diagnosis. One of the components of liquid biopsy is the exosome. The exosome cargos non-coding-RNAs, especially long non-coding RNAs (lncRNAs), circular RNAs (circRNAs), and microRNAs (miRNAs). The lung cancer derived exosomal non-coding RNAs play the pivotal roles of lung cancer in carcinogenesis, diagnosis, therapy, drug resistance and prognosis of lung cancer. Given ceRNA (competitive endogenous RNA) mechanism, lncRNA or circRNA can act as ceRNA to compete to bind miRNAs and alter the expression of the targeted mRNA, contributing to the development and progression of lung cancer. The current research progress of the roles of the exosomal non-coding-RNAs and the interplay of ceRNAs and miRNAs in mediated lung cancer is illustrated in this article. Hence, we presented an experimentally validated lung cancer derived exosomal non-coding RNAs-regulated target gene axis from already existed evidence in lung cancer. Then LncRNA/circRNA-miRNA-mRNA axis may be a potential target for lung cancer treatment and has great potential in the diagnosis and prognosis of lung cancer.

Diagnostic Accuracy of Exosomal Long Noncoding RNAs in Diagnosis of NSCLC: A Meta-Analysis

PURPOSE

Globally, non-small cell lung cancer (NSCLC) is the primary cause of cancer-related mortality, both early and accurate diagnosis are essential for effective treatment and improved patient outcomes. Exosomal noncoding RNAs (ncRNAs) have emerged as promising biomarkers for NSCLC diagnosis. This meta-analysis aims to assess the diagnostic accuracy of exosomal long noncoding RNAs (lncRNAs) for diagnosing NSCLC.

METHODS

A comprehensive literature search was conducted to identify relevant studies that assessed the diagnostic performance of exosomal lncRNAs in NSCLC. Quality assessment and data extraction were performed independently by two reviewers. Pooled sensitivity, specificity, and other relevant diagnostic parameters were calculated using a bivariate random-effects model. Subgroup analyses and meta-regression were conducted to explore potential sources of heterogeneity.

RESULTS

Sixteen studies, comprising 1843 NSCLC cases and 1298 controls, were included in this meta-analysis. The pooled sensitivity and specificity of nine exosomal lncRNAs for diagnosing NSCLC were 0.74 [95% confidence interval (CI) 0.69-0.79] and 0.78 (95% CI 0.68-0.85). The pooled area under the receiver operating characteristic curve (AUC) for fifteen lncRNAs was 0.80 (95% CI 0.768-0.831). Meta-regression could not find any source for interstudy heterogeneity.

CONCLUSION

Exosomal lncRNAs, particularly AL139294.1, GAS5, LUCAT1, and SOX2-OT, have excellent diagnostic accuracy and promising diagnostic potential in NSCLC. Therefore, they can be used as diagnostic tools for early detection of NSCLC.

Autonomous enzymatic synthesis of functional nucleic acids for sensitive measurement of long noncoding RNA in human lung tissues

Aberrant long noncoding RNA (lncRNA) expression is linked to varied pathological processes and malignant tumors, and lncRNA can serve as potential disease biomarkers. Herein, we demonstrate the autonomous enzymatic synthesis of functional nucleic acids for sensitive measurement of lncRNA in human lung tissues on the basis of multiple primer generation-mediated rolling circle amplification (mPG-RCA). This assay involves two padlock probes that act as both a detection probe for recognizing target lncRNA and a domain for producing complementary DNAzyme. Two padlock probes can hybridize with target lncRNA at different sites, followed by ligation to form a circular template with the aid of RNA ligase. The circular template can initiate mPG-RCA to generate abundant Mg2+-dependent DNAzymes that can specifically cleave signal probes to induce the recovery of Cy3 fluorescence. The inherent characteristics of ligase-based ligation reaction and DNAzymes endow this assay with excellent specificity, and the introduction of multiple padlock probes endows this assay with high sensitivity. This strategy can rapidly and sensitively measure lncRNA with a wide linear range of 1 fM - 1 nM and a detection limit of 678 aM within 1.5 h, and it shows distinct advantages of simplicity and immobilization-free without the need of precise temperature control and tedious procedures of nanomaterial preparation. Moreover, it enables accurate measurement of lncRNA level in normal cells and malignant tumor cells as well as differentiation of lncRNA expressions in tissues of non-small cell lung cancer (NSCLC) patients and normal individuals, with promising applications in biomedical studies and disease diagnosis.

Label-free single-vesicle based surface enhanced Raman spectroscopy: A robust approach for investigating the biomolecular composition of small extracellular vesicles

Small extracellular vesicles (sEVs) are cell-released vesicles ranging from 30-150nm in size. They have garnered increasing attention because of their potential for both the diagnosis and treatment of disease. The diversity of sEVs derives from their biological composition and cargo content. Currently, the isolation of sEV subpopulations is primarily based on bio-physical and affinity-based approaches. Since a standardized definition for sEV subpopulations is yet to be fully established, it is important to further investigate the correlation between the biomolecular composition of sEVs and their physical properties. In this study, we employed a platform combining single-vesicle surface-enhanced Raman spectroscopy (SERS) and machine learning to examine individual sEVs isolated by size-exclusion chromatography (SEC). The biomolecular composition of each vesicle examined was reflected by its corresponding SERS spectral features (biomolecular "fingerprints"), with their roots in the composition of their collective Raman-active bonds. Origins of the SERS spectral features were validated through a comparative analysis between SERS and mass spectrometry (MS). SERS fingerprinting of individual vesicles was effective in overcoming the challenges posed by EV population averaging, allowing for the possibility of analyzing the variations in biomolecular composition between the vesicles of similar and/or different sizes. Using this approach, we uncovered that each of the size-based fractions of sEVs contained particles with predominantly similar SERS spectral features. Indeed, more than 84% of the vesicles residing within a particular group were clearly distinguishable from that of the other EV sub-populations, despite some spectral variations within each sub-population. Our results suggest the possibility that size-based EV fractionation methods produce samples where similarly eluted sEVs are correlated with their respective biochemical contents, as reflected by their SERS spectra. Our findings therefore highlight the possibility that the biogenesis and respective biological functionalities of the various sEV fractions may be inherently different.

The Significance and Importance of dPCR, qPCR, and SYBR Green PCR Kit in the Detection of Numerous Diseases

Digital PCR (dPCR) is the latest technique that has become commercially accessible for various types of research. This method uses Taq polymerase in a standard polymerase chain reaction (PCR) to amplify a target DNA fragment from a complex sample, like quantitative PCR (qPCR) and droplet digital PCR (dd- PCR). ddPCR may facilitate microRNA (miRNA) measurement, particularly in liquid biopsy, because it has been proven to be more effective and sensitive, and in this method, ddPCR can provide an unprecedented chance for deoxyribonucleic acid (DNA) methylation research because of its capability to increase sensitivity and precision over conventional PCR-based methods. qPCR has also been found to be a valuable standard technique to measure both copy DNA (cDNA) and genomic DNA (gDNA) levels, although the finding data can be significantly variable and non-reproducible without relevant validation and verification of both primers and samples. The SYBR green quantitative real-time PCR (qPCR) method has been reported as an appropriate technique for quantitative detection and species discrimination, and has been applied profitably in different experiments to determine, quantify, and discriminate species. Although both TaqMan qRT-PCR and SYBR green qRT-PCR are sensitive and rapid, the SYBR green qRT-PCR assay is easy and the TaqMan qRT-PCR assay is specific but expensive due to the probe required. This review aimed to introduce dPCR, qPCR, SYBR green PCR kit, and digital PCR, compare them, and also introduce their advantages in the detection of different diseases.

Comprehensive landscape and future perspective of long noncoding RNAs in non-small cell lung cancer: it takes a village

Long noncoding RNAs (lncRNAs) are a distinct subtype of RNA that lack protein-coding capacity but exert significant influence on various cellular processes. In non-small cell lung cancer (NSCLC), dysregulated lncRNAs act as either oncogenes or tumor suppressors, contributing to tumorigenesis and tumor progression. LncRNAs directly modulate gene expression, act as competitive endogenous RNAs by interacting with microRNAs or proteins, and associate with RNA binding proteins. Moreover, lncRNAs can reshape the tumor immune microenvironment and influence cellular metabolism, cancer cell stemness, and angiogenesis by engaging various signaling pathways. Notably, lncRNAs have shown great potential as diagnostic or prognostic biomarkers in liquid biopsies and therapeutic strategies for NSCLC. This comprehensive review elucidates the significant roles and diverse mechanisms of lncRNAs in NSCLC. Furthermore, we provide insights into the clinical relevance, current research progress, limitations, innovative research approaches, and future perspectives for targeting lncRNAs in NSCLC. By summarizing the existing knowledge and advancements, we aim to enhance the understanding of the pivotal roles played by lncRNAs in NSCLC and stimulate further research in this field. Ultimately, unraveling the complex network of lncRNA-mediated regulatory mechanisms in NSCLC could potentially lead to the development of novel diagnostic tools and therapeutic strategies.

Construction of a Programmable Feedback Network with Continuously Activatable Molecular Beacon Fluorescence for One-Step Quantification of Long Noncoding RNAs in Clinical Breast Tissues

Long noncoding RNAs (lncRNAs) are key regulators in numerous pathological and physiological processes, and their aberrant expression is implicated in many diseases. Herein, we develop a programmable feedback network with continuously activatable molecular beacon (MB) fluorescence for one-step quantification of mammalian-metastasis-associated lung adenocarcinoma transcript 1 (lncRNA MALAT1) in clinical breast tissues. We introduce a functional MB with three domains, including a substrate for lncRNA MALAT1 recognition, a template for strand displacement amplification (SDA), and a reporter for signal output with FAM fluorescence being quenched by BHQ1. When MALAT1 is present, it recognizes and unfolds the MB, leading to the recovery of FAM fluorescence. Once the MB is opened, multiple rounds of SDA reaction are automatically initiated by recruiting primer, KF DNA polymerase, and Nt.BbvCI nicking enzyme, inducing the opening of more MBs and the dissociation of more FAM/BHQ1 pairs. Consequently, a feedback network is constructed through multicycle cascade SDA, achieving the exponential accumulation of fluorescence signals for accurate quantification of MALAT1. In this assay, only two oligonucleotides (i.e., MB and primer) are involved for the establishment of a feedback amplification network, greatly simplifying the design of the reaction system. Moreover, this assay requires only one step to realize the isothermal exponential amplification for real-time monitoring of MALAT1 with attomolar sensitivity. This assay displays single-base mismatch selectivity with high anti-interference capability, and it can further quantify endogenous MALAT1 at the single-cell level and differentiate MALAT1 expression between breast cancer patient tissues and healthy person tissues.

Simultaneous amplification of DNA in a multiplex circular array shaped continuous flow PCR microfluidic chip for on-site detection of bacterial

Based on time to place conversion, continuous flow polymerase chain reaction (CF-PCR) can realize a rapid amplification of DNA by running the PCR reagent in a serpentine microchannel but a larger space is required for each sample, which greatly reduces the efficiency of the CF-PCR. Herein, we propose a multiplex circular array shaped CF-PCR microfluidic chip for on-site detection of bacteria. There were 12 serpentine microchannels which were distributed on the disc in an annular form, and each microchannel consisted of an inlet for sample injection, and an outlet for the detection of the PCR products based on fluorescence. Samples could be simultaneously driven into each inlet by a one-to-twelve diverter through a syringe. Moreover, the method of adding fluorescent dyes at the end of the microchannel can solve the inhibition effect of excessive fluorescent dyes on the PCR reaction. The process finished with simultaneous amplification of 12 different target genes from Porphyromonas gingivalis, Treponema denticola, Tannerella forsythia, and Escherichia coli, and on-site detection of their corresponding positives within 23 min. The fastest detectable PCR reaction time was 5.38 ± 0.2 min at a flow rate of 1 mL h^-1. For E. coli, the minimum detectable concentration was 2.5 × 10^-3 ng μL^-1 in this microfluidic system. Such a system can increase the throughput of CF-PCR for point-of-care testing of pathogens.

Lab-on-a-chip systems for cancer biomarker diagnosis

Lab-on-a-chip (LOC) or micro total analysis system is one of the microfluidic technologies defined as the adaptation, miniaturization, integration, and automation of analytical laboratory procedures into a single instrument or "chip". In this article, we review developments over the past five years in the application of LOC biosensors for the detection of different types of cancer. Microfluidics encompasses chemistry and biotechnology skills and has revolutionized healthcare diagnosis. Superior to traditional cell culture or animal models, microfluidic technology has made it possible to reconstruct functional units of organs on chips to study human diseases such as cancer. LOCs have found numerous biomedical applications over the past five years, including integrated bioassays, cell analysis, metabolomics, drug discovery and delivery systems, tissue and organ physiology and disease modeling, and personalized medicine. This review provides an overview of the latest developments in microfluidic-based cancer research, with pros, cons, and prospects.

Adsorption-Free Self-Priming Direct Digital Dual-crRNA CRISPR/Cas12a-Assisted Chip for Ultrasensitive Detection of Pathogens

Rapid and sensitive pathogen detection methods are critical for disease diagnosis and treatment. RPA-CRISPR/Cas12 systems have displayed remarkable potential in pathogen detection. A self-priming digital PCR chip is a powerful and attractive tool for nucleic detection. However, the application of the RPA-CRISPR/Cas12 system to the self-priming chip still has great challenges due to the problems of protein adsorption and two-step detection mode of RPA-CRISPR/Cas12. In this study, an adsorption-free self-priming digital chip was developed and a direct digital dual-crRNAs (3D) assay was established based on the chip for ultrasensitive detection of pathogens. This 3D assay combined the advantages of rapid amplification of RPA, specific cleavage of Cas12a, accurate quantification of digital PCR, and point-of-care testing (POCT) of microfluidics, enabling accurate and reliable digital absolute quantification of Salmonella in POCT. Our method can provide a good linear relationship of Salmonella detection in the range from 2.58 × 10¹ to 2.58 × 10⁴ cells/mL with a limit of detection ∼0.2 cells/mL within 30 min in a digital chip by targeting the invA gene of Salmonella. Moreover, the assay could directly detect Salmonella in milk without nucleic acid extraction. Therefore, the 3D assay has the significant potential to provide accurate and rapid pathogen detection in POCT. This study provides a powerful nucleic detection platform and facilitates the application of CRISPR/Cas-assisted detection and microfluidic chips.

Mix-and-Detection Assay with Multiple Cyclic Enzymatic Repairing Amplification for Rapid and Ultrasensitive Detection of Long Noncoding RNAs in Breast Tissues

Long noncoding RNAs (lncRNAs) are valuable biomarkers and therapeutic targets, and they play essential roles in various pathological and biological processes. So far, the reported lncRNA assays usually suffer from unsatisfactory sensitivity and time-consuming procedures. Herein, we develop a mix-and-read assay based on multiple cyclic enzymatic repairing amplification (ERA) for sensitive and rapid detection of mammalian metastasis-associated lung adenocarcinoma transcript 1 (lncRNA MALAT1). In this assay, we design two three-way junction (3WJ) probes including a 3WJ template and a 3WJ primer to specifically recognize lncRNA MALAT1, and the formation of a stable 3WJ structure induces cyclic ERA to generate triggers. The resulting triggers subsequently hybridize with a free 3WJ template and act as primers to initiate new rounds of cyclic ERA, generating abundant triggers. The hybridization of triggers with signal probes forms stable double-stranded DNA duplexes that can be specifically cleaved by apurinic/apyrimidinic endonuclease 1 to produce a high fluorescence signal. This assay can be carried out in a mix-and-read manner within 10 min under an isothermal condition (50 °C), which is the rapidest and simplest method reported so far for the lncRNA MALAT1 assay. This method can sensitively detect lncRNA MALAT1 with a limit of detection of 0.87 aM, and it can accurately measure endogenous lncRNA MALAT1 at the single-cell level. Moreover, this method can distinguish lncRNA MALAT1 expression in breast cancer patient tissues and their corresponding healthy adjacent tissues. Importantly, the extension of this assay to different RNAs detection can be achieved by simply replacing the corresponding target recognition sequences.

Advanced technologies for molecular diagnosis of cancer: State of pre-clinical tumor-derived exosome liquid biopsies

Exosomes are membrane-defined extracellular vesicles (EVs) approximately 40-160 ​nm in diameter that are found in all body fluids including blood, urine, and saliva. They act as important vehicles for intercellular communication between both local and distant cells and can serve as circulating biomarkers for disease diagnosis and prognosis. Exosomes play a key role in tumor metastasis, are abundant in biofluids, and stabilize biomarkers they carry, and thus can improve cancer detection, treatment monitoring, and cancer staging/prognosis. Despite their clinical potential, lack of sensitive/specific biomarkers and sensitive isolation/enrichment and analytical technologies has posed a barrier to clinical translation of exosomes. This review presents a critical overview of technologies now being used to detect tumor-derived exosome (TDE) biomarkers in clinical specimens that have potential for clinical translation.

Recent advances in integrated microfluidics for liquid biopsies and future directions

Liquid biopsies have piqued the interest of researchers as a new tumor diagnosis technique due to their unique benefits of non-invasiveness, sensitivity, and convenience. Recent advances in microfluidic technology have integrated separation, purification, and detection, allowing for high-throughput, high-sensitivity, and high-controllability detection of specific biomarkers in liquid biopsies. With the increasing demand for tumor detection and individualized treatment, new challenges are emerging for the ever-improving microfluidic technology. The state-of-the-art microfluidic design and fabrications have been reviewed in this manuscript, and how this technology can be applied to liquid biopsies from the point of view of the detection process. The primary discussion objectives are circulating tumor cells (CTCs), exosomes, and circulating nucleic acid (ctDNA). Furthermore, the challenges and future direction of microfluidic technology in detecting liquid biomarkers have been discussed.

Programmable Ligation-Transcription Circuit-Driven Cascade Amplification Machinery for Multiple Long Noncoding RNAs Detection in Lung Tissues

The measurement of long noncoding RNAs (lncRNAs) is essential to diagnosis and treatment of various diseases such as cancers. Herein, we develop a simple method to simultaneously detect multiple lncRNAs using programmable ligation-transcription circuit-driven cascade amplification and single-molecule counting. The presence of targets lncRNA HOTAIR and lncRNA MALAT1 activates the ligation-transcription circuits to produce two corresponding functional RNAs. The functional RNAs then cyclically initiate the digestion of signal probes by duplex-specific nuclease to liberate Cy5 and Cy3 molecules. After magnetic separation, the liberated Cy5 and Cy3 molecules are measured by single-molecule counting. In this assay, a single lncRNA can activate ligation-transcription circuit to generate abundant functional RNAs, endowing this assay with high sensitivity. Integration of single-molecule counting ensures the high sensitivity. This method shows extremely high sensitivity with a limit of detection (LOD) of 0.043 aM for HOX gene antisense intergenic RNA (lncRNA HOTAIR) and 0.126 aM for mammalian metastasis-related lung adenocarcinoma transcript 1 (lncRNA MALAT1). Importantly, this method enables simultaneous measurement of multiple endogenous lncRNAs at the single-cell level, and it may discriminate the expressions of various lncRNA in lung tumor tissues of nonsmall cell lung cancer (NSCLC) patients and their corresponding healthy adjacent tissues, offering a promising platform for clinical diagnosis and biomedical research.

Long non-coding RNAs (lncRNAs); roles in tumorigenesis and potentials as biomarkers in cancer diagnosis

New research has indicated that long non-coding RNAs (lncRNAs) play critical roles in a broad range of biological processes, including the pathogenesis of many complex human diseases, including cancer. The detailed regulation mechanisms of many lncRNAs in cancer initiation and progression have yet to be discovered, even though a few of lncRNAs' functions in cancer have been characterized. In the present study, we summarize recent advances in the mechanisms and functions of lncRNAs in cancer. We focused on the roles of newly-identified lncRNAs as oncogenes and tumor suppressors, as well as the potential pathways these molecules could play. The paper also discusses their potential uses as biomarkers for the diagnosis and prognosis of cancer.

A Necroptosis-Related lncRNA Signature Predicts Prognosis and Indicates the Immune Microenvironment in Soft Tissue Sarcomas

Background: The necroptosis and long noncoding RNA (lncRNA) are critical in the occurrence and development of malignancy, while the association between the necroptosis-related lncRNAs (NRlncRNAs) and soft tissue sarcoma (STS) remains controversial. Therefore, the present study aims to construct a novel signature based on NRlncRNAs to predict the prognosis of STS patients and investigate its possible role.

Methods: The transcriptome data and clinical characteristics were extracted from The Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression database (GTEx). A novel NRlncRNA signature was established and verified by the COX regression analysis and least absolute shrinkage and selection operator (LASSO) regression analysis. Subsequently, the K-M survival analysis, ROC, univariate, multivariate Cox regression analysis, and nomogram were used to evaluate the predictive value of the signature. Also, a variety of bioinformatic analysis algorithms explored the differences between the potential mechanism, tumor immune status, and drug sensitivity in the two-risk group. Finally, the RT-qPCR was performed to evaluate the expression of signature NRlncRNAs.

Results: A novel signature consisting of seven NRlncRNAs was successfully established and verified with stable prediction performance and general applicability for STS. Next, the GSEA showed that the patients in the high-risk group were mainly enriched with tumor-related pathways, while the low-risk patients were significantly involved in immune-related pathways. In parallel, we found that the STS patients in the low-risk group had a better immune status than that in the high-risk group. Additionally, there were significant differences in the sensitivity to anti-tumor agents between the two groups. Finally, the RT-qPCR results indicated that these signature NRlncRNAs were abnormally expressed in STS.

Conclusion: To the best of our knowledge, it is the first study to construct an NRlncRNA signature for STS. More importantly, the novel signature displays stable value and translational potential for predicting prognosis, tumor immunogenicity, and therapeutic response in STS.

A Cost-Effective Nucleic Acid Detection System Using a Portable Microscopic Device

A fluorescence microscope is one of the most important tools for biomedical research and laboratory diagnosis. However, its high cost and bulky size hinder the application of laboratory microscopes in space-limited and low-resource applications. Here, in this work, we proposed a portable and cost-effective fluorescence microscope. Assembled from a set of 3D print components and a webcam, it consists of a three-degree-of-freedom sliding platform and a microscopic imaging system. The microscope is capable of bright-field and fluorescence imaging with micron-level resolution. The resolution and field of view of the microscope were evaluated. Compared with a laboratory-grade inverted fluorescence microscope, the portable microscope shows satisfactory performance, both in the bright-field and fluorescence mode. From the configurations of local resources, the microscope costs around USD 100 to assemble. To demonstrate the capability of the portable fluorescence microscope, we proposed a quantitative polymerase chain reaction experiment for meat product authenticating applications. The portable and low-cost microscope platform demonstrates the benefits in space-constrained environments and shows high potential in telemedicine, point-of-care testing, and more.

lncRNA SLC9A3-AS1 Promotes Oncogenesis of NSCLC via Sponging microRNA-760 and May Serve as a Prognosis Predictor of NSCLC Patients

Background

Non-small cell lung cancer (NSCLC) is a prevalent type of lung cancer worldwide. Long noncoding RNA (lncRNA) SLC9A3-AS1 is reported to play a carcinogenic role in nasopharyngeal carcinoma, but its full-scale role in NSCLC remains elusive.

Methods

SLC9A3-AS1 expression was detected in serum and tissue of NSLCC patients and NSCLC cell lines. The effects of SLC9A3-AS1 on NSCLC proliferation, migration and invasion were evaluated using CCK-8 and transwell assays. In addition, the potential downstream molecules of SLC9A3-AS1 were searched and explored by bioinformatics analysis, RT-qPCR, dual-luciferase reporter, and rescue experiments.

Results

SLC9A3-AS1 was upregulated in NSCLC tissues and cell lines. SLC9A3-AS1 possessed a favorable ability in diagnosing NSCLC. A high level of SLC9A3-AS1 was associated with poor prognosis in NSCLC patients. Functionally, SLC9A3-AS1 knockdown inhibited cell proliferation, migration, and invasion of NSCLC cells. Mechanistically, SLC9A3-AS1 acted as competing endogenous RNA for miR-760 to regulate NSCLC progression. In addition, rescue assay showed that downregulation of miR-760 could reverse the modulatory activity of SLC9A3-AS1 knockdown on NSCLC cells.

Conclusion

SLC9A3-AS1 was upregulated in NSCLC, and SLC9A3-AS1 knockdown hindered NSCLC progression through targeting miR-760, suggesting that it may prove to be a novel biomarker and therapeutic target for NSCLC.

Exosomes as a new frontier of cancer liquid biopsy

Liquid biopsy, characterized by minimally invasive detection through biofluids such as blood, saliva, and urine, has emerged as a revolutionary strategy for cancer diagnosis and prognosis prediction. Exosomes are a subset of extracellular vesicles (EVs) that shuttle molecular cargoes from donor cells to recipient cells and play a crucial role in mediating intercellular communication. Increasing studies suggest that exosomes have a great promise to serve as novel biomarkers in liquid biopsy, since large quantities of exosomes are enriched in body fluids and are involved in numerous physiological and pathological processes. However, the further clinical application of exosomes has been greatly restrained by the lack of high-quality separation and component analysis methods. This review aims to provide a comprehensive overview on the conventional and novel technologies for exosome isolation, characterization and content detection. Additionally, the roles of exosomes serving as potential biomarkers in liquid biopsy for the diagnosis, treatment monitoring, and prognosis prediction of cancer are summarized. Finally, the prospects and challenges of applying exosome-based liquid biopsy to precision medicine are evaluated.

Integrated microfluidic system for isolating exosome and analyzing protein marker PD-L1

Exosomes are lipid-bilayered nanovesicles secreted by cells to mediate intercellular communication. Various kinds of biomolecules involved in exosomes offer non-invasive approaches for detecting or monitoring disease and developing targeted therapeutics. Here, we present an integrated microfluidic exosome isolation and detection system (EXID system) to analyze the abundance of the exosomal PD-L1 protein marker, which is a transmembrane protein expressed by tumors to suppress immune activation of T cells. By incorporating exosome isolation and biomarker labelling and quantification within a single microfluidic chip, our system reduced the total analysis time below 2 h. Using the EXID system, 7 categories of cell lines including cancer cell lines and control samples were profiled, where significant differences in the fluorescence intensity were observed with the limit of detection (LOD) down to 10.76 per microliter. Such noticeable variations in PD-L1 abundance among cancer cell lines highlighted the need of personalized treatments. Furthermore, 16 clinical samples from 7 post-treated cancer patients, 3 prior-treatment patients and 6 healthy controls, are tested, among which differences in sensitivity toward immune response were subsistent. Because the abundance of PD-L1 reflects the sensibility for immune response, our results provide useful guides to design immunotherapy strategies for different types of tumors.

Multiplexed analysis of small extracellular vesicle-derived mRNAs by droplet digital PCR and machine learning improves breast cancer diagnosis

Breast cancer has become the leading cause of global cancer incidence and a serious threat to women's health. Accurate diagnosis and early treatment are of great importance to prognosis. Although clinically used diagnostic approaches can be used for cancer screening, accurate diagnosis of breast cancer is still a critical unmet need. Here, we report a 4-plex droplet digital PCR technology for simultaneous detection of four small extracellular vesicle (sEV)-derived mRNAs (PGR, ESR1, ERBB2 and GAPDH) in combination with machine learning (ML) algorithms to improve breast cancer diagnosis. We evaluate the diagnsotic results with and without the assistance of the ML models. The results indicate that ML-assisted analysis exhibits higher diagnostic performance even using a single marker for breast cancer diagnosis, and demonstrate improved diagnostic performance under the best combination of biomarkers and suitable ML diagnostic model. Therefore, multiple sEV-derived mRNAs analysis coupled with ML not only provides the best combination of markers for breast cancer diagnosis, but also significantly improves the diagnostic efficiency of breast cancer.

PCAT6 May Be a Whistler and Checkpoint Target for Precision Therapy in Human Cancers

Simple Summary

Prostate cancer-associated transcript 6 (PCAT6), as a newly discovered carcinogenic long non-coding RNA (lncRNA), is abnormally expressed in multiple diseases. With the accumulation of studies on PCAT6, we have a deeper understanding of its biological functions and mechanisms. Therefore, in this review, the various molecular mechanisms by which PCAT6 promotes multiple tumorigenesis and progression are summarized and discussed. Furthermore, its potential diagnostic, prognostic, and immunotherapeutic values are also clarified.

Abstract

LncRNAs are involved in the occurrence and progressions of multiple cancers. Emerging evidence has shown that PCAT6, a newly discovered carcinogenic lncRNA, is abnormally elevated in various human malignant tumors. Until now, PCAT6 has been found to sponge various miRNAs to activate the signaling pathways, which further affects tumor cell proliferation, migration, invasion, cycle, apoptosis, radioresistance, and chemoresistance. Moreover, PCAT6 has been shown to exert biological functions beyond ceRNAs. In this review, we summarize the biological characteristics of PCAT6 in a variety of human malignancies and describe the biological mechanisms by which PCAT6 can facilitate tumor progression. Finally, we discuss its diagnostic and prognostic values and clinical applications in various human malignancies.

A plasmonic gold nanofilm-based microfluidic chip for rapid and inexpensive droplet-based photonic PCR

Polymerase chain reaction (PCR) is a powerful tool for nucleic acid amplification and quantification. However, long thermocycling time is a major limitation of the commercial PCR devices in the point-of-care (POC). Herein, we have developed a rapid droplet-based photonic PCR (dpPCR) system, including a gold (Au) nanofilm-based microfluidic chip and a plasmonic photothermal cycler. The chip is fabricated by adding mineral oil to uncured polydimethylsiloxane (PDMS) to suppress droplet evaporation in PDMS microfluidic chips during PCR thermocycling. A PDMS to gold bonding technique using a double-sided adhesive tape is applied to enhance the bonding strength between the oil-added PDMS and the gold nanofilm. Moreover, the gold nanofilm excited by two light-emitting diodes (LEDs) from the top and bottom sides of the chip provides fast heating of the PCR sample to 230 °C within 100 s. Such a design enables 30 thermal cycles from 60 to 95 °C within 13 min with the average heating and cooling rates of 7.37 ± 0.27 °C/s and 1.91 ± 0.03 °C/s, respectively. The experimental results demonstrate successful PCR amplification of the alcohol oxidase (AOX) gene using the rapid plasmonic photothermal cycler and exhibit the great performance of the microfluidic chip for droplet-based PCR.

Advanced Nanotechnologies for Extracellular Vesicle-Based Liquid Biopsy

Extracellular vesicles (EVs) are emerging as a new source of biomarkers in liquid biopsy because of their wide presence in most body fluids and their ability to load cargoes from disease-related cells. Owing to the crucial role of EVs in disease diagnosis and treatment, significant efforts have been made to isolate, detect, and analyze EVs with high efficiency. A recent overview of advanced EV detection nanotechnologies is discussed here. First, several key challenges in EV-based liquid biopsies are introduced. Then, the related pivotal advances in nanotechnologies for EV isolation based on physical features, chemical affinity, and the combination of nanostructures and chemical affinity are summarized. Next, a summary of high-sensitivity sensors for EV detection and advanced approaches for single EV detection are provided. Later, EV analysis is introduced in practical clinical scenarios, and the application of machine learning in this field is highlighted. Finally, future opportunities for the development of next-generation nanotechnologies for EV detection are presented.

A rapid nucleic acid concentration measurement system with large field of view for a droplet digital PCR microfluidic chip

Droplet digital polymerase chain reaction (ddPCR) is an effective technique, with unparalleled sensitivity, for the absolute quantification of target nucleic acids. However, current commercial ddPCR devices for detecting the gene chip are time consuming due to complex image stitching. To address this issue, we propose a universal concentration determination system and realize one-time gene chip imaging with high resolution. All the functional units are controlled by self-developed software using the PyQt5 module in Python. Without stitching technology, images of the ddPCR chip (28 mm × 18 mm) containing 20 000 independent 0.81 nL micro chambers can be obtained in less than 15 seconds, which saves about 165 seconds. A white laser light source (2 mW cm^-2) was employed as a substitute for the mercury lamp. Its wavelength matches well with typical fluorescent dyes (e.g., HEX, ROX and Cy5), and thus it can strengthen the fluorescence intensity for weak signals. The results also demonstrated that the correlation coefficient for the measured concentration and theoretical value was above 99%, by testing the ddPCR products with COVID-19 virus. Such a system can greatly reduce the time required for image acquisition and DNA concentration determination, and thus is able to speed up the lab-to-application process for ddPCR technology.

Analysis and Construction of a Competitive Endogenous RNA Regulatory Network of Baicalin-Induced Apoptosis in Human Osteosarcoma Cells

BACKGROUND

Baicalin is an extract from the traditional Chinese herb Scutellaria baicalensis and has the potential to treat osteosarcoma (OS). However, the transcriptome-level mechanism of baicalin-mediated antitumor effects in OS has not yet been investigated. The aim of this study was to analyze the competitive endogenous RNA (ceRNA) regulatory network involved in baicalin-induced apoptosis of OS cells.

METHODS

In this study, CCK-8 and flow cytometry assays were used to detect the antitumor effects of baicalin on human OS MG63 cells. Furthermore, transcriptome sequencing was employed to establish the long noncoding RNA (lncRNA), microRNA (miRNA), and mRNA profiles.

RESULTS

Baicalin inhibited MG63 cell proliferation and induced apoptosis. Totals of 58 lncRNAs, 31 miRNAs, and 2136 mRNAs in the baicalin-treated MG63 cells were identified as differentially expressed RNAs compared to those in control cells. Of these, 2 lncRNAs, 3 miRNAs, and 18 mRNAs were included in the ceRNA regulatory network. The differentially expressed RNAs were confirmed by quantitative real-time PCR (qRT-PCR).

CONCLUSIONS

By identifying the ceRNA network, our results provide new information about the possible molecular basis of baicalin, which has potential applications in OS treatment.

Long noncoding RNA SLC9A3‑AS1 increases E2F6 expression by sponging microRNA‑486‑5p and thus facilitates the oncogenesis of nasopharyngeal carcinoma

Long noncoding RNA SLC9A3 antisense RNA 1 (SLC9A3-AS1) plays a central role in lung cancer; yet, its functions in nasopharyngeal carcinoma (NPC) have not been elucidated. The present study revealed the roles of SLC9A3-AS1 in NPC and dissected the mechanisms downstream of SLC9A3-AS1. SLC9A3-AS1 levels in NPC were assessed by applying RT-qPCR. The modulatory role of SLC9A3-AS1 interference on NPC cells was examined using numerous functional experiments. High expression of SLC9A3-AS1 was observed in NPC samples. Patients with NPC with a high level of SLC9A3-AS1 experienced a shorter overall survival than those with a low SLC9A3-AS1 level. Loss of SLC9A3-AS1 reduced NPC cell proliferation, colony formation, migration, and invasion but induced cell apoptosis in vitro. Animal experiments further revealed that the depletion of SLC9A3-AS1 hindered NPC tumour growth in vivo. As a competitive endogenous RNA, SLC9A3-AS1 sponged microRNA-486-5p (miR-486-5p), consequently upregulating E2F transcription factor 6 (E2F6). Finally, the effects of SLC9A3-AS1 silencing on NPC cells were reversed by inhibiting miR-486-5p or overexpressing E2F6. In summary, SLC9A3-AS1 exerted carcinogenic effects on NPC cells by adjusting the miR-486-5p/E2F6 axis. Accordingly, the newly identified SLC9A3-AS1/miR-486-5p/E2F6 pathway may offer attractive therapeutic targets for future development.

Using single-vesicle technologies to unravel the heterogeneity of extracellular vesicles

Extracellular vesicles (EVs) are heterogeneous lipid containers with a complex molecular cargo comprising several populations with unique roles in biological processes. These vesicles are closely associated with specific physiological features, which makes them invaluable in the detection and monitoring of various diseases. EVs play a key role in pathophysiological processes by actively triggering genetic or metabolic responses. However, the heterogeneity of their structure and composition hinders their application in medical diagnosis and therapies. This diversity makes it difficult to establish their exact physiological roles, and the functions and composition of different EV (sub)populations. Ensemble averaging approaches currently employed for EV characterization, such as western blotting or 'omics' technologies, tend to obscure rather than reveal these heterogeneities. Recent developments in single-vesicle analysis have made it possible to overcome these limitations and have facilitated the development of practical clinical applications. In this review, we discuss the benefits and challenges inherent to the current methods for the analysis of single vesicles and review the contribution of these approaches to the understanding of EV biology. We describe the contributions of these recent technological advances to the characterization and phenotyping of EVs, examination of the role of EVs in cell-to-cell communication pathways and the identification and validation of EVs as disease biomarkers. Finally, we discuss the potential of innovative single-vesicle imaging and analysis methodologies using microfluidic devices, which promise to deliver rapid and effective basic and practical applications for minimally invasive prognosis systems.

Simultaneous Enzyme-Free Detection of Multiple Long Noncoding RNAs in Cancer Cells at Single-Molecule/Particle Level

Aberrant change in long noncoding RNA (lncRNA) is associated with various diseases and cancers. So far, simultaneous detection of lncRNAs has remained a great challenge due to their large size and extensive secondary structure. Herein, we develop an enzyme-free single-molecule/particle detection method for simultaneous detection of multiple lncRNAs in cancer cells based on target-catalyzed strand displacement. We designed the magnetic bead-capture probe-multiple Cy5/Cy3-modified reporter unit complexes to isolate and identify lncRNA MALAT1 and lncRNA HOTAIR. The target-catalyzed strand displacement reactions lead to the release of Cy5 and Cy3 fluorescent molecules from the complexes, which can be subsequently quantified by single-molecule/particle detection. The dual-targetability, good selectivity and high sensitivity of this method enables simultaneous detection of multiple lncRNAs in even single cancer cell. Importantly, this method can discriminate cancer cells from normal cells and has significant advantages in the simple sequence design and in being free of enzymes, holding great potential in living cell imaging and early clinical diagnosis.

Review: Multiplexed profiling of biomarkers in extracellular vesicles for cancer diagnosis and therapy monitoring

Extracellular vesicles (EVs) are nanoscale vesicles secreted by normal and pathological cells. The types and levels of surface proteins and internal nucleic acids in EVs are closely related to their original cells, tumor occurrence, and development. Thus, the sensitive and accurate detection of EV biomarkers is a reliable approach for noninvasive disease diagnosis and treatment response monitoring. However, the purification and molecular profiling of these EVs are technically challenging. Much effort has been dedicated to developing new methods for the detection of multiple EV biomarkers. In this review, we summarize the recent progress in EV protein and nucleic acid biomarker analysis. Additionally, we systematically discuss the advantages of multiplexed EV biomarker detection for accurate cancer diagnosis, therapy monitoring, and cancer screening. This article aims to present an overview of all kinds of analytical technologies for assessing EVs and their applications in clinical settings.

Emerging methods in biomarker identification for extracellular vesicle-based liquid biopsy

Extracellular vesicles (EVs) are released by many cell types and distributed within various biofluids. EVs have a lipid membrane-confined structure that allows for carrying unique molecular information originating from their parent cells. The species and quantity of EV cargo molecules, including nucleic acids, proteins, lipids, and metabolites, may vary largely owing to their parent cell types and the pathophysiologic status. Such heterogeneity in EV populations provides immense challenges to researchers, yet allows for the possibility to prognosticate the pathogenesis of a particular tissue from unique molecular signatures of dispersing EVs within biofluids. However, the inherent nature of EV's small size requires advanced methods for EV purification and evaluation from the complex biofluid. Recently, the interdisciplinary significance of EV research has attracted growing interests, and the EV analytical platforms for their diagnostic prospect have markedly progressed. This review summarizes the recent advances in these EV detection techniques and methods with the intention of translating an EV-based liquid biopsy into clinical practice. This article aims to present an overview of current EV assessment techniques, with a focus on their progress and limitations, as well as an outlook on the clinical translation of an EV-based liquid biopsy that may augment current paradigms for the diagnosis, prognosis, and monitoring the response to therapy in a variety of disease settings.

LncRNA PCNAP1 Promotes Hepatoma Cell Proliferation through Targeting miR-340-5p and is Associated with Patient Survival

Hepatocellular carcinoma (HCC) is one of the most common malignancies and causes poor outcome. Dysregulation of long noncoding RNA (lncRNA) is involved in HCC. Upregulation of the lncRNA PCNAP1 has been reported to promote HBV-infectious HCC growth, but its clinical significance and underlying mechanisms in HCC development remain unclear. Here, we report that PCNAP1 expression is increased in both HBV-infectious and noninfectious HCC tissues compared with matched normal tissues, and its upregulation correlates with poor survival rates of HCC patients. Furthermore, we found that PCNAP1 promotes HCC cell proliferation through acting as a competitive endogenous RNA (ceRNA) to sponge miR-340-5p, which has been reported to directly inhibit ATF7 expression in HCC cells. Moreover, the PCNAP1/miR-340-5p/ATF7 signaling associates with the poor survival rates of HCC patients. Collectively, our findings suggest that the PCNAP1/miR-340-5p/ATF7 signaling may be a potential biomarker for the prognosis of HCC patients and a potential therapeutic target for HCC.

Promising role of long non-coding RNA PCAT6 in malignancies

Long non-coding RNAs (lncRNAs), a newly identified class of non-coding RNA (ncRNA), are defined as RNA molecules at least 200 nucleotides in length that are not translated into proteins. LncRNAs contribute to a wide range of biological processes and are master regulators of disease occurrence, development, and response to therapy in human malignancies. The lncRNA prostate cancer‑associated transcript 6 (PCAT6) is upregulated in various human malignancies, including lung cancer, hepatocellular carcinoma, cervical cancer, osteosarcoma, glioblastoma, colorectal cancer, breast cancer, gastric cancer, gastrointestinal stromal tumors, and pancreatic ductal adenocarcinoma. High expression of PCAT6 is closely correlated with aggressive clinicopathological characteristics and poor prognosis in cancer patients, suggesting it is an oncogenic lncRNA. PCAT6 overexpression also facilitates cell proliferation, invasion, and migration while attenuating apoptosis, indicating that it might serve as a new prognostic biomarker and therapeutic target for malignancies. Here, we discuss the molecular mechanisms, regulatory functions, and potential clinical applications of PCAT6 in cancer.