Ultrasensitive ImmunoMag-CRISPR Lateral Flow Assay for Point-of-Care Testing of Urinary Biomarkers

Unique motif Sequences for early diagnosis of preeclampsia

Preeclampsia (PE) is a disease that significantly impacts both maternal and infant health with its prevalence varying across different ethnicities. Current diagnostic methods for PE typically identify the condition after 20 weeks of gestation, often when the disease has already manifested and reached an advanced stage. The situation underscores the urgent need for early biomarkers capable of effective screening and diagnosis. Our review addresses this challenge by utilizing bioinformatics approaches as an alternative method prior to preclinical and clinical studies. Specifically, we focus on FRAGmentomics-based Methylation Analysis (FRAGMA), targeting the CGCGCGG sequence motif for methylation studies in cell-free DNA (cfDNA). Since cfDNA is largely derived from the placenta, the FRAGMA approach is particularly promising, given that the primary pathophysiology of PE originates in the placenta, and methylation patterns are unique to specific tissues. In the previous research, we identified 66 genes containing this sequence motif that are implicated in the pathophysiology of PE, and only six genes - FN1, ITGA2, ITGA5, ITGB1, ITGB3, and VWF - show potential as early detection biomarkers for PE. These genes still require further investigation to confirm their utility as biomarkers for PE in the future studies.

The nucleic acid detection using CRISPR/Cas biosensing system with micro-nano modality for point-of-care applications

Nucleic acid detection is considered the golden standard for diagnosing infectious diseases caused by various pathogens, including viruses, bacteria, and parasites. PCR and other amplification-based technologies are highly sensitive and specific, allowing for accurate detection and identification of low-level causative pathogens by targeting and amplifying their unique genetic segment (DNA or RNA). However, it is important to recognize that machinery-dependent diagnostic methods may only sometimes be available or practical in resource-limited settings, where direct implementation can be challenging. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)-based diagnostics offer a promising alternative for nucleic acid detection. These methods provide gene sequence-specific targeting, multiplexing capability, rapid result disclosure, and ease of operation, making them suitable for point-of-care (POC) applications. CRISPR-Cas-based nucleic acid detection leverages the intrinsic gene-editing capabilities of CRISPR systems to detect specific DNA or RNA sequences with high precision, ensuring high specificity in identifying pathogens. When integrated with micro- and nano-technologies, CRISPR-based diagnostics gain additional benefits, including automated microfluidic processes, enhanced multiplexed detection, improved sensitivity through nanoparticle integration, and combined detection strategies. In this review, we analyze the motivations for tailoring the CRISPR-Cas system with microfluidic formats or nanoscale materials for nucleic acid biosensing and detection. We discuss and categorize current achievements in such systems, highlighting their differences, commonalities, and opportunities for addressing challenges, particularly for POC diagnostics. Micro- and nano-technologies can significantly enhance the practical utility of the CRISPR-Cas system, enabling more comprehensive diagnostic and surveillance capabilities. By integrating these technologies, CRISPR-based diagnostics can achieve higher levels of automation, sensitivity, and multiplexing, making them invaluable tools in the global effort to diagnose and control infectious diseases.

Origami Paper-Based Immunoassay Device with CRISPR/Cas12a Signal Amplification

In clinical diagnosis, the determination of target proteins at low concentration levels is generally performed by immunoassays, such as the enzyme-linked immunosorbent assay (ELISA), which is a time-consuming process. To date, paper-based ELISA platforms enabling faster and less expensive analysis have been developed, but their important issue for clinical applications is the limited sensitivity compared to conventional ELISA. To address this challenge, this paper introduces a simple, rapid, and highly sensitive detection method for non-nucleic acid targets achieved by integrating the CRISPR/Cas12a system into paper-based ELISA. An origami-type paper-based device enabling simple assay operation has been designed, and the detection of targets on the paper substrates is based on observing the fluorescence signal induced by the CRISPR/Cas12a enzyme cleaving a probe single-stranded DNA (ssDNA) labeled with fluorophore and quencher (FQ reporter). To enhance sensitivity, antibodies labeled with a network of multiple DNA activating the CRISPR/Cas12a enzyme have been utilized as detection antibodies. As a result, the developed device successfully boosted the detection sensitivity for both human IgG and the hepatitis B virus surface antigen (HBsAg). In particular, the limit of detection (LOD) for HBsAg was estimated to be 12 pg/mL, representing over 10-fold higher sensitivity compared with commercially available HBsAg ELISA kits (LOD: 200 pg/mL). In addition, the fluorescence response toward porcine whole blood samples containing different HBsAg concentrations was also confirmed by capturing images with a smartphone, followed by quantitative data analysis. These results demonstrate the potential applicability of the proposed platform for clinical tests at the point of care.

Biomarkers in Kidney Transplantation: A Rapidly Evolving Landscape

The last decade has seen an explosion in clinical research focusing on the use of noninvasive biomarkers in kidney transplantation. Much of the published literature focuses on donor-derived cell-free DNA (dd-cfDNA). Although initially studied as a noninvasive means of identifying acute rejection, it is now clear that dd-cfDNA is more appropriately described as a marker of severe injury and irrespective of the etiology, elevated dd-cfDNA ≥0.5% portends worse graft outcomes. Blood gene expression profiling is also commercially available and has mostly been studied in the context of early identification of subclinical rejection, although additional data is needed to validate these findings. Torque teno virus, a ubiquitous DNA virus, has emerged as a biomarker of immunosuppression exposure as peripheral blood Torque teno virus copy numbers might mirror the intensity of host immunosuppression. Urinary chemokine tests including C-X-C motif chemokine ligand 9 and C-X-C motif chemokine ligand 10 have recently been assessed in large clinical trials and hold promising potential for early diagnosis of both subclinical and acute rejection, as well as, for long-term prognosis. Urinary cellular messenger RNA and exosome vesicular RNA based studies require additional validation. Although current data does not lend itself to conclusion, future studies on multimodality testing may reveal the utility of serial surveillance for individualization of immunosuppression and identify windows of opportunity to intervene early and before the irreversible allograft injury sets in.

Rapid and visual detection of hepatitis B virus using the ERA/Cas12f1_ge4.1-based lateral flow assay system

Hepatitis B virus (HBV) is a major pathogen posing significant challenges to global public health, making early diagnosis critical for preventing severe liver diseases. We previously developed a fluorescent biosensor named PAM-dependent dsDNA Target-activated Cas12f1 Trans Reporter (PDTCTR). However, its reliance on specialized fluorescence equipment and lack of visual readout limited its application in resource-limited settings. To address these limitations, we developed a lateral flow assay (LFA) that integrates enzymatic recombinase amplification (ERA) with the Cas12f1_ge4.1 system. This approach enables the specific amplification of the HBV target gene through ERA and leverages the precise cleavage activity of Cas12f1_ge4.1 for enhanced signal amplification. The entire detection process is completed within 50 minutes, with results readily interpretable through visual inspection. The assay achieves a minimum detection limit of 100 copies per μL and demonstrates high specificity, showing no cross-reactivity with related viruses. In a validation study involving 71 clinical samples, the system achieved a sensitivity of 94.23%, specificity of 100%, and a kappa value of 0.90 compared to quantitative PCR (qPCR), indicating high reliability. This method thus shows promise as an effective tool for early HBV diagnosis, particularly suited for rapid, on-site detection in resource-constrained environments, and holds broad potential for diverse applications.

Leveraging Synthetic Antibody-DNA Conjugates to Expand the CRISPR-Cas12a Biosensing Toolbox

We report here the use of antibody-DNA conjugates (Ab-DNA) to activate the collateral cleavage activity of the CRISPR-Cas12a enzyme. Our findings demonstrate that Ab-DNA conjugates effectively trigger the collateral cleavage activity of CRISPR-Cas12a, enabling the transduction of antibody-mediated recognition events into fluorescence outputs. We developed two different immunoassays using an Ab-DNA as activator of Cas12a: the CRISPR-based immunosensing assay (CIA) for detecting SARS-CoV-2 spike S protein, which shows superior sensitivity compared with the traditional enzyme-linked immunosorbent assay (ELISA), and the CRISPR-based immunomagnetic assay (CIMA). Notably, CIMA successfully detected the SARS-CoV-2 spike S protein in undiluted saliva with a limit of detection (LOD) of 890 pM in a 2 h assay. Our results underscore the benefits of integrating Cas12a-based signal amplification with antibody detection methods. The potential of Ab-DNA conjugates, combined with CRISPR technology, offers a promising alternative to conventional enzymes used in immunoassays and could facilitate the development of versatile CRISPR analytical platforms for the detection of non-nucleic acid targets.

Highly Sensitive One-Pot Isothermal Assay Combining Rolling Circle Amplification and CRISPR/Cas12a for Aflatoxin B1 Detection

Occurrences of mycotoxins in cereals are widespread throughout the world. However, the lack of efficient and ultrasensitive tests has largely impeded the identification of these substances in actual samples. Herein, a novel one-pot isothermal assay that integrates rolling-circle amplification (RCA) and CRISPR/Cas12a to detect aflatoxin B1 (AFB1) is reported. Upon addition of AFB1 to the magnetic bead functionalized with a duplex of the AFB1 aptamer and its complementary DNA (cDNA), the specific recognition of AFB1 by the aptamer causes the release of cDNA to activate the RCA reaction. Subsequently, the RCA amplicon initiates both trans-cleavage and cis-cleavage activities of the endonuclease Cas12a. The synergistic coupling of RCA and CRISPR/Cas12a enables exponential amplification of cDNA, which further promotes CRISPR/Cas12a to nonspecifically cleave the single-stranded DNA reporters with enhanced detection signals. Remarkably, the CRISPR/Cas12a-assisted one-pot isothermal assay can not only achieve ultrasensitive quantitative detection through fluorescence detection, but also achieve visual detection through a lateral flow strip, which improves accessibility to mycotoxin detection in resource-limited regions. The limit of detection was 0.016 and 0.408 ng/mL, respectively. The proposed assay successfully applies in real samples with satisfactory recoveries from 90 to 114%. This study presents a powerful and versatile method for reliable and ultrasensitive detection of mycotoxins in various applications.

CRISPR/Cas and Argonaute-powered lateral flow assay for pathogens detection

Pathogens contamination is a pressing global public issue that has garnered significant attention worldwide, especially in light of recent outbreaks of foodborne illnesses. Programmable nucleases like CRISPR/Cas and Argonaute hold promise as tools for nucleic acid testing owning to programmability and the precise target sequence specificity, which has been utilized for the development pathogens detection. At present, fluorescence, as the main signal output method, provides a simple response mode for sensing analysis. However, the dependence of fluorescence output on large instruments and correct analysis of output data limited its use in remote areas. Lateral flow strips (LFS), emerging as a novel flexible substrate, offer a plethora of advantages, encompassing easy-to-use, rapidity, visualization, low-cost, portability, etc. The integration of CRISPR/Cas and Argonaute with LFS, lateral flow assay (LFA), rendered a new and on-site mode for pathogens detection. In the review, we introduced two programmable nucleases CRISPR/Cas and Argonaute, followed by the structure, principle and advantages of LFA. Then diversified engineering detection pattens for viruses, bacteria, parasites, and fungi based on CRISPR/Cas and Argonaute were introduced and summarized. Finally, the challenge and perspectives involved in on-site diagnostic assays were discussed.

Lateral flow assays: Progress and evolution of recent trends in point-of-care applications

Paper based point-of-care (PoC) detection platforms applying lateral flow assays (LFAs) have gained paramount approval in the diagnostic domain as well as in environmental applications owing to their ease of utility, low cost, and rapid signal readout. It has centralized the aspect of self-evaluation exhibiting promising potential in the last global pandemic era of Covid-19 implementing rapid management of public health in remote areas. In this perspective, the present review is focused towards landscaping the current framework of LFAs along with integration of components and characteristics for improving the assay by pushing the detection limits. The review highlights the synergistic aspects of assay designing, sample enrichment strategies, novel nanomaterials-based signal transducers, and high-end analytical techniques that contribute significantly towards sensitivity and specificity enhancement. Various recent studies are discussed supporting the innovations in LFA systems that focus upon the accuracy and reliability of rapid PoC testing. The review also provides a comprehensive overview of all the possible difficulties in commercialization of LFAs subjecting its applicability to pathogen surveillance, water and food testing, disease diagnostics, as well as to agriculture and environmental issues.

Biomarkers in Kidney Transplantation

Currently in the United States, there are more than 250,000 patients with a functioning kidney allograft and over 100,000 waitlisted patients awaiting kidney transplant, with a burgeoning number added to the kidney transplant wait list every year. Although early post-transplant care is delivered at the transplant center, the increasing number of kidney transplant recipients requires general nephrologists to actively participate in the long-term care of these patients. Serum creatinine and proteinuria are imperfect traditional biomarkers of allograft dysfunction and lag behind subclinical allograft injury. This manuscript reviews the various clinically available biomarkers in the field of kidney transplantation for a general nephrologist with a focus on the utility of donor-derived cell-free DNA, as a marker of early allograft injury. Blood gene expression profiling, initially studied in the context of early identification of subclinical rejection, awaits validation in larger multicentric trials. Urinary cellular messenger ribonucleic acid and chemokine CXCL10 hold promising potential for early diagnosis of both subclinical and acute rejection. Torque tenovirus, a ubiquitous DNA virus is emerging as a biomarker of immunosuppression exposure as peripheral blood torque tenovirus copy numbers might mirror the intensity of host immunosuppression. Although high-quality evidence is still being generated, evidence and recommendations are provided to aid the general nephrologist in implementation of novel biomarkers in their clinical practice.

Development of Aptamer-Functionalized Gold Nanoparticles as Probes in Point-of-Care Diagnostic Device for Rapid Detection of Multidrug-Resistant Bacteria in Bombyx mori L.

The sericulture industry suffers severe crop losses due to various silkworm diseases, necessitating the development of further technologies for rapid pathogen detection. Here, we report an all-in-one portable biosensor that combines conjugated gold nanoparticles (Au NPs) with an aptamer-based lateral flow assay (LFA) platform for the real-time analysis of Mammaliicoccus sp. and Pseudomonas sp. Our platform enables sample-to-answer naked eye detection within 5 min without any cross-reactivity with other representatives of the silkworm pathogenic bacterial group. This assay was based on the sandwich-type format using a bacteria-specific primary aptamer (Apt1) conjugated with 23 nm ± 1.27 nm Au NPs as a signal probe and another bacteria-specific secondary aptamer (Apt2)-coated nitrocellulose membrane as a capture probe. The hybridization between the signal probe and the capture probe in the presence of bacteria develops a red band in the test line, whose intensity is directly proportional to the bacterial concentration. Under the optimal experimental conditions, the visual limit of detection of the strip for Mammaliicoccus sp. and Pseudomonas sp. was 1.5 × 104 CFU/mL and 1.5 × 103 CFU/mL, respectively. Additionally, the performance of the LFA device was validated by using a colorimetric assay, and the results from the colorimetric assay are consistent with those obtained from the LFA. Our findings indicate that the developed point-of-care diagnostic device has significant potential for providing a cost-effective, scalable alternative for the rapid detection of silkworm pathogens.

CRISPR-Based Biosensors for Medical Diagnosis: Readout from Detector-Dependence Detection Toward Naked Eye Detection

The detection of biomarkers (such as DNA, RNA, and protein) plays a vital role in medical diagnosis. The CRISPR-based biosensors utilize the CRISPR/Cas system for biometric recognition of targets and use biosensor strategy to read out biological signals without the employment of professional operations. Consequently, the CRISPR-based biosensors demonstrate great potential for the detection of biomarkers with high sensitivity and specificity. However, the signal readout still relies on specialized detectors, limiting its application in on-site detection for medical diagnosis. In this review, we summarize the principles and advances of the CRISPR-based biosensors with a focus on medical diagnosis. Then, we review the advantages and progress of CRISPR-based naked eye biosensors, which can realize diagnosis without additional detectors for signal readout. Finally, we discuss the challenges and further prospects for the development of CRISPR-based biosensors.

"Three-in-One" Plasmonic Au@PtOs Nanocluster Driven Lateral Flow Assay for Multimodal Cancer Exosome Biosensing

Exploiting the multiple properties of nanozymes for the multimode lateral flow assay (LFA) is urgently required to improve the accuracy and versatility. Herein, we developed a novel plasmonic Au nanostar@PtOs nanocluster (Au@PtOs) as a multimode signal tag for LFA detection. Based on the PtOs bimetallic nanocluster doping strategy, Au@PtOs can indicate both excellent SERS enhancement and nanozyme catalytic activity. Meanwhile, Au@PtOs displays a better photothermal effect than that of Au nanostars. Therefore, catalytic colorimetric/SERS/temperature three-mode signals can be read out based on the Au@PtOs nanocomposite. The Au@PtOs was combined with LFA and applied for breast cancer exosome detection. The detection limit for the colorimetric/SERS/temperature mode was 2.6 × 103/4.1 × 101/4.6 × 102 exosomes/μL, respectively, which was much superior to the common Au nanoparticles LFA (∼105 exosomes/μL). Moreover, based on the fingerprint molecular recognition ability of the SERS mode, exosome phenotypes derived from different breast cancer cell lines can be discriminated easily. Based on the convenient visual colorimetric mode and sensitive SERS/temperature quantitative modes, Au@PtOs driven LFA can satisfy the requirements of accurate and flexible multimodal sensing in different application scenarios.

An autophagy-associated diagnostic signature based on peripheral blood for antibody-mediated rejection in renal transplantation

BACKGROUND

Antibody-mediated rejection (ABMR) emerged as a major cause of graft loss in renal transplantation. Needle biopsy is the gold standard for diagnosis of ABMR in renal allografts. Thus, noninvasive diagnosis methods of ABMR with high accuracy are urgently needed to prevent unnecessary biopsies.

METHODS

We collected peripheral blood transcriptome data from two independent renal transplantation cohorts with patients with ABMR, stable well-functioning transplants (STA), and T-cell mediated rejection (TCMR). Differentially expressed genes (DEGs) were identified by comparing the ABMR group with the STA group. In addition, functional enrichment analysis and gene set enrichment analysis were performed to seek new key underlying mechanisms in ABMR. Subsequently, we utilized a Boruta algorithm and least absolute shrinkage and selection operator logistic algorithm to establish a diagnostic model which was then evaluated and validated in an independent cohort.

RESULTS

According to functional enrichment analysis, autophagy was found to be the primary upregulated biological process in ABMR. Based on algorithms, three autophagy-associated genes, ubiquitin specific peptidase 33 (USP33), Ras homolog mTORC1 binding (RHEB), and ABL proto-oncogene 2 (ABL2), were selected to establish the diagnostic model in the training cohort. This autophagy-related gene model possessed good diagnostic value in distinguishing ABMR from STA blood samples in the training cohort (AUC = 0.907) and in the validation cohort (AUC = 0.972). In addition, this model also showed good discernibility in distinguishing ABMR from TCMR in the training and validation cohorts (AUCs = 0.908 and 0.833).

CONCLUSION

We identified and validated an autophagy-associated diagnostic model with high accuracy for renal transplant patients with ABMR. Our study provided a new potential test for the non-invasive diagnosis of ABMR in clinical practice and highlighted the importance of autophagy in ABMR.