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The field of lipidomics has been significantly advanced by mass spectrometric analysis. The distinction and quantitation of the unsaturated lipid isomers, however, remain a long-standing challenge. In this study, we have developed an analytical tool for both identification and quantitation of lipid C=C location isomers from complex mixtures using online Paternò–Büchi reaction coupled with tandem mass spectrometry (MS/MS). The potential of this method has been demonstrated with an implementation into shotgun lipid analysis of animal tissues. Among 96 of the unsaturated fatty acids and glycerophospholipids identified from rat brain tissue, 50% of them were found as mixtures of C=C location isomers; for the first time, to our knowledge, the quantitative information of lipid C=C isomers from a broad range of classes was obtained. This method also enabled facile cross-tissue examinations, which revealed significant changes in C=C location isomer compositions of a series of fatty acids and glycerophospholipid (GP) species between the normal and cancerous tissues.

Plasma SARS-CoV-2 RNA may represent a viable diagnostic alternative to respiratory RNA levels, which rapidly decline after infection. Quantitative PCR with reverse transcription (RT–qPCR) reference assays exhibit poor performance with plasma, probably reflecting the dilution and degradation of viral RNA released into the circulation, but these issues could be addressed by analysing viral RNA packaged into extracellular vesicles. Here we describe an assay approach in which extracellular vesicles directly captured from plasma are fused with reagent-loaded liposomes to sensitively amplify and detect a SARS-CoV-2 gene target. This approach accurately identified patients with COVID-19, including challenging cases missed by RT–qPCR. SARS-CoV-2-positive extracellular vesicles were detected at day 1 post-infection, and plateaued from day 6 to the day 28 endpoint in a non-human primate model, while signal durations for 20–60 days were observed in young children. This nanotechnology approach uses a non-infectious sample and extends virus detection windows, offering a tool to support COVID-19 diagnosis in patients without SARS-CoV-2 RNA detectable in the respiratory tract. Measuring the levels of circulating SARS-CoV-2 RNA in plasma might represent a more accurate way to detect lower respiratory tract and extrapulmonary infections, which classical COVID-19 detection assays based on nasopharyngeal swabs might miss. Here, the authors accurately detect SARS-CoV-2 RNA in plasma-circulating extracellular vesicles using a CRISPR–Cas-based strategy that shows promising characteristics for potential clinical application.

Neurological manifestations are a significant complication of coronavirus disease (COVID-19), but underlying mechanisms aren’t well understood. The development of animal models that recapitulate the neuropathological findings of autopsied brain tissue from patients who died from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection are critical for elucidating the neuropathogenesis of infection and disease. Here, we show neuroinflammation, microhemorrhages, brain hypoxia, and neuropathology that is consistent with hypoxic-ischemic injury in SARS-CoV-2 infected non-human primates (NHPs), including evidence of neuron degeneration and apoptosis. Importantly, this is seen among infected animals that do not develop severe respiratory disease, which may provide insight into neurological symptoms associated with “long COVID”. Sparse virus is detected in brain endothelial cells but does not associate with the severity of central nervous system (CNS) injury. We anticipate our findings will advance our current understanding of the neuropathogenesis of SARS-CoV-2 infection and demonstrate SARS-CoV-2 infected NHPs are a highly relevant animal model for investigating COVID-19 neuropathogenesis among human subjects. COVID-19 can result in neurological manifestations and animal models could provide insights into the mechanisms. Here, the authors describe neuroinflammation, microhemorrhages and brain hypoxia in SARS-CoV-2 infected non-human primates, including in animals that don’t develop severe respiratory disease.

Extracellular vesicles (EVs) from biological fluids can provide critical information for minimally invasive diagnostics and treatment monitoring, but their nanoscale size, low biomarker abundance, and heterogeneity pose challenges. Here, we integrate rolling circle amplification with expansion microscopy (RCA–ExM) to achieve super-resolution multi-omics profiling of single EVs using conventional fluorescence microscopy. Sensitive multimodal biomarker detection is achieved by employing RCA to detect switch hairpin probe-labeled EV membrane proteins, and EV-liposome fusion to detect EV miRNAs via delivery of specific molecular beacons and a signal-amplifying enzyme circuit. Next, hydrogel-mediated expansion is employed to enlarge the fused EVs to permit single-EV detections. RCA–ExM quantitation of miRNA-21 levels in EpCAM + PD-L1 + plasma EVs from a clinical cohort ( n  = 86) successfully distinguishes cancer patients from healthy donors and differentiates 3 categories of immunotherapy efficacy. RCA–ExM therefore exhibits significant promise for more sensitive and specific diagnostics, and treatment monitoring applications. Extracellular vesicles (EVs) can provide critical information for diagnostics, but analysis can be difficult. Here, the authors develop a super-resolution imaging method that combines rolling circle amplification with expansion microscopy to reveal surface/internal markers in single EVs for cancer diagnosis and immunotherapy prediction.

Chloroquine — an approved malaria drug — is known in nanomedicine research for the investigation of nanoparticle uptake in cells, and may have potential for the treatment of COVID-19.

Despite major advances in HIV testing, ultrasensitive detection of early infection remains challenging, especially for the viral capsid protein p24, which is an early virological biomarker of HIV-1 infection. Here, To improve p24 detection in patients missed by immunological tests that dominate the diagnostics market, we show a click chemistry amplified nanopore (CAN) assay for ultrasensitive quantitative detection. This strategy achieves a 20.8 fM (0.5 pg/ml) limit of detection for HIV-1 p24 antigen in human serum, demonstrating 20~100-fold higher analytical sensitivity than nanocluster-based immunoassays and clinically used enzyme-linked immunosorbent assay, respectively. Clinical validation of the CAN assay in a pilot cohort shows p24 quantification at ultra-low concentration range and correlation with CD4 count and viral load. We believe that this strategy can improve the utility of p24 antigen in detecting early infection and monitoring HIV progression and treatment efficacy, and also can be readily modified to detect other infectious diseases. Accurate detection of antigen p24 for HIV−1 early diagnosis remains challenging. Here the authors present a click chemistry amplified nanopore (CAN) assay that allows p24 quantification at ultralow concentration range in clinical samples.

Tuberculosis (TB) remains a major underdiagnosed public health threat worldwide, being responsible for more than 10 million cases and one million deaths annually. TB diagnosis has become more rapid with the development and adoption of molecular tests, but remains challenging with traditional TB diagnosis, but there has not been a critical review of this area. Here, we systematically review these approaches to assess their diagnostic potential and issues with the development and clinical evaluation of proposed CRISPR-based TB assays. Based on these observations, we propose constructive suggestions to improve sample pretreatment, method development, clinical validation, and accessibility of these assays to streamline future assay development and validation studies.

Six ebolavirus species are reported to date, including human pathogens Bundibugyo virus (BDBV), Ebola virus (EBOV), Sudan virus (SUDV), and Taï Forest virus (TAFV); non-human pathogen Reston virus (RESTV); and the plausible Bombali virus (BOMV). Since there are differences in the disease severity caused by different species, species identification and viral burden quantification are critical for treating infected patients timely and effectively. Here we developed an immunoprecipitation-coupled mass spectrometry (IP-MS) assay for VP40 antigen detection and quantification. We carefully selected two regions of VP40, designated as peptide 8 and peptide12 from the protein sequence that showed minor variations among Ebolavirus species through MS analysis of tryptic peptides and antigenicity prediction based on available bioinformatic tools, and generated high-quality capture antibodies pan-specific for these variant peptides. We applied this assay to human plasma spiked with recombinant VP40 protein from EBOV, SUDV, and BDBV and virus-like particles (VLP), as well as EBOV infected NHP plasma. Sequence substitutions between EBOV and SUDV, the two species with highest lethality, produced affinity variations of 2.6-fold for p8 and 19-fold for p12. The proposed IP-MS assay differentiates four of the six known EBV species in one assay, through a combination of p8 and p12 data. The IP-MS assay limit of detection (LOD) using multiple reaction monitoring (MRM) as signal readout was determined to be 28 ng/mL and 7 ng/mL for EBOV and SUDV respectively, equivalent to ~1.625–6.5×10 5 Geq/mL, and comparable to the LOD of lateral flow immunoassays currently used for Ebola surveillance. The two peptides of the IP-MS assay were also identified by their tandem MS spectra using a miniature MALDI-TOF MS instrument, greatly increasing the feasibility of high specificity assay in a decentralized laboratory.

Numerous groups have employed the special properties of CRISPR/Cas systems to develop platforms that have broad potential applications for sensitive and specific detection of nucleic acid (NA) targets. However, few of these approaches have progressed to commercial or clinical applications. This review summarizes the properties of known CRISPR/Cas systems and their applications, challenges associated with the development of such assays, and opportunities to improve their performance or address unmet assay needs using nano‐/micro‐technology platforms. These include rapid and efficient sample preparation, integrated single‐tube, amplification‐free, quantifiable, multiplex, and non‐NA assays. Finally, this review discusses the current outlook for such assays, including remaining barriers for clinical or point‐of‐care applications and their commercial development. CRISPR assays that permit sensitive detection of various new targets continue to evolve and have exciting potential for future clinical and commercial applications. However, while much has been done to improve the performance and workflows of these assays, significant challenges remain for their widespread commercial and clinical adoption, although lessons from nucleic acid amplification assays could facilitate this process.

Emerging evidence underscores biophysical characteristics of cancer cells as key modulators of cancer progression and metastasis. Herein, we reported a cell-mechanophenotyping screening microfluidic chip (termed LesM) for the high-efficient capture of circulating tumor cells (CTCs) and evaluation of single-cell deformation to reveal the hematogenous metastatic potential of bacteria-infected breast cancer. LesM employs L-shaped traps to capture single cells, leveraging bacteria-infected CTCs with cytoskeletal reorganization traverse narrowed channels while rigid native cells are retained. The platform demonstrates an average single-cell capture efficiency of 95.42% and specificity of 85.34% in discriminating infected versus non-infected breast cancer cells, validated through parallel in vivo metastatic assays. LesM enables high-throughput sensing up to 10,240 cells of mechanical signatures and microbial cargo, correlating with metastatic risk and antibiotic response. By bridging biomechanics and intratumoral microbiota detection, LesM offers a transformative liquid biopsy tool for predicting distant metastasis and guiding antimicrobial therapies in bacteria-infected breast cancers. Emerging evidence underscores biophysical characteristics of cancer cells as key modulators of cancer metastasis. Here, the authors reported a single-cell mechanophenotyping chip that screens deformable CTCs to reveal the hematogenous metastatic potential of bacteria-infected breast cancer.