GAGE-seq concurrently profiles multiscale 3D genome organization and gene expression in single cells.

The organization of mammalian genomes features a complex, multiscale three-dimensional (3D) architecture, whose functional significance remains elusive because of limited single-cell technologies that can concurrently profile genome organization and transcriptional activities. Here, we introduce genome architecture and gene expression by sequencing (GAGE-seq), a scalable, robust single-cell co-assay measuring 3D genome structure and transcriptome simultaneously within the same cell. Applied to mouse brain cortex and human bone marrow CD34+ cells, GAGE-seq characterized the intricate relationships between 3D genome and gene expression, showing that multiscale 3D genome features inform cell-type-specific gene expression and link regulatory elements to target genes. Integration with spatial transcriptomic data revealed in situ 3D genome variations in mouse cortex. Observations in human hematopoiesis unveiled discordant changes between 3D genome organization and gene expression, underscoring a complex, temporal interplay at the single-cell level. GAGE-seq provides a powerful, cost-effective approach for exploring genome structure and gene expression relationships at the single-cell level across diverse biological contexts.

A Bioinspired and Cost-Effective Device for Minimally Invasive Blood Sampling.

Conventional venipuncture is invasive and challenging in low and middle-income countries. Conversely, point-of-care devices paired with fingersticks, although less invasive, suffer from high variability and low blood volume collection. Recently approved microsampling devices address some of these issues but remain cost-prohibitive for resource-limited settings. In this work, a cost-effective microsampling device is described for the collection of liquid blood with minimal invasiveness and sufficient volume retrieval for laboratory analyses or immediate point-of-care testing. Inspired by the anatomy of sanguivorous leeches, the single-use device features a storage compartment for blood collection and a microneedle patch hidden within a suction cup. Finite Element Method simulations, corroborated by mechanical analyses, guide the material selection for device fabrication and design optimization. In piglets, the device successfully collects ≈195 µL of blood with minimal invasiveness. Additionally, a tailor-made lid and adapter enable safe fluid transportation and integration with commercially available point-of-care systems for on-site analyses, respectively. Taken together, the proposed platform holds significant promise for enhancing healthcare in the pediatric population by improving patient compliance and reducing the risk of needlestick injuries through concealed microneedles. Most importantly, given its cost-effective fabrication, the open-source microsampling device may have a meaningful impact in resource-limited healthcare settings.

Clot Retraction and Its Correlation with the Function of Platelet Integrin αIIbß3.

Clot retraction results from retractions of platelet filopodia and fibrin fibers and requires the functional platelet αIIbß3 integrin. This assay is widely used to test the functions of platelets and fibrinogen as well as the efficacy of fibrinolysis. Changes in clot retraction have been found in a variety of hemostatic abnormalities and, more recently, in arterial thrombosis. Despite its broad clinical use and low cost, many aspects of clot retraction are poorly understood. In the present study, we performed two clinical standard clot retraction assays using whole-blood and platelet-rich plasma (PRP) samples to determine how clot retraction correlates with platelet counts and mean volume, the density of αIIbß3 integrin and PLA genotypes, and plasma fibrinogen levels. We found that clot retraction was affected by platelet counts, but not mean platelet volume. It correlated with the surface density of the integrin αIibß3, but not PLA genotypes. These results indicate that clot retraction measures a unique aspect of platelet function and can serve as an additional means to detect functional changes in platelets.

Concurrent profiling of multiscale 3D genome organization and gene expression in single mammalian cells.

The organization of mammalian genomes within the nucleus features a complex, multiscale three-dimensional (3D) architecture. The functional significance of these 3D genome features, however, remains largely elusive due to limited single-cell technologies that can concurrently profile genome organization and transcriptional activities. Here, we report GAGE-seq, a highly scalable, robust single-cell co-assay that simultaneously measures 3D genome structure and transcriptome within the same cell. Employing GAGE-seq on mouse brain cortex and human bone marrow CD34+ cells, we comprehensively characterized the intricate relationships between 3D genome and gene expression. We found that these multiscale 3D genome features collectively inform cell type-specific gene expressions, hence contributing to defining cell identity at the single-cell level. Integration of GAGE-seq data with spatial transcriptomic data revealed in situ variations of the 3D genome in mouse cortex. Moreover, our observations of lineage commitment in normal human hematopoiesis unveiled notable discordant changes between 3D genome organization and gene expression, underscoring a complex, temporal interplay at the single-cell level that is more nuanced than previously appreciated. Together, GAGE-seq provides a powerful, cost-effective approach for interrogating genome structure and gene expression relationships at the single-cell level across diverse biological contexts.

Recombinant ADAMTS-13 Improves Survival of Mice Subjected to Endotoxemia.

When stimulated by proinflammatory mediators, endothelial cells release ultra-large von Willebrand factor (ULVWF) multimers that are hyperactive in activating and aggregating platelets. These ULVWF multimers can accumulate in the circulation and on the inflamed endothelium because they are insufficiently cleaved by the metalloprotease ADAMTS-13, which becomes moderately deficient under conditions of systemic inflammation. This moderate ADAMTS-13 deficiency may lead to thrombotic complications that contribute to ischemic tissue injury and organ failure that are associated with severe infections. To test this hypothesis, we investigated whether recombinant ADAMTS-13 improves the pathological course of endotoxemia in lipopolysaccharide (LPS)-treated mice. C57BL/J6 mice received a bolus infusion of either 5 µg/mouse of ADAMTS-13 or vehicle control 30 min after LPS challenge and were monitored for seven-day survival. During the monitoring period, platelet counts, VWF antigen, and ADAMTS-13 activity were measured. Thrombosis was also examined by the immunohistochemistry in the liver. We found that ADAMTS-13 reduced mortality from 66% to 34.9%. The improved survival was associated with a greater recovery from thrombocytopenia, higher plasma ADAMTS-13 activity, and less thrombotic vascular occlusion. These results suggest that systemic inflammation could result in deficient ULVWF proteolysis by ADAMTS-13 and that ADAMTS-13 improves the outcomes of endotoxemia-induced inflammation.

LRP-1 Binds Fibrinogen in a Sialylation-Dependent Manner: A Quartz Crystal Microbalance Study.

Cardiovascular disease (CVD) is the leading cause of mortality in the United States. Atherosclerosis, the dominant condition leading to CVD, is characterized by fibrofatty plaque formation. Fibrinogen, an important clotting factor, has been known to promote atherogenesis as it retains the ability to trigger smooth muscle cell proliferation, localize in areas crucial to plaque progression, and bind both platelets and leukocytes. Yet, these consequences can be suppressed through anti-inflammatory receptors like LRP-1─an endocytic receptor part of the LDLR family responsible for the endocytosis of cell debris and protein degradation products. However, the continual progression of atherosclerosis in many patients indicates that such clearance mechanisms, deemed efferocytosis, are impaired during atherosclerosis. Using the quartz crystal microbalance with dissipation monitoring (QCM-D) as a platform to investigate receptor-ligand interactions, we identify fibrinogen to be a ligand of LRP-1 and characterize its binding with LRP-1. By examining a key player in atherosclerosis development─the effect of sialidase on receptor efficacy─we found that the desialylation of LRP-1 reduces its ability to bind fibrinogen. Protein docking simulations highlighted the N-terminus portion of fibrinogen's α domain as the LRP-1 docking site. The sialylated O-linked glycans at T894 and T935 have the potential to mediate direct binding of LRP-1 to fibrinogen and support the tertiary structure of LRP-1. These phenomena are important in showing a probable cause of defective efferocytosis that occurs readily during atherosclerosis.

Light Extinction by Agglomerates of Gold Nanoparticles: A Plasmon Ruler for Sub-10 nm Interparticle Distances.

Plasmon rulers relate the shift of resonance wavelength, λl, of gold agglomerates to the average distance, s, between their constituent nanoparticles. These rulers are essential for monitoring the dynamics of biomolecules (e.g., proteins and DNA) by determining their small (<10 nm) coating thickness. However, existing rulers for dimers and chains estimate coating thicknesses smaller than 10 nm with rather large errors (more than 200%). Here, the light extinction of dimers, 7- and 15-mers of gold nanoparticles with diameter dp = 20-80 nm and s = 1-50 nm is simulated. Such agglomerates shift λl up to 680 nm due to plasmonic coupling, in excellent agreement with experimental data by microscopy, dynamic light scattering, analytical centrifugation, and UV-visible spectroscopy. Subsequently, a new plasmon ruler is derived for gold nanoagglomerates that enables the accurate determination of sub-10 nm coating thicknesses, in excellent agreement also with tedious microscopy measurements.

Host-to-Host Group A Streptococcus Transmission Causes Infection of the Lamina Propria but Not Epithelium of the Upper Respiratory Tract in MyD88-Deficient Mice.

To understand protective immune responses against the onset of group A Streptococcus respiratory infection, we investigated whether MyD88 KO mice were susceptible to acute infection through transmission. After commingling with mice that had intranasal group A Streptococcus (GAS) inoculation, MyD88-/- recipient mice had increased GAS loads in the nasal cavity and throat that reached a mean throat colonization of 6.3 × 106 CFU/swab and mean GAS load of 5.2 × 108 CFU in the nasal cavity on day 7. Beyond day 7, MyD88-/- recipient mice became moribund, with mean 1.6 × 107 CFU/swab and 2.5 × 109 CFU GAS in the throat and nasal cavity, respectively. Systemic GAS infection occurred a couple of days after the upper respiratory infection. GAS infects the lip, the gingival sulcus of the incisor teeth, and the lamina propria of the turbinate but not the nasal cavity and nasopharyngeal tract epithelia, and C57BL/6J recipient mice had no or low levels of GAS in the nasal cavity and throat. Direct nasal GAS inoculation of MyD88-/- mice caused GAS infection, mainly in the lamina propria of the turbinate. In contrast, C57BL/6J mice with GAS inoculation had GAS bacteria in the nasal cavity but not in the lamina propria of the turbinates. Thus, MyD88-/- mice are highly susceptible to acute and lethal GAS infection through transmission, and MyD88 signaling is critical for protection of the respiratory tract lamina propria but not nasal and nasopharyngeal epithelia against GAS infection.

The Risk of Mortality Associated With Opioid Use in Patients With Acute Heart Failure: Systematic Review and Meta-analysis.

AIMS: The impact of opioids in acute heart failure (AHF) is unclear. This systematic review with meta-analysis aimed to evaluate the mortality risk associated with opioid use in AHF. METHODS AND RESULTS: An electronic search was performed in MEDLINE, CENTRAL, Web of Science Core Collection, and SCIELO (December 2019) for randomized controlled trials and observational studies evaluating the impact of opioids in in-hospital and 30-day mortality in patients with AHF. Data were screened, extracted, and appraised by 2 independent reviewers. A random-effects meta-analysis to estimate the pooled odds ratios (OR) with 95% confidence intervals (CI) was performed and heterogeneity was evaluated using the I2 statistics. Six observational retrospective studies with 151,735 participants were included. Pooled results showed a statistical significant association between morphine and in-hospital mortality (OR 1.78; 95% CI 1.01-3.13; I2 = 92%; 6 studies) and 30-day mortality (OR 1.56; 95% CI 1.14-2.15; I2 = 0; 2 studies). Both outcomes were rated as having a serious risk of bias and had a very low Grading of Recommendation, Assessment, Development, and Evaluation evidence. CONCLUSIONS: Opioids seem to be associated with an increased risk of short-term mortality in AHF patients; however, the confidence in the estimated effect is very low, which highlights the need of further research to evaluate this question.