Severely Ill COVID-19 Patients Display Impaired Exhaustion Features in SARS-CoV-2-Reactive CD8+ T Cells
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How CD8+ T cells respond to SARS-CoV-2 infection is not fully known. Investigators reported on the single-cell transcriptomes of >80,000 virus-reactive CD8+ T cells, obtained using a modified Antigen-Reactive T cell Enrichment assay, from 39 COVID-19 patients and 10 healthy subjects. COVID-19 patient cells were segregated into two groups based on whether the dominant CD8+ T cell response to SARS-CoV-2 was “exhausted” or not.
A Modular Master Regulator Landscape Controls Cancer Transcriptional Identity
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The mechanisms linking genomic alterations to transcriptional identity of cancer cells remain elusive. Integrative genomic analysis, using a network-based approach, identified 407 master regulator (MR) proteins responsible for canalizing the genetics of individual samples from 20 cohorts in The Cancer Genome Atlas into 112 transcriptionally distinct tumor subtypes. MR proteins could be further organized into 24 pan-cancer, MR block modules (MRBs), each regulating key cancer hallmarks and predictive of patient outcome in multiple cohorts.
Gut Microbiome Dysbiosis in Antibiotic-Treated COVID-19 Patients Is Associated with Microbial Translocation and Bacteremia
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The investigators demonstrated that SARS-CoV-2 infection induced gut microbiome dysbiosis in male mice. Samples collected from human COVID-19 patients of both sexes also revealed substantial gut microbiome dysbiosis. Analysis of blood culture results testing for secondary microbial bloodstream infections with paired microbiome data indicated that bacteria might translocate from the gut into the systemic circulation of COVID-19 patients. These results were consistent with a direct role for gut microbiome dysbiosis in enabling dangerous secondary infections during COVID-19.
Cell-Specific Regulation of Gene Expression Using Splicing-Dependent Frameshifting
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Precise and reliable cell-specific gene delivery remains technically challenging. Investigators report a splicing-based approach for controlling gene expression whereby separate translational reading frames are coupled to the inclusion or exclusion of mutated, frameshifting cell-specific alternative exons. Candidate exons are identified by analyzing thousands of publicly available RNA sequencing datasets and filtering by cell specificity, conservation, and local intron length.
Neuroinflammatory Transcriptional Programs Induced in Rhesus Pre‑Frontal Cortex White Matter During Acute SHIV Infection
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Neuroinflammation has evolved as a protective immune response within the central nervous system (CNS), but chronic neuroinflammation leads to oxidative stress, cellular damage, and neurodegeneration. People living with HIV are at increased risk for age-related neurodegenerative diseases. Using rhesus macaques of both sexes, the researchers characterized the molecular underpinnings of acute neuroinflammation following simian–human immunodeficiency virus (SHIV) infection.
Isoniazid and Rifapentine Treatment Effectively Reduces Persistent M. tuberculosis Infection in Macaque Lungs
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People with HIV and asymptomatic latent tuberculosis (TB) coinfection are at risk of developing active TB symptoms. The Centers for Disease Control and Prevention recommends a weekly dose of isoniazid and rifapentine for 3 months (3HP) for treatment of latent TB infection, but the sterilizing efficacy of the regimen has not been demonstrated previously. Using rhesus macaques of both sexes, researchers evaluated the efficacy of the 3HP regimen in eradicating persistent Mycobacterium tuberculosis infection.
Wastewater Sequencing Reveals Early Cryptic SARS-CoV-2 Variant Transmission
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The investigators explored the use of SARS-CoV-2 RNA concentration in wastewater as a practical approach to estimate community prevalence of COVID-19, detect emerging variants, and track regional infection dynamics. Two obstacles must be overcome to leverage wastewater-based genomic surveillance: low-quality sequence data and inability to estimate relative lineage abundance in mixed samples. The investigators developed and deployed improved virus concentration protocols and deconvolution software to fully resolve multiple virus strains from wastewater.
Distinct Metabolic States Guide Maturation of Inflammatory and Tolerogenic Dendritic Cells
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The investigators mapped single-cell metabolic states and immune profiles of inflammatory and tolerogenic monocytic dendritic cells using recently developed multiparametric approaches. Activation scores revealed simultaneous engagement of multiple metabolic pathways in distinct monocytic dendritic cell differentiation stages (e.g., rapid reprogramming of glycolytic monocytes and transient co-activation of mitochondrial pathways followed by maturation of dendritic cells). This data set provides insights into metabolic pathways that affect the immune profiles of human dendritic cells.
Mosaic RBD Nanoparticles Protect Against Challenge by Diverse Sarbecoviruses in Animal Models
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Two animal coronaviruses from the SARS-like betacoronavirus (sarbecovirus) lineage—SARS-CoV and SARS-CoV-2—have caused epidemics or pandemics in humans during the past 20 years. New SARS-CoV-2 variants have prolonged the COVID-19 pandemic, and the discovery of diverse sarbecoviruses in bats raises the possibility of another coronavirus pandemic. Vaccines and therapeutics are needed to protect against both SARS-CoV-2 variants and zoonotic sarbecoviruses with the potential to infect humans.
Recreating the Heart’s Helical Structure–Function Relationship With Focused Rotary Jet Spinning
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The investigators developed a tissue engineering approach that enables rapid deposition of cardiomyocyte microfibers with programmable alignments in 3D geometries. Using this focused rotary jet spinning (FRJS) method, they reproduced tissue scaffolds with contractile cells' helical alignments, resembling complex structures of the musculature and properties of a natural heart. This work represents an important advance towards biofabrication of tissue models for healthy and diseased hearts by manipulating orientation of specific fibers.