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Opposing regulation of TNF responses by IFN-γ and a PGE2-cAMP axis that is apparent in rheumatoid and immune checkpoint inhibitor-induced arthritis human IL-1β+ macrophages
IL-1β-expressing macrophages have been described in rheumatoid arthritis (RA), immune checkpoint inhibitor-induced inflammatory arthritis (ICI-arthritis), and pancreatic cancer and proposed to be pathogenic. IL-1β+ macrophages express genes cooperatively induced by PGE2 and TNF signaling, but …
Read PDFHLA Class Ib and MICA/MICB Expression in Human Tissues and Cell Types: Reshuffling Immune Players
Abnormal expression of HLA class Ib, MICA and MICB molecules is associated with the evolution of pathological conditions and clinical settings. Here, we use RNA-sequencing data from two publicly-available projects, from different human organs and …
Read PDFSingle-nucleus transcriptional and chromatin accessibility analyses of maturing mouse Achilles tendon uncover the molecular landscape of tendon stem/progenitor cells
Tendons and ligaments are crucial connective tissues linking bones and muscles, yet achieving full functional recovery after injury remains challenging. We investigated the characteristics of tendon stem/progenitor cells (TSPCs) by focusing on the declining tendon …
Read PDFThe effect of cold ischemia time on hypoxia, EMT, and apoptosis pathways in normal colon mucosa
Cold ischemia time (CIT), the interval between tissue excision and preservation, is a critical preanalytical variable that profoundly impacts gene expression profiles. Variability in CIT can lead to inconsistent transcriptomic results, making study interpretation challenging …
Read PDFThe use of Benzonase to produce ribosome footprints simplifies translational levels quantification by Ribo-seq
Gene expression quantification through genomics methods is crucial for understanding diverse biological contexts. Among these methods, ribosome profiling (Ribo-seq) stands out as a valuable tool for uncovering post-transcriptional gene expression regulation by providing a comprehensive …
Read PDFBRPtools: An AutoML-Powered web platform for multiclass disease prediction from bulk blood RNA-seq data
Blood-based transcriptomic profiling provides a minimally invasive approach for disease diagnosis; however, the integration of large-scale, heterogeneous RNA sequencing (RNA-seq) datasets remains challenging. Here, we manually curated and uniformly reprocessed 134 publicly available human RNA-seq …
Read PDFDelta family protocadherins contribute to protoglomerular targeting of olfactory sensory neuron axons in the olfactory bulb
To understand how neural circuits are assembled, it is essential to identify and characterize the axonal guidance cues and receptors that determine the axonal trajectories and connections between neurons. We performed single-cell RNA sequencing of …
Read PDF<i>Characterization</i> of a Novel Family of Contilisant + Belinostat Multitarget Small Molecules in Glioblastoma
<b>Background</b>: Glioblastoma is the most common and malignant primary brain tumor in adults, with current treatment presenting limited effectiveness. Therapeutic resistance stems largely from its marked molecular and cellular heterogeneity. Multitarget small molecules (MSMs) have …
Read PDFSingle-Cell Transcriptome Profiling Reveals Dynamic Cell Populations and Immune Infiltration in Moyamoya Disease
<h4>Background</h4>The cellular composition and molecular mechanisms of the pathological arteries in Moyamoya disease (MMD) remain poorly understood. To improve our understanding of pathogenesis in MMD, we aimed to comprehensively map the cellular composition and molecular …
Read PDFA method of comprehensive sequencing analysis of the small RNA fragmentome (RiboMarker)
Small RNAs and RNA fragments (sRNAs) found in blood and other biofluids have emerged as promising biomarkers for cancer and other pathologies. Sequencing analysis of sRNAs representing the entire RNA fragmentome could improve understanding of …
Read PDFTissue microenvironment dictates the state of human iPSC-derived endothelial cells of distinct developmental origin in 3D cardiac microtissues
Each tissue and organ in the body has its own type of vasculature. Here, we demonstrate that organotypic vasculature for the heart can be recreated in a three-dimensional cardiac microtissue (MT) model composed of human …
Read PDFSystemic lupus pregnancies are characterized by an intrinsic pro-inflammatory monocyte transcriptome, driven by an aberrant miRNA signature
<h4>Objective</h4>Pregnancy induces profound immunological adaptations that usually promote tolerance and reduce autoimmune activity. However, women with systemic lupus erythematosus (SLE) remain at increased risk of disease flares and pregnancy complications, whereas rheumatoid arthritis (RA) often …
Read PDFIntegrative GWAS and transcriptomic analyses reveal markers and candidate genes associated with resistance to <i>Botrytis cinerea</i> fruit rot in blueberry
<i>Botrytis cinerea</i> is a broad host range fungal pathogen causing gray mold disease and crop losses worldwide. In blueberries, symptoms include blossom blight in the field and postharvest fruit rot, affecting the entire supply chain. …
Read PDFBulk RNAseq Analysis of Cardiac Myosin-Specific CD4<sup>+</sup> and CD8<sup>+</sup> T Cells Reveals Distinct Transcriptomic Profiles Between Myocarditis-Resistant and Susceptible Mice
<b>Background</b>: We recently generated T cell receptor (TCR) transgenic (Tg) mice specific to cardiac myosin heavy chain-α (Myhc-α 334-352) on both myocarditis-resistant (C57BL/6) and susceptible (A/J) genetic backgrounds. We noted that the antigen-specific TCRs were …
Read PDFVEGF-A blockade overcomes liver metastases resistance to chemoimmunotherapy in patients with advanced non-squamous NSCLC
<h4>Purpose</h4>Liver metastases (LMs) confer resistance to immune checkpoint blockade in advanced non-squamous non-small cell lung cancer (ns-NSCLC), likely through an immunosuppressive tumor microenvironment (TME). We hypothesized that vascular endothelial growth factor (VEGF)-A blockade, by remodeling …
Read PDFIdentification of a Small-Molecule Modulator of Astrocyte Reactivity for Optic Nerve Protection
<h4>Purpose</h4>Injury of the optic nerve leads to retinal ganglion cells (RGCs) apoptosis and irreversible vision loss, in which reactive astrocytes play a central role. The aim of this study is to modulate pathological reactive astrocytes …
Read PDFLithium ameliorates neural differentiation restoring cell death balance in Cornelia de Lange syndrome 2D and 3D models
Cornelia de Lange syndrome (CdLS) is a rare genetic disorder that affects almost any organ, including the central nervous system. It leads to a wide range of neurodevelopmental delays, and there are currently no available …
Read PDFAdvanced human organoid-on-chip with physiological cellular complexity reveals bidirectional secretion patterns
Intestinal epithelial cells are essential for maintaining gut homeostasis, serving as a physical barrier separating luminal content from the immune compartment. They are crucial for balancing tolerance to commensal and protection from pathogenic bacteria and …
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