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Accurate estimation of cell-type composition from bulk RNA sequencing (RNA-seq) is critical for dissecting the cellular basis of disease. Single-cell RNA sequencing (scRNA-seq) has emerged as a preferred reference for cell-type deconvolution. However, in practice, …
Read PDFRenal-resident macrophages (RMs) are essential regulators of kidney homeostasis and repair, yet the mechanisms governing RM niche regeneration after acute depletion remain poorly defined. To overcome these limitations, we have developed an inducible human CD59- …
Read PDF<h4>Objective</h4>Medulloblastoma (MB) is one of the most prevalent solid brain tumors in the pediatric population. Although hundreds of Differentially Expressed Genes (DEGs) have been identified as diagnostic molecules and therapeutic targets for Medulloblastoma (MB), the …
Read PDFTestosterone is the most studied androgen in hormone replacement therapy in postmenopausal women. Many transgender men also receive long-term testosterone replacement therapy (TRT) and have high serum testosterone levels compared to the low levels seen …
Read PDF<h4>Background</h4>Atypical teratoid rhabdoid tumors (ATRTs) are highly aggressive pediatric central nervous system tumors defined by the inactivation of the SMARCB1 gene. Despite the identification of three distinct molecular subtypes, each defined by unique clinical and …
Read PDF<h4>Introduction</h4>Allele-specific expression (ASE), preferential expression of one allele at a heterozygous locus, is implicated in various brain diseases but remains largely uncharacterized in Alzheimer's disease (AD).<h4>Methods</h4>We performed a genome-wide characterization of ASE variants across seven …
Read PDFOur understanding of the causal mechanisms of disorders such as anxiety and depression remains rudimentary. There is a pressing need to develop disease-modifying and preventative therapies that can be administered early and reduce symptom emergence. …
Read PDFRupture of unstable atherosclerotic plaques is a major cause of mortality. Endothelial-to-mesenchymal transition associates with advanced atherosclerotic plaques and contributes to plaque progression. We examined the role of Twist1, a transcription factor that drives endothelial-to-mesenchymal …
Read PDFMechanistic crosstalk between the DNA-damage response (DDR) and the innate immune system is essential to maintain genomic integrity, tissue homeostasis, and organismal resilience. However, the origin and diversity of this crosstalk among animal lineages remain …
Read PDFPooled perturbation screens can reveal cellular regulatory networks, yet scaling these techniques for large-scale screens in animals remains challenging. Here we present MIC-Drop-seq, a technique that addresses these challenges by combining high-throughput CRISPR gene disruption …
Read PDFLymph nodes (LNs) along the murine gastrointestinal tract are immunologically distinct. Here, we investigate whether such an immune dichotomy globally defines gut LN identity and what drives the regional differences. However, we find that, transcriptionally, …
Read PDFDrug-induced acute kidney injury (AKI) affects about 20 % of hospitalized AKI patients, a significant contributor to morbidity and mortality. The lack of understanding of the kidney system and functioning of nephrotoxic drugs contributes to …
Read PDF<h4>Background & aims</h4>Metabolic dysfunction-associated steatohepatitis (MASH) increasingly drives hepatocellular carcinoma (HCC) development. We characterized inflammatory infiltrates in liver biopsies from MASH patients who developed HCC versus controls to identify predictive immune signatures.<h4>Method</h4>Formalin-fixed paraffin-embedded (FFPE) liver …
Read PDF<h4>Background</h4>Acute lymphoblastic leukemia (ALL) is a hematologic malignancy characterized by malignant transformation of lymphoid precursor cells. ALL prognosis differs considerably, especially between pediatric patients and adult patients, with poor response to therapy in adults. MicroRNAs …
Read PDFCD4+ T helper (TH)-17 cells play a pivotal role in mucosal immune defense and are implicated in autoimmune diseases and cancer. Although Th17 cell plasticity is well-studied in mice, the factors driving their transition between …
Read PDFCancer stem cells (CSCs) constitute a subpopulation of malignant cells with self-renewal and differentiation capabilities that drive tumorigenicity, metabolic adaptability, immune evasion, and therapeutic resistance, key factors contributing to metastasis and poor clinical outcomes. While …
Read PDFThe hypothalamus is a conserved structure in the brain of vertebrates that plays key roles in the organism's homeostasis through different functions, including regulation of temperature, sleep, energy balance and reproduction. The hypothalamus is composed …
Read PDFLymphocyte-activation gene 3 (LAG3) is an immune checkpoint expressed on the surface of T cells. We conducted a comprehensive molecular characterization and clinical analysis of LAG3 expression in gliomas. Across the CGGA and TCGA glioma …
Read PDF<h4>Introduction</h4>The cellular mechanisms underlying Long COVID (LC) associated with myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) remain poorly understood.<h4>Methods</h4>We performed single-cell RNA sequencing (scRNA-seq) on peripheral blood mononuclear cells collected 12 months after acute COVID-19 infection from …
Read PDFAlthough genetic risk in coronary artery disease (CAD) is linked to changes in gene expression, recent discoveries have revealed a major role for A-to-I RNA editing in CAD. ADAR1 edits immunogenic double-stranded RNA (dsRNA), preventing …
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