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Chronic Lymphocytic Leukemia (CLL) is characterized by clinical and biological heterogeneity, with a subset of patients progressing to Richter Transformation (RT), an aggressive lymphoma. This study explores MYC target gene activation across various CLL stages …
Read PDFOrofacial clefting (OFC) is among the most common birth defects and can occur either as part of a syndrome or in isolation (nonsyndromic, ns). Cleft palate only (CPO) is an OFC subtype. Here, we searched …
Read PDFThe prevalence of both osteoporosis and sarcopenia increases with age and about 60% of elderly sarcopenia patients also develop osteoporosis. However, the co-occurrence of osteoporosis and sarcopenia remains unclear. We performed single-cell 5' RNA-seq on …
Read PDFCells release heterogeneous extracellular vesicles and particles (EVPs) into circulation, carrying RNA and proteins that reflect their origin. Recently, brain-derived EVs have gained significant attention as non-invasive biomarkers for Alzheimer's disease (AD). Here, we identified …
Read PDFChitinase-3-like protein 1 (CHI3L1) is a secreted, non-enzymatic glycoprotein that interacts with cell-surface and extracellular-matrix proteins, proteoglycans, and polysaccharides. Many studies reported the overexpression of CHI3L1 in various cancers, but its exact role in tumorigenesis/cancer …
Read PDFDeterioration of the blood-brain barrier (BBB), including impaired neurovascular uncoupling, contributes to cognitive decline in aging. The BBB is formed principally by brain microvascular endothelial cells (ECs), and ECs throughout the body are enriched for …
Read PDFMüller glia arise from late-stage retinal progenitor cells (RPCs) as a distinct lineage that diverges from neurogenic trajectories. Here, we identify the maternally imprinted gene Plagl1 as a key transcriptional regulator of gliogenesis in the …
Read PDFHigh-grade serous ovarian cancer (HGSC) is a heterogeneous disease. RNA sequencing (RNAseq) of bulk solid tissue is of limited use in these populations due to heterogeneity. Single-cell RNA-seq (scRNA-seq) allows for the identification of diverse …
Read PDFCombining allele-specific expression (ASE) analysis with single-cell RNA-seq can elucidate how genomic variation affects RNA expression at the single-cell level. We explore how experimental and computational choices impact the power of ASE-based methods and develop …
Read PDFColorectal cancer (CRC) is the second most frequently diagnosed cancer worldwide and represents a major challenge for public health. Despite advances in molecular profiling, important gaps remain in our understanding of tumorigenesis and the regulatory …
Read PDFTumor-infiltrating T cells have been the primary focus of cancer immunotherapy; however, accumulating evidence points to a critical role for B cells and plasma cells in shaping responses to immune checkpoint blockade. In this study, …
Read PDFThe epithelial-mesenchymal transition (EMT) is a metastasis-promoting process whose heterogeneity has been extensively studied at a gene expression level. EMT involves reprogramming of lipid metabolism; however, there has been little focus lipid level heterogeneity. Here, …
Read PDFCardiovascular and cerebrovascular diseases, often caused by atherosclerosis, are the stern cause of death worldwide, and carotid plaque play a crucial role in the development of these diseases. Tryptophan metabolism is an important pathway involved …
Read PDFCell segmentation in imaging-based spatial transcriptomics (ST) relies on stained image segmentation or transcript clustering, but current methods are limited by dependence on manual annotations, sensitivity to staining quality and cell density, and lack of …
Read PDFBronchopulmonary dysplasia (BPD) is the most common chronic lung disease in preterm infants and is characterized by aberrant late-stage lung development driven by multiple factors. Although previous studies have demonstrated that BPD is associated with …
Read PDFAging is a dominant risk factor for chronic diseases characterized by the functional decline of tissues and organs. During aging, the hematopoietic system declines in regenerative capacity-seemingly attributable to increases in DNA damage, replicative stress, …
Read PDFDuring zebrafish embryonic body elongation, differentiation of mesodermal progenitors into presomitic mesoderm requires the transcription factors tbx16 and mesogenin 1. Here, by using temporally controlled tbx16 and mesogenin 1 overexpression and RNAseq to identify immediate …
Read PDFGene up(down)regulation findings in single-cell and spatial RNA sequencing can be inconsistent despite remarkable progress in technology. Inconsistent findings in high-quality samples raise concerns about assumptions behind widely accepted data analysis approaches. We, therefore, propose …
Read PDFThe oxymonads are anaerobic protist symbionts of animals with spectacular morphological complexity and variability, but because only a handful of species have been cultured, very little data are available for the group. This includes molecular …
Read PDFDinoflagellates are an abundant and diverse group of protists representing a wealth of unique biology and ecology. While many dinoflagellates are photosynthetic or mixotrophic, many taxa are heterotrophs, often with complex feeding strategies. Compared to …
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