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Single-cell transcriptomic profiling of malignant peripheral nerve sheath tumors
Malignant peripheral nerve sheath tumors (MPNSTs) are aggressive sarcomas arising from Schwann cells and characterized by marked cellular and molecular heterogeneity. Although bulk multi-omic studies have provided valuable insights into MPNST biology, recent advances in …
Read PDFSingle-cell RNA sequencing unravels T cell exhaustion underlying the chronicity of chromoblastomycosis
<h4>Introduction</h4>Chromoblastomycosis (CBM) is a chronic, neglected tropical fungal infection. Its immunopathogenesis, particularly the mechanism underlying its chronicity, remains poorly understood.<h4>Methods</h4>We performed single-cell RNA sequencing (scRNA-seq) on lesional skin from a CBM patient, followed by comprehensive …
Read PDFMethodologies for Sample Multiplexing and Computational Deconvolution in Single-Cell Sequencing
Single-cell sequencing is revolutionizing biological research by enabling unprecedented cellular resolution, yet traditional multi-sample experiments are often constrained by high costs and batch effects. Sample multiplexing offers a critical solution by uniquely tagging individual cells …
Read PDFCausal Effects and Single-Cell Microenvironmental Implications of Germline Variant-Regulated Lactylation-Related Pro-Oncogenic Genes in Colorectal Cancer
<h4>Background</h4>Colorectal cancer (CRC) is shaped by inherited genetic susceptibility, metabolic reprogramming, epigenetic regulation, and tumor microenvironment (TME) heterogeneity. Lactylation has recently emerged as an epigenetic mechanism that links lactate accumulation to chromatin remodeling and transcriptional …
Read PDFUnraveling lncRNA diversity at a single cell resolution and in a spatial context across different cancer types
Long noncoding RNAs (lncRNAs) participate in gene regulation underlying development and disease. Overcoming inherent limitations of bulk sequencing lncRNA analysis, we leveraged single-cell and spatial transcriptomics (ST) data to analyze 219,442 potential lncRNAs identified by …
Read PDFInterpretable learning of temporal cellular dynamics from single-cell data
Reconstructing temporal cellular dynamics from static single-cell transcriptomics remains a major challenge. Methods based on RNA velocity are useful, but interpreting their results to learn new biology remains difficult, and their predictive power is limited. …
Read PDFKey cellular subpopulations and mechanisms of propranolol in infantile hemangioma: insights from single-cell omics
Infantile hemangioma (IH) is the most common benign vascular tumor in infancy, characterized by rapid proliferation followed by spontaneous involution. Despite propranolol being established as first-line therapy, the cellular basis of this biphasic behavior and …
Read PDFIntelligent label-free droplet microfluidic sorting system for single-cell encapsulation and morphology-guided screening
The label-free extraction of cellular morphological data from within droplet microenvironments, and its subsequent translation into reliable, high-precision sorting, continues to pose a central challenge in the field of droplet microfluidics. Here, we develop an …
Read PDFSingle-cell landscape of sex-specific drivers of Alzheimer's disease
<h4>Introduction</h4>We investigated sex-specific gene expression associations with the neuropathology and cognitive manifestation of Alzheimer's disease (AD) leveraging single-nucleus transcriptomic datasets including 2.84 million nuclei from the dorsolateral prefrontal cortex (DLPFC).<h4>Methods</h4>We delineated the full scope of …
Read PDFPitfalls in analysis and interpretation of single-cell RNA-seq data in cancer
Single-cell and single-nuclei RNA-seq (sc/snRNA-seq) have become a central approach in cancer research, and their widespread impact has been enabled by various computational tools developed specifically for sc/snRNA-seq analysis. Nevertheless, proper analysis and interpretation of …
Read PDFGraph Topology Reframes the Coherence of Cell-State Manifold Inference under Heterogeneous Single-Cell Observations
Manifold-based single-cell omics analyses assume that high-dimensional observations can fall into a low-dimensional space encoding biological constraints. In practice, per-cell observation is highly heterogeneous: Shallowly and deeply observed cells coexist. In an empirical single-cell RNA …
Read PDFSingle-cell phenotypic heterogeneity shapes quorum signaling dynamics in Pseudomonas aeruginosa
Quorum sensing (QS) coordinates collective bacterial behavior, yet how individuality arises within a system built to unify action remains unclear. Using imaging-transcriptomics, we profile the QS response of Pseudomonas aeruginosa at single-cell resolution and uncover …
Read PDFscUmaper: An automated framework for doublet removal and cell-type annotation in single-cell transcriptomics
Single-cell RNA sequencing can resolve cellular heterogeneity but is sensitive to heterotypic doublets and often requires expert-driven preprocessing and annotation. We developed single cell utility matrices processing engine (scUmaper), an R/Seurat-native workflow that integrates quality …
Read PDFSingle-Cell Analysis Identified a Recurrent Malignant-Associated Transcriptional State in Colorectal Cancer
Colorectal cancer (CRC) exhibits substantial molecular heterogeneity, yet detailed single-cell transcriptomic data from Japanese patients remain limited. Here, we performed single-cell RNA sequencing (scRNA-seq) on tumor tissues and adjacent normal tissues from four Japanese CRC …
Read PDFResearch Progress of Interstitial Lung Disease Based on Single-Cell Sequencing Technology
Interstitial lung disease (ILD) refers to a collection of respiratory conditions characterized by inflammation of the lung parenchyma, alveolar irritation, and fibrosis of the interstitial tissue. Traditional research methods are often unable to completely reveal …
Read PDFBrain Single-Cell Transcriptional Responses to Bexarotene-Activated RXR in an Alzheimer's Disease Model
Pharmacological activation of brain Retinoid X Receptors (RXRs) enhances cognition and facilitates amyloid-beta (Aβ) clearance in Alzheimer's disease (AD) mouse models, partly by upregulating apolipoprotein E (<i>Apoe</i>), a major AD genetic risk factor. However, the …
Read PDFMachine learning predictions surpass individual mRNAs as a proxy of single-cell protein expression
<h4>Background</h4>Expansive repositories of scRNA-seq data are now available. These are often analysed assuming that mRNA abundance reflects expression of the cognate protein. However, post-transcriptional/translational regulation and the sparsity of measurements in single-cell data make mRNA …
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