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Single-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 PDFPredicting Macrophage Spatial Localization from Single-Cell Transcriptomes to Uncover Disease Mechanisms
When cells are isolated for single-cell RNA sequencing (scRNA-seq), their positional information is inevitably lost. Here, an algorithm termed MERLIN is described that can reconstruct such information in organs with compartmentalized anatomy, such as the …
Read PDFA sequence knowledge-guided deep learning method for single-cell multi-omics translation
<h4>Background</h4>Analysis of proteins is key to understanding biological processes, disease pathogenesis, and advancing therapeutic development. However, proteome profiling remains significantly limited when compared to the exponential growth of single-cell RNA sequencing data, owing to technical …
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 PDFA single-cell transcriptome atlas reveals the transcriptionally earliest state in rice callus
<h4>Background</h4>The cell fate transition of pluripotent callus from somatic cells plays an important role in plant development studies and crop genetic improvement. Embryonic callus is a group of totipotent cells derived from the founder cells …
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 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 PDFSingle-Cell Transcriptomics Reveal Microenvironment Alterations in Canine Peri-Implantitis
<h4>Background</h4>Peri-implantitis, a major contributor to dental implant failure, lacks comprehensive insights into tissue-specific heterogeneity as current researches predominantly focus on the whole peri-implant tissue rather than distinct molecular and cellular dynamics in gingiva and alveolar …
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 PDFTime-series single-cell transcriptomics reveals pervasive daily rhythmicity and nocturnal spermatogenesis in the zebrafish testis
The vertebrate testis has long been regarded as lacking strong cellular daily rhythmicity. Here, we use time-series single-cell RNA sequencing to construct a temporal atlas of the adult zebrafish testis. We identify previously unknown cell-type-specific …
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 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 …
Read PDFMachine learning approaches for biomarker discovery using single-cell RNA sequencing
The application of single-cell RNA sequencing (scRNA-seq) for biomarker discovery promises unprecedented resolution in identifying potential biomarkers by capturing and analysing cellular heterogeneity. Traditionally, biomarker discovery efforts within single-cell transcriptomics have primarily relied on conventional …
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