Spatiotemporal metabolomic approaches to the cancer-immunity panorama: a methodological perspective

Molecular Cancer, Год журнала: 2024, Номер 23(1)

Опубликована: Сен. 18, 2024

Язык: Английский

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Multiplexed Random Access Approach to DNA Microspheres for High‐Capacity Data Storage

Advanced Functional Materials, Год журнала: 2024, Номер 34(48)

Опубликована: Окт. 6, 2024

Abstract With the rapid growth of modern information data, DNA has emerged as a novel medium for data storage due to its durability, replicability, sustainability, and high density. This study focuses on compatibility, capacity, random access systems. A calcium phosphate (CaP) mineralized fluorescent SiO 2 (FSD@CaP) microspheres is developed by encapsulating fluorescence‐labeled encoding files onto surface that are intrinsically sized addressed two‐dimensional (2D) barcodes. The various sizes forming 2D barcodes FSD@CaP. enhance system's compatibility while allowing multiplexed files. high‐capacity permits effective single file using minimal number FSD@CaP microspheres, without impacting matrix system. Ultimately, arbitrary within complex pool distinct barcode‐tagged demonstrated utilizing flow cytometer sorting. Consequently, strategy this system provides scalable concept sets.

Язык: Английский

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CAFE: An Integrated Web App for High-Dimensional Analysis and Visualisation in Spectral Flow Cytometry

Опубликована: Янв. 7, 2025

Spectral flow cytometry provides greater insights into cellular heterogeneity by simultaneous measurement of up to 50 markers. However, analyzing such high-dimensional (HD) data is complex through traditional manual gating strategy. To address this gap, we developed CAFE as an open-source Python-based web application with a graphical user interface. Built Streamlit, incorporates libraries Scanpy for single-cell analysis, Pandas and PyArrow efficient handling, Matplotlib, Seaborn, Plotly creating customizable figures. Its robust toolset includes density-based down-sampling, dimensionality reduction, batch correction, Leiden-based clustering, cluster merging annotation. Using CAFE, demonstrated analysis human PBMC dataset 350,000 cells identifying 16 distinct cell clusters. can generate publication-ready figures in real time via interactive slider controls dropdown menus, eliminating the need coding expertise making HD accessible all. licensed under MIT freely available at https://github.com/mhbsiam/cafe.

Язык: Английский

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30-Color Longitudinal Full-Spectrum Immunophenotyping and Sorting of Human Circulating Immune Cell Subsets Implicated in Systemic Autoimmune Rheumatic Diseases

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2025, Номер unknown

Опубликована: Янв. 13, 2025

Purpose and Appropriate Sample Types This 30-color panel was developed to enable the enumeration purification of distinct circulating immune cell subsets implicated in pathogenesis systemic autoimmune diseases including rheumatoid arthritis (RA), lupus erythematosus (SLE), sclerosis (SSc; scleroderma), Sjögren’s disease (SjD), idiopathic inflammatory myopathy (IIM), others. While designed for application peripheral blood mononuclear cells, inclusion CD45 coupled with ability extract cellular autofluorescence spectral signatures enables this other tissue types. Of 30 total markers, employs 18 markers profile T consisting different memory helper polarities, > 10 B double-negative a 8 lineage identify lineages monocyte natural killer subsets, conventional dendritic plasmacytoid basophils. reproducibly identifies target populations excellent resolution over several months data acquisition minimal batch effects, offering investigators practical approach sort interest downstream applications while simultaneously collecting high parameter immunophenotypic information using limited sample quantity.

Язык: Английский

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Lymphocyte Subset Imbalance in Cardiometabolic Diseases: Are T Cells the Missing Link?

International Journal of Molecular Sciences, Год журнала: 2025, Номер 26(3), С. 868 - 868

Опубликована: Янв. 21, 2025

Cardiometabolic and cardiovascular diseases (CVDs) remain the leading cause of death worldwide, with well-established risk factors such as smoking, obesity, diabetes contributing to plaque formation chronic inflammation. However, emerging evidence suggests that immune system plays a more significant role in development progression CVD than previously thought. Specifically, finely tuned regulation lymphocyte subsets governs post-injury inflammation tissue damage resolution orchestrates functions activation endothelial cells, cardiomyocytes, fibroblasts CVD-associated lesions (e.g., atherosclerotic plaques). A deeper understanding system’s involvement will provide new insights into disease biology uncover novel therapeutic targets aimed at re-establishing homeostasis. In this review, we summarize current state knowledge on distribution CVD, including atherosclerosis, diabetes, hypertension, myocardial infarction, stroke.

Язык: Английский

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Key Considerations on CITE‐Seq for Single‐Cell Multiomics

PROTEOMICS, Год журнала: 2025, Номер unknown

Опубликована: Фев. 9, 2025

CITE-Seq (Cellular Indexing of Transcriptomes and Epitopes by Sequencing) is an advanced single-cell sequencing method to profile both gene expression protein abundance simultaneously in individual cells using mRNA techniques alongside antibody-derived tags (ADTs), for detection. The characterization the transcriptome proteome from same provides a powerful multiomic approach understanding mechanisms complex biological processes. This review focuses on workflow microwell-based analysis system as example key considerations staining with ADTs. By highlighting critical information library preparation, sequencing, data analysis, this practical guide which perform comprehensive workflow.

Язык: Английский

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Cytometry at the Intersection of Metabolism and Epigenetics in Lymphocyte Dynamics

Cytometry Part A, Год журнала: 2025, Номер unknown

Опубликована: Март 7, 2025

Landmark studies at the turn of century revealed metabolic reprogramming as a driving force for lymphocyte differentiation and function. In addition to changes, differentiating lymphocytes must remodel their epigenetic landscape properly rewire gene expression. Recent discoveries have shown that shifts can shape fate by altering state, bringing together these two areas inquiry. The ongoing evolution high-dimensional cytometry has enabled increasingly comprehensive analyses landscapes in transcend technical limitations past. Here, we review recent insights into interplay between metabolism epigenetics how its dysregulation lead immunological dysfunction disease. We also discuss latest advances anticipate will advance future work this area.

Язык: Английский

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OMIP‐112: 42‐Parameter (40‐Color) Spectral Flow Cytometry Panel for Comprehensive Immunophenotyping of Human Peripheral Blood Leukocytes

Cytometry Part A, Год журнала: 2025, Номер unknown

Опубликована: Март 17, 2025

ABSTRACT Profiling the human immune system is essential to understanding its role in disease, but it requires advanced and novel technologies. Spectral flow cytometry (SFM) enables deep profiling at single‐cell level. It able detect many fluorescent parameters within one measurement; therefore, vastly useful when patient material limited. However, designing analyzing these high‐dimensional datasets remains complex. We optimized a 42‐parameter panel (40 commercially available fluorochromes, stacked fluorochrome an autofluorescent (AF) parameter) that identification of innate adaptive cell composition. first on peripheral whole blood, outperforms other published OMIPs 40 colors terms complexity. With this panel, we are identify neutrophils, basophils, eosinophils, monocytes, dendritic cells, CD4 T CD8 regulatory mucosal‐associated invariant (MAIT) γδ B NK lymphoid cells (ILCs). Furthermore, with utilization co‐stimulatory, checkpoint, activation, homing, maturation markers, deeper phenotyping. Within measurement, more than 80 distinct subsets were identified by FlowSOM annotated manually. In conclusion, SFM aim generate profiles understand disease monitor therapy response.

Язык: Английский

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Development of a Spectral Flow Cytometry Analysis Pipeline for High-dimensional Immune Cell Characterization

The Journal of Immunology, Год журнала: 2024, Номер 213(11), С. 1713 - 1724

Опубликована: Окт. 25, 2024

Abstract Flow cytometry is used for immune cell analysis composition and function. Spectral flow allows high-dimensional of cells, overcoming limitations conventional cytometry. However, analyzing data from large Ab panels challenging using traditional biaxial gating strategies. We present, to our knowledge, a novel pipeline improve spectral employ this method identify rare T populations in aging. isolated splenocytes young (2–3 mo old) aged (18–19 female C57BL/6N mice then stained these with panel 20 fluorescently labeled Abs. performed processing Python within Jupyter Notebook environment perform dimensionality reduction, batch correction, unsupervised clustering, differential expression analysis. Our 3,776,804 cells 11 spleens revealed 35 distinct clusters identified by surface marker expression. observed significant differences between mice, enriched one age group over the other. Naive, effector memory, central memory CD8+ CD4+ subsets exhibited age-associated changes abundance also demonstrate utility human PBMC dataset that 50–fluorescent color panel. By leveraging methods, we provide insights into aging process. This approach offers robust easily implemented may facilitate discovery therapeutic targets age-related dysfunction.

Язык: Английский

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Development of a Spectral Flow Cytometry Analysis Pipeline for High-Dimensional Immune Cell Characterization

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Июнь 22, 2024

Flow cytometry is a widely used technique for immune cell analysis, offering insights into composition and function. Spectral flow allows high-dimensional analysis of cells, overcoming limitations conventional cytometry. However, analyzing data from large antibody panels can be challenging using traditional bi-axial gating strategies. Here, we present novel pipeline designed to improve spectral We employ this method identify rare T populations in aging. isolated splenocytes young (2-3 months) aged (18-19 female mice then stained these with panel 20 fluorescently labeled antibodies. was performed, followed by processing Python within Jupyter Notebook environment perform batch correction, unsupervised clustering, dimensionality reduction, differential expression analysis. Our 3,776,804 cells 11 spleens revealed 34 distinct clusters identified surface marker expression. observed significant differences between mice, certain enriched one age group over the other. Naïve, effector memory, central memory CD8

Язык: Английский

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