Multi Omics Applications in Biological Systems

Current Issues in Molecular Biology, Год журнала: 2024, Номер 46(6), С. 5777 - 5793

Опубликована: Июнь 11, 2024

Traditional methodologies often fall short in addressing the complexity of biological systems. In this regard, system biology omics have brought invaluable tools for conducting comprehensive analysis. Current sequencing capabilities revolutionized genetics and genomics studies, as well characterization transcriptional profiling dynamics several species sample types. Biological systems experience complex biochemical processes involving thousands molecules. These occur at different levels that can be studied using mass spectrometry-based (MS-based) analysis, enabling high-throughput proteomics, glycoproteomics, glycomics, metabolomics, lipidomics Here, we present most up-to-date techniques utilized completion Additionally, include some interesting examples applicability multi to a variety

Язык: Английский

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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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A single-cell RNA sequencing dataset of peripheral blood cells in long COVID patients on herbal therapy

Scientific Data, Год журнала: 2025, Номер 12(1)

Опубликована: Янв. 30, 2025

Язык: Английский

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Comprehensive review on single-cell RNA sequencing: A new frontier in Alzheimer's disease research

Ageing Research Reviews, Год журнала: 2024, Номер 100, С. 102454 - 102454

Опубликована: Авг. 12, 2024

Язык: Английский

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Performance comparison of high throughput single-cell RNA-Seq platforms in complex tissues

Heliyon, Год журнала: 2024, Номер 10(17), С. e37185 - e37185

Опубликована: Авг. 30, 2024

Single-cell transcriptomics has emerged as the preferred tool to define cell identity through analysis of gene expression signatures. However, there are limited studies that have comprehensively compared performance different scRNAseq systems in complex tissues. Here, we present a systematic comparison two well-established high throughput 3'-scRNAseq platforms: 10× Chromium and BD Rhapsody, using tumours diversity. Our experimental design includes both fresh artificially damaged samples from same tumours, which also provides comparable dataset examine their under challenging conditions. The metrics used this study consist sensitivity, mitochondrial content, reproducibility, clustering capabilities, type representation ambient RNA contamination. These analyses showed Rhapsody similar while highest content. Interestingly, found detection biases between platforms, including lower proportion endothelial myofibroblast cells sensitivity granulocytes for Chromium. Moreover, source noise was plate-based droplet-based platforms. In conclusion, our reported platform differential should be considered selection method during designs.

Язык: Английский

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Tumor cells that resist neutrophil anticancer cytotoxicity acquire a prometastatic and innate immune escape phenotype

Cellular and Molecular Immunology, Год журнала: 2025, Номер unknown

Опубликована: Март 28, 2025

In the tumor host, neutrophils may exhibit protumor or antitumor activity. It is hypothesized that in response to host-derived therapy-induced factors, adopt diverse functional states ultimately execute these differential functions. Here, we provide an alternative scenario which of individual cell population determines overall versus outcome neutrophil‒tumor interactions. Experimentally, show human neutrophils, are sequentially stimulated with bacteria and secreted factors from cells, kill a certain proportion target cells. However, majority cells remained resistant this neutrophil-mediated killing underwent functional, phenotypic transcriptomic switch was reminiscent partial epithelial‒to-mesenchymal transition. This biological associated physical escape NK-mediated resulted enhanced metastasis lymph nodes preclinical orthotopic mouse model. Mechanistically, identified antimicrobial neutrophil granule proteins elastase (NE) matrix metalloprotease-9 (MMP-9) as molecular mediators switch. We validated data patients head neck cancer bacterially colonized intratumoral niches were enriched for mesenchymal expressing NE MMP-9. Our reveal parallel execution cytotoxic prometastatic activity by activated identify MMP-9 node metastasis. The mechanism explains dichotomy tumor-associated at level has implications superinfected cancers dysbiotic microenvironment.

Язык: Английский

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Human genital dendritic cell heterogeneity confers differential rapid response to HIV-1 exposure

Frontiers in Immunology, Год журнала: 2024, Номер 15

Опубликована: Окт. 25, 2024

Dendritic cells (DCs) play critical roles in HIV pathogenesis and require further investigation the female genital tract, a main portal of entry for infection. Here we characterized DC populations at single cell level how subsets respond to immediately following exposure. We found that CD11c

Язык: Английский

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Profiling low-mRNA content cells in complex human tissues using BD Rhapsody single-cell analysis

STAR Protocols, Год журнала: 2024, Номер 5(4), С. 103475 - 103475

Опубликована: Дек. 1, 2024

Язык: Английский

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Copper chelation redirects neutrophil function to enhance anti-GD2 antibody therapy in neuroblastoma

Nature Communications, Год журнала: 2024, Номер 15(1)

Опубликована: Дек. 12, 2024

Abstract Anti-disialoganglioside (GD2) antibody therapy has provided clinical benefit to patients with neuroblastoma however efficacy is likely impaired by the immunosuppressive tumor microenvironment. We have previously defined a link between intratumoral copper levels and immune evasion. Here, we report that adjuvant chelation potentiates anti-GD2 confer durable control in immunocompetent models of neuroblastoma. Mechanistic studies reveal creates an immune-primed microenvironment through enhanced infiltration activity Fc-receptor-bearing cells, specifically neutrophils which are emerging as key effectors therapy. Moreover, sequestration attenuates neutrophil function can be successfully reversed using increase pro-inflammatory effector functions. Importantly, repurpose clinically approved chelating agent Cuprior non-toxic, efficacious immunomodulatory strategy. Collectively, our findings provide evidence for testing enhance improve outcomes

Язык: Английский

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Comparison of Fixed Single Cell RNA-seq Methods to Enable Transcriptome Profiling of Neutrophils in Clinical Samples

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

Опубликована: Авг. 17, 2024

Summary Monitoring neutrophil gene expression is a powerful tool for understanding disease mechanisms, developing new diagnostics, therapies and optimizing clinical trials. Neutrophils are sensitive to the processing, storage transportation steps that involved in sample analysis. This study first evaluate capabilities of technologies from 10X Genomics, PARSE Biosciences, HIVE (Honeycomb Biotechnologies) generate high-quality RNA data human blood-derived neutrophils. Our comparative analysis shows all methods produced high quality data, importantly capturing transcriptomes FLEX cell populations particular showed close concordance with flow cytometry data. Here, we establish reliable single-cell sequencing workflow neutrophils trials: offer guidelines on collection preserve demonstrate how each method performs practice.

Язык: Английский

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