Advancements in single-cell RNA sequencing and spatial transcriptomics: transforming biomedical research

Acta Biochimica Polonica, Journal Year: 2025, Volume and Issue: 72

Published: Feb. 5, 2025

In recent years, significant advancements in biochemistry, materials science, engineering, and computer-aided testing have driven the development of high-throughput tools for profiling genetic information. Single-cell RNA sequencing (scRNA-seq) technologies established themselves as key dissecting sequences at level single cells. These reveal cellular diversity allow exploration cell states transformations with exceptional resolution. Unlike bulk sequencing, which provides population-averaged data, scRNA-seq can detect subtypes or gene expression variations that would otherwise be overlooked. However, a limitation is its inability to preserve spatial information about transcriptome, process requires tissue dissociation isolation. Spatial transcriptomics pivotal advancement medical biotechnology, facilitating identification molecules such their original context within sections single-cell level. This capability offers substantial advantage over traditional techniques. valuable insights into wide range biomedical fields, including neurology, embryology, cancer research, immunology, histology. review highlights approaches, technological developments, associated challenges, various techniques data analysis, applications disciplines microbiology, neuroscience, reproductive biology, immunology. It critical role characterizing dynamic nature individual

Language: Английский

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Revealing microRNA regulation in single cells

Trends in Genetics, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 1, 2025

MicroRNAs (miRNAs) are key regulators of gene expression and control cellular functions in physiological pathophysiological states. miRNAs play important roles disease, stress, development, now being investigated for therapeutic approaches. Alternative processing during biogenesis results the generation miRNA isoforms (isomiRs) which further diversify regulation. Single-cell RNA-sequencing (scsRNA-seq) technologies, together with computational strategies, enable exploration miRNAs, isomiRs, interacting RNAs at level. By integration other miRNA-associated single-cell modalities, can be resolved different stages In this review we discuss (i) experimental assays that measure isomiR abundances, (ii) methods their analysis to investigate mechanisms post-transcriptional

Language: Английский

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Bioinformatics perspectives on transcriptomics: A comprehensive review of bulk and single‐cell RNA sequencing analyses

Quantitative Biology, Journal Year: 2025, Volume and Issue: 13(2)

Published: Jan. 6, 2025

Abstract The transcriptome, the complete set of RNA molecules within a cell, plays critical role in regulating physiological processes. advent sequencing (RNA‐seq) facilitated by Next Generation Sequencing (NGS) technologies, has revolutionized transcriptome research, providing unique insights into gene expression dynamics. This powerful strategy can be applied at both bulk tissue and single‐cell levels. Bulk RNA‐seq provides profile sample. Conversely, (scRNA‐seq) offers resolution cellular level, allowing uncovering heterogeneity, identification rare cell types, distinction between distinct populations. As computational tools, machine learning techniques, NGS platforms continue to evolve, field research is poised for significant advancements. Therefore, fully harness this potential, comprehensive understanding scRNA‐seq including their advantages, limitations, considerations, crucial. review systematic comparison processes involved scRNA‐seq, highlighting fundamental principles, applications, strengths, while outlining future directions research.

Language: Английский

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Comparison of spatial transcriptomics technologies using tumor cryosections

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: April 5, 2024

Abstract Background Spatial transcriptomics ( ST ) technologies are revolutionizing our understanding of intra-tumor heterogeneity and the tumor microenvironment by revealing single-cell molecular profiles within their spatial tissue context. The rapid evolution methods, each with unique features, presents a challenge in selecting most appropriate technology for specific research objectives. Here, we compare four imaging-based methods – RNAscope HiPlex, Molecular Cartography, MERFISH/Merscope, Xenium together sequencing-based (Visium). These were used to study cryosections medulloblastoma extensive nodularity (MBEN), chosen its distinct microanatomical features. Results Our analysis reveals that automated well suited delineating intricate MBEN microanatomy, capturing cell-type-specific transcriptome profiles. We devise approaches sensitivity specificity different attributes guide method selection based on aim. Furthermore, demonstrate how reimaging slides after can markedly improve cell segmentation accuracy integrate additional transcript protein readouts expand analytical possibilities depth insights. Conclusions This highlights key distinctions between various provides set parameters evaluating performance. findings aid informed choice delineate enhancing resolution breadth transcriptomic analyses, thereby contributing advancing applications solid research.

Language: Английский

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Advances in long-read single-cell transcriptomics

Human Genetics, Journal Year: 2024, Volume and Issue: 143(9-10), P. 1005 - 1020

Published: May 24, 2024

Abstract Long-read single-cell transcriptomics (scRNA-Seq) is revolutionizing the way we profile heterogeneity in disease. Traditional short-read scRNA-Seq methods are limited their ability to provide complete transcript coverage, resolve isoforms, and identify novel transcripts. The protocols developed for long-read sequencing platforms overcome these limitations by enabling characterization of full-length techniques initially suffered from comparatively poor accuracy compared short read scRNA-Seq. However, with improvements accuracy, accessibility, cost efficiency, long-reads gaining popularity field This review details advances scRNA-Seq, an emphasis on library preparation downstream bioinformatics analysis tools.

Language: Английский

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Applications of Nanopore sequencing in precision cancer medicine

International Journal of Cancer, Journal Year: 2024, Volume and Issue: 155(12), P. 2129 - 2140

Published: July 19, 2024

Oxford Nanopore Technologies sequencing, also referred to as stands at the forefront of a revolution in clinical genetics, offering potential for rapid, long read, and real-time DNA RNA sequencing. This technology is currently making sequencing more accessible affordable. In this comprehensive review, we explore its regarding precision cancer diagnostics treatment. We encompass critical analysis cases where was successfully applied identify point mutations, splice variants, gene fusions, epigenetic modifications, non-coding RNAs, other pivotal biomarkers that defined subsequent treatment strategies. Additionally, address challenges applications discuss current efforts overcome them.

Language: Английский

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Single-cell RNA sequencing in stroke and traumatic brain injury: Current achievements, challenges, and future perspectives on transcriptomic profiling

Journal of Cerebral Blood Flow & Metabolism, Journal Year: 2024, Volume and Issue: unknown

Published: Dec. 9, 2024

Single-cell RNA sequencing (scRNA-seq) is a high-throughput transcriptomic approach with the power to identify rare cells, discover new cellular subclusters, and describe novel genes. scRNA-seq can simultaneously reveal dynamic shifts in phenotypes heterogeneities subtypes. Since publication of first protocol on 2009, this evolving technology has continued improve, through use cell-specific barcodes, adoption droplet-based systems, development advanced computational methods. Despite induction stress response during tissue dissociation process, remains popular technology, commercially available methods have been applied brain. Recent advances spatial transcriptomics now allow researcher capture positional context transcriptional activity, strengthening our knowledge organization cell-cell interactions spatially intact tissues. A combination data proteomic, metabolomic, or chromatin accessibility promising direction for future research. Herein, we provide an overview workflow, analyses methods, pros cons technology. We also summarize latest achievements stroke acute traumatic brain injury, applications transcriptomics.

Language: Английский

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Advancing Single-Cell Detection of Senescent Cells: Laboratory Methods and Clinical Applications

OBM Geriatrics, Journal Year: 2025, Volume and Issue: 09(02), P. 1 - 32

Published: April 14, 2025

Cellular senescence (aging) is a physiological process that plays role in tissue remodeling, wound healing, and embryogenesis. Prolonged of cells can have detrimental effects trigger secretory phenotype (SASP, senescence-associated phenotype), degenerative disorders, cancer, age-related diseases. Suitable biomarkers range different laboratory methods are used to investigate these complex relationships vitro vivo. Since universal biomarker for cell has not yet been identified, numerous identify senescent cell. The detection quantification their SASP provide the basis targeted treatment patient. In parallel, single-cell analysis also required quantitative assessment therapy result. Depending on facilities performing analysis, wide available. this review, we general overview accessible techniques such as immunohistochemistry using microscopy automated flow cytometry introduce new possibilities by modern like mass spectrometry or genetic method single cells. focus here use routine laboratories. classical with enzyme immunoassays, measurement products (IL-6, IL-8), part work. This review discusses ideas visualisation clinical patient data gerontology. An outlook potential future optimization improve rejuvenate status patients cellular organ-specific level discussed.

Language: Английский

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Single-cell RNA Sequencing in the Study of Human Retinal Organoids

Experimental Eye Research, Journal Year: 2025, Volume and Issue: 256, P. 110417 - 110417

Published: May 2, 2025

Language: Английский

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Allometry of cell types in planarians by single-cell transcriptomics

Science Advances, Journal Year: 2025, Volume and Issue: 11(19)

Published: May 7, 2025

Allometry explores the relationship between an organism’s body size and its various components, offering insights into ecology, physiology, metabolism, disease. The cell is basic unit of biological systems, yet study cell-type allometry remains relatively unexplored. Single-cell RNA sequencing (scRNA-seq) provides a promising tool for investigating allometry. Planarians, capable growing degrowing following allometric scaling rules, serve as excellent model these studies. We used scRNA-seq to examine in asexual planarians different sizes, revealing that they consist same types but varying proportions. Notably, gut basal cells are most responsive changes size, suggesting role energy storage. capture regulated gene modules distinct response size. This research sheds light on molecular cellular aspects underscores utility investigations.

Language: Английский

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