High-throughput gene expression analysis with TempO-LINC sensitively resolves complex brain, lung and kidney heterogeneity at single-cell resolution DOI Creative Commons

Dennis J. Eastburn,

Kevin S. White,

Nathan D. Jayne

et al.

Scientific Reports, Journal Year: 2024, Volume and Issue: 14(1)

Published: Dec. 28, 2024

Abstract We report the development and performance of a novel genomics platform, TempO-LINC, for conducting high-throughput transcriptomic analysis on single cells nuclei. TempO-LINC works by adding cell-identifying molecular barcodes onto highly selective high-sensitivity gene expression probes within fixed cells, without having to first generate cDNA. Using an instrument-free combinatorial indexing approach, all same cell receive identical barcode, enabling reconstruction single-cell profiles across as few several hundred up 100,000 + per sample. The approach is easily scalable based number rounds barcoding performed; however, experiments reported in this study, assay utilized over 5.3 million unique barcodes. offers robust protocol fixing banking displays detection from multiple diverse sample types. show that has multiplet rate less than 1.1% capture ~ 50%. Although can accurately profile whole transcriptome (19,683 human, 21,400 mouse 21,119 rat genes), it be targeted measure only actionable/informative genes pathways interest – thereby reducing sequencing requirements. In we applied transcriptomes more 90,000 species types, including nuclei lung, kidney brain tissues. data demonstrated ability identify annotate 50 populations positively correlate type-specific markers them. new technology ideal large-scale applications/studies with high quality.

Language: Английский

Identification of a novel disulfidptosis-related gene signature in osteoarthritis using bioinformatics analysis and experimental validation DOI Creative Commons

Mingjie Wei,

Xiangwen Shi,

Wenbao Tang

et al.

Scientific Reports, Journal Year: 2025, Volume and Issue: 15(1)

Published: Jan. 8, 2025

Osteoarthritis (OA) is a degenerative bone disease characterized by the destruction of joint cartilage and synovial inflammation, involving intricate immune regulation processes. Disulfidptosis, novel form programmed cell death, has recently been identified; however, effects roles disulfidptosis-related genes (DR-DEGs) in OA remain unclear. We obtained six datasets from GEO database, using four as training sets two validation sets. Differential expression analysis was employed to identify DR-DEGs, unique molecular subtypes were constructed based on these DR-DEGs. Subsequently, microenvironment patients comprehensively analyzed "CIBERSORT" algorithm for infiltration. Various machine learning algorithms utilized screen characteristic nomogram models ROC curves built genes. The scRNA dataset (GSE169454) used classify chondrocytes samples into distinct types, further exploring gene distribution correlation DR-DEGs with specific subpopulations. Moreover, levels validated through rat models. In our study, we identified 10 significant differences within samples. Based recognized (cluster 1 2). ZNF484 NDUFS1 found be significantly overexpressed subtype 1, while infiltration abundance activated mast cells markedly elevated 2. observed proportions 11 types between control samples, 9 demonstrating substantial correlations levels. Further revealed that SLC3A2 NDUFC1 predominantly expressed preHTC subpopulation. All exhibited notably higher EC subpopulation across various types. proportion subgroups high increased, mainly enriching pathways related such IL-17 signaling pathway TGF-beta pathway. Using learning, which, combination models, demonstrated promising performance diagnosis OA. Additionally, vivo confirmed elevation PPM1F This study potential biomarkers classification provided preliminary understanding their role microenvironment. However, experimental clinical studies are required validate diagnostic value therapeutic potential.

Language: Английский

Citations

1
Applications of single-cell technologies in drug discovery for tumor treatment DOI Creative Commons
Bingyu Liu, Shunfeng Hu, Xin Wang

et al.

iScience, Journal Year: 2024, Volume and Issue: 27(8), P. 110486 - 110486

Published: July 11, 2024

Language: Английский

Citations

4
Flexible and stretchable bioelectronics for organoids DOI Creative Commons

Jaeyong Lee,

Jia Liu

Med-X, Journal Year: 2025, Volume and Issue: 3(1)

Published: Feb. 1, 2025

Abstract Organoids have gained significant interest due to their ability recapitulate the structural, molecular, and functional complexity of corresponding organs. While methods been developed characterize benchmark organoid structural molecular properties, capturing development maturation organoids remains challenging. To address this, multifunctional bioelectronics for interfacing with has actively pursued. However, conventional electronics face limitations in achieving recording control across entire three-dimensional (3D) volume a long-term stable manner large morphological cellular composition changes during development. In this review, we first discuss application interfacing. We then focus on flexible stretchable designed create organoid/electronics hybrids chronically interfaces. also review recent advancements charting multimodal cell activities throughout Furthermore, explore integration other characterization modalities comprehensive cells within 3D tissues. Finally, potential integrating artificial intelligence into system through embedded electronics, harnessing biosymbiotic computational systems. These could provide valuable tools characterizing maturation, establishing patient-specific models, developing therapeutic opportunities, exploring novel strategies. Graphical abstract

Language: Английский

Citations

0
Single-cell RNA sequencing reveals the impaired epidermal differentiation and pathological microenvironment in diabetic foot ulcer DOI Creative Commons
Y. Liu, Peng Wang, Jingting Li

et al.

Burns & Trauma, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 17, 2025

Diabetic foot ulcer (DFU) is one of the most common and complex complications diabetes, but underlying pathophysiology remains unclear. Single-cell RNA sequencing (scRNA-seq) has been conducted to explore novel cell types or molecular profiles DFU from various perspectives. This study aimed comprehensively analyze potential mechanisms impaired re-epithelization in a single-cell perspective. We scRNA-seq on tissues human normal skin, acute wound, investigate epidermal differentiation pathological microenvironment. Pseudo-time lineage inference analyses revealed distinct states transition trajectories cells under different conditions. Transcription factor analysis regulatory mechanism key subtypes keratinocytes. Cell-cell interaction network between proinflammatory microenvironment cells. Laser-capture microscopy coupled with (LCM-seq) multiplex immunohistochemistry were used validate expression location Our research provided comprehensive map phenotypic dynamic changes that occur during differentiation, alongside corresponding networks DFU. Importantly, we identified two keratinocytes: basal (BC-2) diabetes-associated keratinocytes (DAK) might play crucial roles impairment homeostasis. BC-2 DAK showed marked increase DFU, an inactive state insufficient motivation for differentiation. was involved cellular response apoptosis processes, high TXNIP, IFITM1, IL1R2. Additionally, pro-differentiation transcription factors downregulated indicating process be inhibited associated glucose Furthermore, increased CCL2 + CXCL2+ fibroblasts, VWA1+ vascular endothelial cells, GZMA+CD8+ T detected These wound could regulate fate through TNFSF12-TNFRSF12A, IFNG-IFNGR1/2, IL-1B-IL1R2 pathways, which result persistent inflammation findings offer insights into present therapeutic targets improve care treatment outcomes patients.

Language: Английский

Citations

0
Recent progress in single-cell transcriptomic studies in plants DOI Creative Commons
Yuhan Cho, Ulhas Sopanrao Kadam,

Bogun Park

et al.

Plant Biotechnology Reports, Journal Year: 2025, Volume and Issue: unknown

Published: April 3, 2025

Language: Английский

Citations

0
From whole bodies to single cells: A guide to transcriptomic approaches for ecology and evolutionary biology DOI Creative Commons
Katja M. Hoedjes, Sonja Grath, Nico Posnien

et al.

Molecular Ecology, Journal Year: 2024, Volume and Issue: unknown

Published: June 10, 2024

Abstract RNA sequencing (RNAseq) methodology has experienced a burst of technological developments in the last decade, which opened up opportunities for studying mechanisms adaptation to environmental factors at both organismal and cellular level. Selecting most suitable experimental approach specific research questions model systems can, however, be challenge researchers ecology evolution are commonly faced with choice whether study gene expression variation whole bodies, tissues, and/or single cells. A wide range sometimes polarised opinions exists over is best. Here, we highlight advantages disadvantages each these approaches provide guide help make informed decisions maximise power their study. Using illustrative examples various ecological evolutionary questions, readers through different RNAseq them identify design own projects.

Language: Английский

Citations

3
Single-Cell Omics for Transcriptome CHaracterization (SCOTCH): isoform-level characterization of gene expression through long-read single-cell RNA sequencing DOI Creative Commons
Zhuoran Xu, Hui‐Qi Qu, Joe Chan

et al.

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

Published: April 30, 2024

Recent development involving long-read single-cell transcriptome sequencing (lr-scRNA-Seq) represents a significant leap forward in genomics. With the recent introduction of R10 flowcells by Oxford Nanopore, we propose that previous computational methods designed to handle high error rates are less relevant, and traditional approach using short reads compile "barcode space" (candidate barcode list) de-multiplex long no longer necessary. Instead, should now shift focus on harnessing unique benefits analyze complexity. In this context, introduce comprehensive suite named Single-Cell Omics for Transcriptome CHaracterization (SCOTCH). SCOTCH supports both Nanopore PacBio platforms, is compatible with library preparation protocols from 10X Genomics Parse Biosciences. Through sub-exon identification strategy dynamic thresholding read mapping scores, precisely aligns known isoforms discover novel isoforms, efficiently addressing ambiguous challenges commonly encountered data. By multiple issue probabilistic inference, allows powerful isoform differential transcript usage analysis. Comprehensive simulations real data analyses across platforms (including Bioscience, paired Illumina or technologies R9 flowcells, as well sequencing) demonstrated outperforms existing accuracy, quantification accuracy detection, while also uncovering biological insights complexity at level.

Language: Английский

Citations

2
Single-Cell Sequencing Technology in Ruminant Livestock: Challenges and Opportunities DOI Creative Commons

Avery Lyons,

J. J. Brown,

Kimberly M Davenport

et al.

Current Issues in Molecular Biology, Journal Year: 2024, Volume and Issue: 46(6), P. 5291 - 5306

Published: May 27, 2024

Advancements in single-cell sequencing have transformed the genomics field by allowing researchers to delve into intricate cellular heterogeneity within tissues at greater resolution. While omics are more widely applied model organisms and humans, their use livestock species is just beginning. Studies cattle, sheep, goats already leveraged single-nuclei RNA-seq as well ATAC-seq delineate diversity tissues, track changes cell populations gene expression over developmental stages, characterize immune important for disease resistance resilience. Although challenges exist of this technology ruminant livestock, such precise annotation unique spatial resolution cells a tissue, there vast potential enhance our understanding molecular mechanisms underpinning traits essential healthy productive livestock. This review intends highlight insights gained from published studies goats, particularly those with publicly accessible data. Further, manuscript will discuss opportunities how it may contribute enhanced profitability sustainability animal agriculture future.

Language: Английский

Citations

2
Tackling neurodegeneration in vitro with omics: a path towards new targets and drugs DOI Creative Commons
Caterina Carraro,

Jessica V. Montgomery,

Julien Klimmt

et al.

Frontiers in Molecular Neuroscience, Journal Year: 2024, Volume and Issue: 17

Published: June 17, 2024

Drug discovery is a generally inefficient and capital-intensive process. For neurodegenerative diseases (NDDs), the development of novel therapeutics particularly urgent considering long list late-stage drug candidate failures. Although our knowledge on pathogenic mechanisms driving neurodegeneration growing, additional efforts are required to achieve better ultimately complete understanding pathophysiological underpinnings NDDs. Beyond etiology NDDs being heterogeneous multifactorial, this process further complicated by fact that current experimental models only partially recapitulate major phenotypes observed in humans. In such scenario, multi-omic approaches have potential accelerate identification new or repurposed drugs against multitude underlying One advantage for implementation these overarching tools able disentangle disease states model perturbations through comprehensive characterization distinct molecular layers (i.e., genome, transcriptome, proteome) up single-cell resolution. Because recent advances increasing their affordability scalability, use omics technologies drive nascent, but rapidly expanding neuroscience field. Combined with increasingly advanced vitro models, which benefited from introduction human iPSCs, multi-omics shaping paradigm NDDs, prediction screening. review, we discuss examples, main advantages open challenges targets therapies

Language: Английский

Citations

1
The shared role of neutrophils in ankylosing spondylitis and ulcerative colitis DOI
Tianyou Chen,

Weiming Tan,

Xinli Zhan

et al.

Genes and Immunity, Journal Year: 2024, Volume and Issue: 25(4), P. 324 - 335

Published: July 25, 2024

Language: Английский

Citations

1