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

Scientific Reports, Год журнала: 2025, Номер 15(1)

Опубликована: Янв. 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.

Язык: Английский

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Applications of single-cell technologies in drug discovery for tumor treatment

iScience, Год журнала: 2024, Номер 27(8), С. 110486 - 110486

Опубликована: Июль 11, 2024

Язык: Английский

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Flexible and stretchable bioelectronics for organoids

Med-X, Год журнала: 2025, Номер 3(1)

Опубликована: Фев. 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

Язык: Английский

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Single-cell RNA sequencing reveals the impaired epidermal differentiation and pathological microenvironment in diabetic foot ulcer

Burns & Trauma, Год журнала: 2025, Номер unknown

Опубликована: Фев. 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.

Язык: Английский

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Recent progress in single-cell transcriptomic studies in plants

Plant Biotechnology Reports, Год журнала: 2025, Номер unknown

Опубликована: Апрель 3, 2025

Язык: Английский

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From whole bodies to single cells: A guide to transcriptomic approaches for ecology and evolutionary biology

Molecular Ecology, Год журнала: 2024, Номер unknown

Опубликована: Июнь 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.

Язык: Английский

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Single-Cell Omics for Transcriptome CHaracterization (SCOTCH): isoform-level characterization of gene expression through long-read single-cell RNA sequencing

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

Опубликована: Апрель 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.

Язык: Английский

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Single-Cell Sequencing Technology in Ruminant Livestock: Challenges and Opportunities

Current Issues in Molecular Biology, Год журнала: 2024, Номер 46(6), С. 5291 - 5306

Опубликована: Май 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.

Язык: Английский

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Tackling neurodegeneration in vitro with omics: a path towards new targets and drugs

Frontiers in Molecular Neuroscience, Год журнала: 2024, Номер 17

Опубликована: Июнь 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

Язык: Английский

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The shared role of neutrophils in ankylosing spondylitis and ulcerative colitis

Genes and Immunity, Год журнала: 2024, Номер 25(4), С. 324 - 335

Опубликована: Июль 25, 2024

Язык: Английский

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