Spatial biology – unravelling complexity within the glioblastoma microenvironment

Trends in Molecular Medicine, Год журнала: 2025, Номер unknown

Опубликована: Фев. 1, 2025

HighlightsThe ability to understand molecular differences at a single cell level, and with increasing granularity, through spatial profiling is starting unravel the complexity of glioblastoma tumour microenvironment (TME).Identifying variations in distribution different types providing novel insights into biology leading identification TME-based subtypes.Greater understanding relationships between types, rare, but biologically important, states identifying new biomarkers for predicting an individual's response treatment suggesting resistance mechanisms.AbstractThe advent refinement state-of-the-art technologies have facilitated analysis that combines advantages high-throughput techniques preserve tissue architecture. This combination cellular phenotyping retained context provides much greater interactions within (TME). For glioblastoma, its significant intra-tumoural heterogeneity, plasticity, complex TME, appreciating these patterns may prove key improving patient outcomes. review examines advances techniques, discusses how methodologies are being applied study explores information improves TME. Ultimately, it this will accelerate more effective treatments glioblastoma.

Язык: Английский

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A review of advances in in vitro RNA preparation by ssRNAP

International Journal of Biological Macromolecules, Год журнала: 2025, Номер 304, С. 141002 - 141002

Опубликована: Фев. 12, 2025

Язык: Английский

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Divergence in cellular markers observed in single-cell transcriptomics datasets between cultured primary trabecular meshwork cells and tissues

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

Опубликована: Фев. 14, 2025

Abstract The trabecular meshwork within the outflow apparatus is critical in maintaining intraocular pressure homeostasis. In vitro studies employing primary cell cultures of human (hTM) have conventionally served as surrogates for investigating pathobiology TM dysfunction. Despite its abundant use, translation outcomes from to ex vivo and/or remains a challenge. Given heterogeneity, performing single-cell RNA sequencing comparing hTM tissue may provide important insights on cellular identity and translatability, such an approach has not been reported before. this study, we assembled total 14 samples across passages 1–4, including 4 individuals diagnosed with glaucoma. This dataset offers comprehensive transcriptomic resource scRNA-seq data study global changes gene expression comparison cells situ . We performed extensive preprocessing quality control, allowing research community access utilize public resource.

Язык: Английский

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Single-cell genomics and spatial transcriptomics in islet transplantation for diabetes treatment: advancing towards personalized therapies

Frontiers in Immunology, Год журнала: 2025, Номер 16

Опубликована: Фев. 20, 2025

Diabetes mellitus (DM) is a global health crisis affecting millions, with islet transplantation emerging as promising treatment strategy to restore insulin production. This review synthesizes the current research on single-cell and spatial transcriptomics in context of transplantation, highlighting their potential revolutionize DM management. Single-cell RNA sequencing, offers detailed look into diversity functionality within grafts, identifying specific cell types states that influence graft acceptance function. Spatial complements this by mapping gene expression tissue's context, crucial for understanding microenvironment surrounding transplanted islets interactions host tissues. The integration these technologies comprehensive view cellular microenvironments, elucidating mechanisms underlying function, survival, rejection. instrumental developing targeted therapies enhance performance patient outcomes. emphasizes significance avenues informing clinical practices improving outcomes patients through more effective strategies. Future directions include application personalized medicine, developmental biology, regenerative predict disease progression responses. Addressing ethical technical challenges will be successful implementation integrated approaches practice, ultimately enhancing our ability manage improve quality life.

Язык: Английский

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Spatial transcriptomics in autoimmune rheumatic disease: potential clinical applications and perspectives

Inflammation and Regeneration, Год журнала: 2025, Номер 45(1)

Опубликована: Фев. 20, 2025

Spatial transcriptomics is a cutting-edge technology that analyzes gene expression at the cellular level within tissues while integrating spatial location information. This concept, which combines high-plex RNA sequencing with data, emerged in early 2010s. has rapidly expanded development of technologies such as situ hybridization, sequencing, barcoding, and microdissection-based methods. Each technique offers advanced mapping resolution precise assessments single-cell level. Over past decade, use on clinical samples enabled researchers to identify expressions specific diseased foci, significantly enhancing our understanding interactions disease processes. In field rheumatology, complex elusive pathophysiology diseases rheumatoid arthritis, systemic lupus erythematosus, Sjögren's syndrome remains challenge for personalized treatment. provides insights into how different cell populations interact synovial tissue, kidneys, salivary glands. review summarizes current autoimmune rheumatic diseases, focusing immune distribution tissues. We also explore potential from perspective discuss possibilities translating this bedside.

Язык: Английский

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Integration of single-nuclei and spatial transcriptomics to decipher tumor phenotype predictive of relapse-free survival in Wilms tumor

Frontiers in Immunology, Год журнала: 2025, Номер 16

Опубликована: Март 3, 2025

Background Wilms tumor (WT) is the most common childhood renal malignancy, with recurrence linked to poor prognosis. Identifying molecular features of phenotypes that drive and discovering novel targets are crucial for improving treatment strategies enhancing patient outcomes. Methods Single-nuclei RNA sequencing (snRNA-seq), spatial transcriptomics (ST), bulk RNA-seq, mutation/copy number data were curated from public databases. The Seurat package was used process snRNA-seq ST data. Scissor analysis applied identify subpopulations associated relapse-free survival (RFS). Univariate Cox LASSO analyses utilized reduce features. A prognostic ensemble machine learning model developed. Immunohistochemistry validate expression key in tissues. CellChat Commot infer cellular interactions. PERCEPTION computational pipeline predict response cells chemotherapy targeted therapies. Results By integrating RNA-seq data, we identified a subtype Scissor+ RFS, predominantly derived cap mesenchyme-like blastemal fibroblast-like subgroups. These displayed nephron progenitor signatures cancer stem cell markers. constructed based on signature accurately RFS. TGFA as significant feature this validated by immunohistochemistry. Cellular communication revealed strong associations between cancer-associated fibroblasts (CAFs) through IGF, SLIT, FGF, PDGF pathways. primarily located immune-desert niche surrounded CAFs. Despite reduced responsiveness conventional chemotherapy, sensitive EGFR inhibitors, providing insights into clinical intervention WT patients at high risk recurrence. Conclusion This study relapse-associated resembling cells, residing niches interactions proposed could relapse, offering promising method stratification. Targeting these combination may provide potential therapeutic strategy patients.

Язык: Английский

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From morphology to single-cell molecules: high-resolution 3D histology in biomedicine

Molecular Cancer, Год журнала: 2025, Номер 24(1)

Опубликована: Март 3, 2025

Язык: Английский

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Expression of angiogenic factors in the mammalian senescent cell sustaining Trichinella spp. muscle larvae

Histochemistry and Cell Biology, Год журнала: 2025, Номер 163(1)

Опубликована: Март 3, 2025

Язык: Английский

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Identification and comparison of orthologous cell types from primate embryoid bodies shows limits of marker gene transferability

Опубликована: Март 24, 2025

The identification of cell types remains a major challenge. Even after decade single-cell RNA sequencing (scRNA-seq), reasonable type annotations almost always include manual non-automated steps. orthologous across species complicates matters even more, but at the same time strengthens confidence in assignment. Here, we generate and analyze dataset consisting embryoid bodies (EBs) derived from induced pluripotent stem cells (iPSCs) four primate species: humans, orangutans, cynomolgus, rhesus macaques. This kind data includes continuum developmental types, multiple batch effects (i.e. individuals) uneven compositions hence poses many challenges. We developed semi-automated computational pipeline combining classification marker based cluster annotation to identify primates. approach enabled investigation cross-species conservation gene expression. Consistent with previous studies, our confirm that broadly expressed genes are more conserved than type-specific genes, raising question how - inherently are. Our analyses reveal human less effective macaques vice versa, highlighting limited transferability markers species. Overall, study advances species, provides well-curated reference for future vitro studies informs

Язык: Английский

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Identification and comparison of orthologous cell types from primate embryoid bodies shows limits of marker gene transferability

Опубликована: Март 24, 2025

The identification of cell types remains a major challenge. Even after decade single-cell RNA sequencing (scRNA-seq), reasonable type annotations almost always include manual non-automated steps. orthologous across species complicates matters even more, but at the same time strengthens confidence in assignment. Here, we generate and analyze dataset consisting embryoid bodies (EBs) derived from induced pluripotent stem cells (iPSCs) four primate species: humans, orangutans, cynomolgus, rhesus macaques. This kind data includes continuum developmental types, multiple batch effects (i.e. individuals) uneven compositions hence poses many challenges. We developed semi-automated computational pipeline combining classification marker based cluster annotation to identify primates. approach enabled investigation cross-species conservation gene expression. Consistent with previous studies, our confirm that broadly expressed genes are more conserved than type-specific genes, raising question how - inherently are. Our analyses reveal human less effective macaques vice versa, highlighting limited transferability markers species. Overall, study advances species, provides well-curated reference for future vitro studies informs

Язык: Английский

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