Identifying similar populations across independent single cell studies without data integration DOI Creative Commons
Óscar González-Velasco, Malte Simon, Rüstem Yilmaz

et al.

NAR Genomics and Bioinformatics, Journal Year: 2025, Volume and Issue: 7(2)

Published: March 29, 2025

Abstract Supervised and unsupervised methods have emerged to address the complexity of single cell data analysis in context large pools independent studies. Here, we present ClusterFoldSimilarity (CFS), a novel statistical method design quantify similarity between groups across any number datasets, without need for correction or integration. By bypassing these processes, CFS avoids introduction artifacts loss information, offering simple, efficient, scalable solution. This match cells that exhibit conserved phenotypes including different tissues species, multimodal scenario, single-cell RNA-Seq, ATAC-Seq, proteomics, or, more broadly, exhibiting differential abundance effects among cells. Additionally, performs feature selection, obtaining cross-dataset markers similar observed, providing an inherent interpretability relationships populations. To showcase effectiveness our methodology, generated single-nuclei RNA-Seq from motor cortex spinal cord adult mice. using CFS, identified three distinct sub-populations astrocytes on both tissues. includes various visualization interpretation scores

Language: Английский

Three-dimensional genome organization in immune cell fate and function DOI
Sergi Cuartero, Grégoire Stik, Ralph Stadhouders

et al.

Nature reviews. Immunology, Journal Year: 2022, Volume and Issue: 23(4), P. 206 - 221

Published: Sept. 20, 2022

Language: Английский

Citations

33
CD4 + T cells produce GM-CSF and drive immune-mediated glomerular disease by licensing monocyte-derived cells to produce MMP12 DOI
Hans‐Joachim Paust, Ning Song, Donatella De Feo

et al.

Science Translational Medicine, Journal Year: 2023, Volume and Issue: 15(687)

Published: March 15, 2023

GM-CSF in glomerulonephritis Despite being an immune-mediated disease, the contributions of individual immune cell types are not clear. To address this gap knowledge, Paust et al . characterized pathological cells samples from patients with and mice disease. The authors found that CD4+ T producing granulocyte-macrophage colony-stimulating factor (GM-CSF) licensed monocytes to promote disease by matrix metalloproteinase 12 disrupting glomerular basement membrane. Targeting inhibit axis reduced severity mice, implicating cytokine as a potential therapeutic target for glomerulonephritis. —CM

Language: Английский

Citations

16
Dissection and integration of bursty transcriptional dynamics for complex systems DOI
Cheng Gao,

Suriyanarayanan Vaikuntanathan,

Samantha J. Riesenfeld

et al.

Proceedings of the National Academy of Sciences, Journal Year: 2024, Volume and Issue: 121(18)

Published: April 26, 2024

RNA velocity estimation is a potentially powerful tool to reveal the directionality of transcriptional changes in single-cell RNA-sequencing data, but it lacks accuracy, absent advanced metabolic labeling techniques. We developed an approach,

Language: Английский

Citations

5
Machine learning integrative approaches to advance computational immunology DOI Creative Commons
Fabiola Curion, Fabian J. Theis

Genome Medicine, Journal Year: 2024, Volume and Issue: 16(1)

Published: June 11, 2024

Abstract The study of immunology, traditionally reliant on proteomics to evaluate individual immune cells, has been revolutionized by single-cell RNA sequencing. Computational immunologists play a crucial role in analysing these datasets, moving beyond traditional protein marker identification encompass more detailed view cellular phenotypes and their functional roles. Recent technological advancements allow the simultaneous measurements multiple components—transcriptome, proteome, chromatin, epigenetic modifications metabolites—within single including spatial contexts within tissues. This led generation complex multiscale datasets that can include multimodal from same cells or mix paired unpaired modalities. Modern machine learning (ML) techniques for integration “omics” data without need extensive independent modelling each modality. review focuses recent ML integrative approaches applied immunological studies. We highlight importance methods creating unified representation collections, particularly profiling technologies. Finally, we discuss challenges holistic how they will be instrumental development common coordinate framework studies, thereby accelerating research enabling discoveries computational immunology field.

Language: Английский

Citations

5
HTCA: a database with an in-depth characterization of the single-cell human transcriptome DOI Creative Commons
Lu Pan,

Shaobo Shan,

Roman Tremmel

et al.

Nucleic Acids Research, Journal Year: 2022, Volume and Issue: 51(D1), P. D1019 - D1028

Published: Sept. 21, 2022

Abstract Single-cell RNA-sequencing (scRNA-seq) is one of the most used single-cell omics in recent decades. The exponential growth data has immense potential for large-scale integration and in-depth explorations that are more representative study population. Efforts have been made to consolidate published data, yet extensive characterization still lacking. Many focused on raw-data database constructions while others concentrate mainly gene expression queries. Hereby, we present HTCA (www.htcatlas.org), an interactive constructed based ∼2.3 million high-quality cells from ∼3000 scRNA-seq samples comprised phenotype profiles 19 healthy adult matching fetal tissues. provides a one-stop query signatures, transcription factor (TF) activities, TF motifs, receptor–ligand interactions, enriched ontology (GO) terms, etc. across cell types At same time, encompasses splicing variant 16 tissues, spatial transcriptomics 11 ATAC-sequencing (scATAC-seq) 27 Besides, online analysis tools perform major steps typical analysis. Altogether, allows real-time multi-omics phenotypic flexible

Language: Английский

Citations

22
Deconstructing iNKT cell development at single-cell resolution DOI Creative Commons
Thomas Baranek, Carolina de Amat Herbozo, Thierry Mallevaey

et al.

Trends in Immunology, Journal Year: 2022, Volume and Issue: 43(7), P. 503 - 512

Published: May 31, 2022

Language: Английский

Citations

21
Sanguisorba officinalis ethyl acetate extract attenuates ulcerative colitis through inhibiting PI3K-AKT/NF-κB/ STAT3 pathway uncovered by single-cell RNA sequencing DOI
Congcong Li,

Lei-Qiang Gong,

Yu Jiang

et al.

Phytomedicine, Journal Year: 2023, Volume and Issue: 120, P. 155052 - 155052

Published: Sept. 7, 2023

Language: Английский

Citations

12
Single-cell transcriptomics reveals striking heterogeneity and functional organization of dendritic and monocytic cells in the bovine mesenteric lymph node DOI Creative Commons
G. Tuba Barut,

Marco Kreuzer,

Rémy Bruggmann

et al.

Frontiers in Immunology, Journal Year: 2023, Volume and Issue: 13

Published: Jan. 6, 2023

Dendritic and monocytic cells co-operate to initiate shape adaptive immune responses in secondary lymphoid tissue. The complexity of this system is poorly understood, also because the high phenotypic functional plasticity cells. We have sequenced mononuclear phagocytes mesenteric lymph nodes (LN) three adult cows at single-cell level, revealing ten dendritic-cell (DC) clusters seven monocyte/macrophage with clearly distinct transcriptomic profiles. Among DC, we defined LN-resident subsets their progenitors, as well highly activated migratory DC differing transcript levels for T-cell attracting chemokines. Our analyses revealed a potential differentiation path cDC2, resulting cluster inflammatory cDC2 close transcriptional similarity putative DC3 monocyte-derived DC. Monocytes macrophages displayed sub-clustering mainly driven by pro- or anti-inflammatory expression signatures, including small cycling, presumably self-renewing, macrophages. With snapshot LN-derived phagocytes, reveal properties trajectories “command center immunity”, identify elements that are conserved across species.

Language: Английский

Citations

11
Revisiting Aire and tissue-restricted antigens at single-cell resolution DOI Creative Commons
Minoru Matsumoto, Hideyuki Yoshida, Koichi Tsuneyama

et al.

Frontiers in Immunology, Journal Year: 2023, Volume and Issue: 14

Published: May 3, 2023

The thymus is a highly specialized organ that plays an indispensable role in the establishment of self-tolerance, process characterized by “education” developing T-cells. To provide competent T-cells tolerant to self-antigens, medullary thymic epithelial cells (mTECs) orchestrate negative selection ectopically expressing wide range genes, including various tissue-restricted antigens (TRAs). Notably, recent advancements high-throughput single-cell analysis have revealed remarkable heterogeneity mTECs, giving us important clues for dissecting mechanisms underlying TRA expression. We overview how studies furthered our understanding with focus on Aire inducing mTEC encompass TRAs.

Language: Английский

Citations

11
Spatio-temporal heterogeneity in cancer evolution and tumor microenvironment of renal cell carcinoma with tumor thrombus DOI
Sian Zhou, Junhua Zheng, Wei Zhai

et al.

Cancer Letters, Journal Year: 2023, Volume and Issue: 572, P. 216350 - 216350

Published: Aug. 12, 2023

Language: Английский

Citations

10