An atlas of cells in the human tonsil.
Ontology highlight
ABSTRACT:
SUBMITTER: Massoni-Badosa R
PROVIDER: S-EPMC10869140 | biostudies-literature | 2024 Feb
REPOSITORIES: biostudies-literature
Publications
An atlas of cells in the human tonsil.
Massoni-Badosa Ramon R Aguilar-Fernández Sergio S Nieto Juan C JC Soler-Vila Paula P Elosua-Bayes Marc M Marchese Domenica D Kulis Marta M Vilas-Zornoza Amaia A Bühler Marco Matteo MM Rashmi Sonal S Alsinet Clara C Caratù Ginevra G Moutinho Catia C Ruiz Sara S Lorden Patricia P Lunazzi Giulia G Colomer Dolors D Frigola Gerard G Blevins Will W Romero-Rivero Lucia L Jiménez-Martínez Víctor V Vidal Anna A Mateos-Jaimez Judith J Maiques-Diaz Alba A Ovejero Sara S Moreaux Jérôme J Palomino Sara S Gomez-Cabrero David D Agirre Xabier X Weniger Marc A MA King Hamish W HW Garner Lucy C LC Marini Federico F Cervera-Paz Francisco Javier FJ Baptista Peter M PM Vilaseca Isabel I Rosales Cecilia C Ruiz-Gaspà Silvia S Talks Benjamin B Sidhpura Keval K Pascual-Reguant Anna A Hauser Anja E AE Haniffa Muzlifah M Prosper Felipe F Küppers Ralf R Gut Ivo Glynne IG Campo Elias E Martin-Subero José Ignacio JI Heyn Holger H
Immunity 20240131 2
Palatine tonsils are secondary lymphoid organs (SLOs) representing the first line of immunological defense against inhaled or ingested pathogens. We generated an atlas of the human tonsil composed of >556,000 cells profiled across five different data modalities, including single-cell transcriptome, epigenome, proteome, and immune repertoire sequencing, as well as spatial transcriptomics. This census identified 121 cell types and states, defined developmental trajectories, and enabled an understa ...[more]
Similar Datasets
Project description:Palatine tonsils are secondary lymphoid organs representing the first line of immunological defense against inhaled or ingested pathogens. Here, we provide a comprehensive census of cell types forming the human tonsil by applying single cell transcriptome, epigenome, proteome and adaptive immune repertoire as well as spatial transcriptomics, resulting in an atlas of >350,000 cells. We provide a glossary of over one hundred annotated cell types and states, and disentangle gene regulatory mechanisms that drive cells through specialized lineage trajectories. Exemplarily, we stratify multiple tonsil-resident myeloid slancyte subtypes, establish a distant BCL6 superenhancer as locally active in both follicle-associated T and B cells, and describe SIX5 as a potentially novel transcriptional regulator of plasma cell maturation. Further, our atlas is a reference map to understand alterations observed in disease, here we discover immune-phenotype plasticity in tumoral cells and microenvironment shifts of mantle cell lymphomas (MCL). To facilitate such reference-based analysis, we develop HCATonsilData and SLOcatoR, a computational framework that provides programmatic and modular access to our dataset; and allows the straightforward annotation of future single-cell profiles from secondary lymphoid organs.
| EGAS00001006375 | EGA
Project description:This repository contains all the FASTQ files for the five data modalities (scRNA-seq, scATAC-seq, Multiome, CITE-seq+scVDJ-seq, and spatial transcriptomics) used in the article \\"An Atlas of Cells in The Human Tonsil,\\" published in Immunity in 2024. Inspired by the TCGA barcodes, we have named each fastq file with the following convention: [TECHNOLOGY].[DONOR_ID].[SUBPROJECT].[GEM_ID].[LIBRARY_ID].[LIBRARY_TYPE].[LANE].[READ].fastq.gz which allows to retrieve all metadata from the name itself. Here is a full description of each field: - TECHNOLOGY: scRNA-seq, scATAC-seq, Multiome, CITE-seq+scVDJ-seq, and spatial transcriptomics (Visium). We also include the fastq files associated with the multiome experiments performed on two mantle cell lymphoma patients (MCL). - DONOR_ID: identifier for each of the 17 patients included in the cohort. We provide the donor-level metadata in the file \\"tonsil_atlas_donor_metadata.csv\\", including the hospital, sex, age, age group, cause for tonsillectomy and cohort type for every donor. - SUBPROJECT: each subproject corresponds to one run of the 10x Genomics Chromium™ Chip. - GEM_ID: each run of the 10x Genomics Chromium™ Chip consists of up to 8 \\"GEM wells\\" (see https://www.10xgenomics.com/support/software/cell-ranger/getting-started/cr-glossary): a set of partitioned cells (Gel Beads-in-emulsion) from a single 10x Genomics Chromium™ Chip channel. We give a unique identifier to each of these channels. - LIBRARY_ID: one or more sequencing libraries can be derived from a GEM well. For instance, multiome yields two libraries (ATAC and RNA) and CITE-seq+scVDJ yields 4 libraries (RNA, ADT, BCR, TCR). - LIBRARY_TYPE: the type of library for each library_id. Note that we used cell hashing () for a subset of the scRNA-seq libraries, and thus the library_type can be \\"not_hashed\\", \\"hashed_cdna\\" (RNA expression) or \\"hashed_hto\\" (the hashtag oligonucleotides). - LANE: to increase sequencing depth, each library was sequenced in more than one lane. Important: all lanes corresponding to the same sequencing library need to be inputed together to cellranger, because they come from the same set of cells. - READ: for scATAC-seq we have three reads (R1, R2 or R3), see cellranger-atac's documentation. While we find these names to be the most useful, they need to be changed to follow cellranger's conventions. We provide a code snippet in the README file of the GitHub repository associated with the tonsil atlas to convert between both formats (https://github.com/Single-Cell-Genomics-Group-CNAG-CRG/TonsilAtlas/). Besides the fastq files, cellranger (and other mappers) require additional files, which we also provide in this repository: - cell_hashing_metadata.csv: as mentioned above, we ran cell hashing (10.1186/s13059-018-1603-1) to detect doublets and reduce cost per cell. This file provides the sequence of the hashtag oligonucleotides in cellranger convention to allow demultiplexing. - cite_seq_feature_reference.csv: similar to the previous file, this one links each protein surface marker to the hashtag oligonucleotide that identified it in the CITE-seq experiment. - V10M16-059.gpr and V19S23-039.gpr: these correspond to the two slides of the two Visium experiments performed in the tonsil atlas. They are needed to run spaceranger. - [GEM_ID]_[SLIDE]_[CAPTURE_AREA].jpg: 8 images associated with the Visium experiments. Here, GEM_ID refers to each of the 4 capture areas in each slide. - [TECHNOLOGY]_sequencing_metadata.csv: the GEM-level metadata for each technology. It includes the relationship between subproject, gem_id, library_id, library_type and donor_id. These are the other repositories associated with the tonsil atlas: - Expression and accessibility matrices: https://zenodo.org/records/10373041 - Seurat objects: https://zenodo.org/records/8373756 - HCATonsilData package: https://bioconductor.org/packages/release/data/experiment/html/HCATonsilData.html - Azimuth: https://azimuth.hubmapconsortium.org/ - Github: https://github.com/Single-Cell-Genomics-Group-CNAG-CRG/TonsilAtlas
2024-05-02 | E-MTAB-13687 | biostudies-arrayexpress
Project description:Fibroblastic reticular cells (FRCs), the T-cell zone stromal cell subtype in the lymph nodes, create a scaffold for adhesion and migration of immune cells, thus allowing them to communicate. Although known to be important for the initiation of immune responses, studies about FRCs and their interactions have been impeded because FRCs are limited in availability and lose their function upon culture expansion. To circumvent these limitations, stromal cell precursors can be mechanotranduced to form mature FRCs. Here, we used a library of designed surface topographies to trigger FRC differentiation from tonsil-derived stromal cells (TSCs). Undifferentiated TSCs were seeded on a TopoChip containing 2176 different topographies in culture medium without differentiation factors, then monitored cell morphology and the levels of ICAM-1, a marker of FRC differentiation. We identified 112 and 72 surfaces that upregulated and downregulated, respectively, ICAM-1 expression. By monitoring cell morphology, and expression of the FRC differentiation marker ICAM-1 via image analysis and machine learning, we discovered correlations between ICAM-1 expression, cell shape and design of surface topographies and confirmed our findings by using flow cytometry. Our findings confirmed that TSCs are mechano-responsive cells and identified particular topographies that can be used to improve FRC differentiation protocols.
| S-EPMC6031747 | biostudies-literature
Project description:The human vascular system, comprising endothelial cells (ECs) and mural cells, covers a vast surface area in the body, providing a critical interface between blood and tissue environments. Functional differences exist across specific vascular beds, but their molecular determinants across tissues remain largely unknown. In this study, we integrated single-cell transcriptomics data from 19 human organs and tissues and defined 42 vascular cell states from approximately 67,000 cells (62 donors), including angiotypic transitional signatures along the arterial endothelial axis from large to small caliber vessels. We also characterized organotypic populations, including splenic littoral and blood-brain barrier ECs, thus clarifying the molecular profiles of these important cell states. Interrogating endothelial-mural cell molecular crosstalk revealed angiotypic and organotypic communication pathways related to Notch, Wnt, retinoic acid, prostaglandin and cell adhesion signaling. Transcription factor network analysis revealed differential regulation of downstream target genes in tissue-specific modules, such as those of FOXF1 across multiple lung vascular subpopulations. Additionally, we make mechanistic inferences of vascular drug targets within different vascular beds. This open-access resource enhances our understanding of angiodiversity and organotypic molecular signatures in human vascular cells, and has therapeutic implications for vascular diseases across tissues.
| S-EPMC11645277 | biostudies-literature
Project description:Obesity, which has become a major global health problem, involves a constitutive increase in adipocyte differentiation signaling. Previous studies show that mesenchymal stem cells (MSCs) induce weight loss and glycemic control. However, the mechanisms by which MSCs regulate adipocyte differentiation are not yet known. In this study, we investigated the effects of conditioned medium obtained from human tonsil-derived MSCs (T-MSC CM) on adipocyte differentiation. We found that T-MSC CM attenuated adipocyte differentiation from early stages via inhibiting glucocorticoid signaling. T-MSC CM also increased the phosphorylation of p38 mitogen-activated protein kinase and glucocorticoid receptors and decreased the subsequent nucleus translocation of glucocorticoid receptors. Chronic treatment of mice with synthetic glucocorticoids induced visceral and bone marrow adipose tissue expansion, but these effects were not observed in mice injected with T-MSC CM. Furthermore, T-MSC CM injection protected against reductions in blood platelet counts induced by chronic glucocorticoid treatment, and enhanced megakaryocyte differentiation was also observed. Collectively, these results demonstrate that T-MSC CM exerts inhibitory effects on adipocyte differentiation by regulating glucocorticoid signal transduction. These findings suggest that the therapeutic application of T-MSC CM could reduce obesity by preventing adipose tissue expansion.
| S-EPMC9159628 | biostudies-literature
Project description:Mesenchymal stem cells (MSCs) are capable of self-renewal and differentiation and are thus a valuable source for the replacement of diseased or damaged organs. Previously, we reported that the tonsils can be an excellent reservoir of MSCs for the regeneration of skeletal muscle (SKM) damage. However, the mechanisms involved in the differentiation from tonsil-derived MSCs (T-MSCs) to myocytes via myoblasts remain unclear. To clarify these mechanisms, we analyzed gene expression profiles of T-MSCs during differentiation into myocytes compared with human skeletal muscle cells (hSKMCs). Total RNA was extracted from T-MSCs, T-MSC-derived myoblasts and myocytes, and hSKMCs and was subjected to analysis using a microarray. Microarray analysis of the three phases of myogenic differentiation identified candidate genes associated with myogenic differentiation. The expression pattern of undifferentiated T-MSCs was distinguishable from the myogenic differentiated T-MSCs and hSKMCs. In particular, we selected FNBP1L, which among the upregulated genes is essential for antibacterial autophagy, since autophagy is related to SKM metabolism and myogenesis. T-MSCs differentiated toward myoblasts and skeletal myocytes sequentially, as evidenced by increased expression of autophagy-related markers (including Beclin-1, LC3B and Atg5) and decreased expression of Bcl-2. Furthermore, we reconfirmed that autophagy has an effect on the mechanism of skeletal myogenic differentiation derived from T-MSCs by treatment with 5-azacytidine and bafilomycin A1. These data suggest that the transcriptome of the T-MSC-derived myocytes is similar to that of hSKMCs, and that autophagy has an important role in the mechanism of myogenic differentiation of T-MSCs.
| S-EPMC5360438 | biostudies-literature
Project description:Mesenchymal stromal cells (MSCs) from various sources exhibit different potential for stemness and therapeutic abilities. Recently, we reported a unique MSCs from human palatine tonsil (TMSCs) and their superior proliferation capacity compared to MSCs from other sources. However, unique characteristics of each MSC are not yet precisely elucidated. We investigated the role of stanniocalcin-1 (STC1), an anti-oxidative hormone, in the functions of TMSCs. We found that STC1 was highly expressed in TMSC compared with MSCs from bone marrow or adipose tissue. The proliferation, senescence and differentiation of TMSCs were assessed after the inhibition of STC1 expression. STC1 inhibition resulted in a significant decrease in the proliferation of TMSCs and did not affect the differentiation potential. To reveal the anti-oxidative ability of STC1 in TMSCs themselves or against other cell types, the generation of mitochondrial reactive oxygen species (ROS) in TMSC or ROS-mediated production of interleukin (IL)-1β from macrophage-like cells were detected. Interestingly, the basal level of ROS generation in TMSCs was significantly elevated after STC1 inhibition. Moreover, down-regulation of STC1 impaired the inhibitory effect of TMSCs on IL-1β production in macrophages. Taken together, these findings indicate that STC1 is highly expressed in TMSCs and plays a critical role in proliferating and ROS-regulatory abilities.
| S-EPMC7140534 | biostudies-literature
Project description:Pharyngitis is an inflammation of the pharynx caused by viral, bacterial, or non-infectious factors. In the present study, the anti-inflammatory efficacy of carvacrol was assessed using an in vitro model of streptococcal pharyngitis using human tonsil epithelial cells (HTonEpiCs) induced with Streptococcus pyogenes cell wall antigens. HTonEpiCs were stimulated by a mixture of lipoteichoic acid (LTA) and peptidoglycan (PGN) for 4 h followed by exposure to carvacrol for 20 h. Following exposure, interleukin (IL)-6, IL-8, human beta defensin-2 (HBD-2), epithelial-derived neutrophil-activating protein-78 (ENA-78), granulocyte chemotactic protein-2 (GCP-2), cyclooxygenase-2 (COX-2), tumor necrosis factor-alpha (TNF-α), and prostaglandin (PGE2) were measured by enzyme-linked immunosorbent assays (ELISA). The levels of pro-inflammatory cytokines, IL-6, IL-8, ENA-78, and GCP-2 were decreased in a carvacrol dose-dependent manner. The production of HBD-2 was significantly suppressed over 24 h carvacrol treatments. PGE2 and COX-2 levels in the cell suspensions were affected by carvacrol treatment. TNF-α was not detected. The cell viability of all the tested carvacrol concentrations was greater than 80%, with no morphological changes. The results suggest that carvacrol has anti-inflammatory properties, and carvacrol needs to be further assessed for potential clinical or healthcare applications to manage the pain associated with streptococcal pharyngitis.
| S-EPMC8840435 | biostudies-literature
Project description:BackgroundPharyngitis is an inflammatory condition of the pharynx and associated structures commonly caused by the Group A streptococci (GAS). There is a growing interest in discovering plant-based anti-inflammatory compounds as potential alternatives to conventional drugs. This study evaluated anti-inflammatory activity of phytochemical-rich extracts prepared from 12 herbal plants using human tonsil epithelial cells (HTonEpiC) in vitro.MethodsThe HTonEpiC were induced by a mixture of lipoteichoic acid (LTA) and peptidoglycan (PGN) (10 µg/mL; bacterial antigens) for 4 h and then exposed to ethanol extracts (EE) or aqueous extracts (AE) for 20 h. The secretion of four pro-inflammatory cytokines was measured using enzyme-linked immunosorbent assays (ELISA). Total phenolic and total flavonoid contents of the extracts were determined using spectrophotometric methods.ResultsThe herbal plant extracts (≤5 µg/mL) were not cytotoxic to HTonEpiC. The extracts exhibited a broad range of reduction (1.2%-92.6%) of secretion of interleukin-8 (IL-8), human beta defensin-2 (hBD-2), epithelial-derived neutrophil activating protein-78 (ENA-78), and granulocyte chemotactic protein-2 (GCP-2). Both EE and AE of clove, ginger, and echinacea flower and EE from danshen root significantly inhibited the pro-inflammatory cytokine production as induced by LTA and PGN in HTonEpiCs at the concentrations of 1 and 5 µg/mL.DiscussionOur observations indicate that danshen root, clove, ginger, and echinacea flower extracts exhibit an anti-inflammatory effect in HTonEpiCs. The most efficacious extracts from danshen root, clove, ginger and echinacea flowers have potential to be used as natural sources for developing phytotherapeutic products in the management of painful inflammation due to streptococcal pharyngitis.
| S-EPMC5483044 | biostudies-literature