Mardiyyah/TAPT_data_V2_split · Datasets at Hugging Face

PMCID stringclasses 24 values	Title stringclasses 24 values	Sentences stringlengths 2 40.7k
PMC7612735	Cross-tissue immune cell analysis reveals tissue-specific features in humans.	Furthermore, CellTypist clearly resolved monocytes and macrophages, which often form a transcriptomic continuum in scRNA-seq datasets due to their functional plasticity.
PMC7612735	Cross-tissue immune cell analysis reveals tissue-specific features in humans.	Thus CellTypist was successfully able to identify major groups of cell populations with different abundances in our dataset (fig. S1C).
PMC7612735	Cross-tissue immune cell analysis reveals tissue-specific features in humans.	To automatically annotate fine-grained immune sub-populations, we next applied the low-hierarchy (high-resolution, 91 cell types and subtypes) classifier, which was able to classify cells into 43 specific subtypes including subsets of T cells, B cells, ILCs, and mononuclear phagocytes (Fig. 1E).
PMC7612735	Cross-tissue immune cell analysis reveals tissue-specific features in humans.	This revealed a high degree of heterogeneity within the T cell compartment, not only distinguishing between αβ and γδ T cells, but also between CD4+ and CD8+ T cell subtypes and their more detailed effector and functional phenotypes.
PMC7612735	Cross-tissue immune cell analysis reveals tissue-specific features in humans.	Specifically, the CD4+ T cell cluster was classified into helper, regulatory and cytotoxic subsets, and the CD8+ T cell clusters contained unconventional T cell subpopulations such as MAIT cells.
PMC7612735	Cross-tissue immune cell analysis reveals tissue-specific features in humans.	In the B cell compartment, a clear distinction was observed between naive and memory B cells.
PMC7612735	Cross-tissue immune cell analysis reveals tissue-specific features in humans.	Moreover, CellTypist revealed three distinct subsets of dendritic cells (DC) - DC1, DC2 and migratory DCs (migDCs) (25, 26), again highlighting the granularity CellTypist can achieve.
PMC7612735	Cross-tissue immune cell analysis reveals tissue-specific features in humans.	This fine-grained dissection of each compartment also allowed for the cross-validation and consolidation of cell types by examining the expression of marker genes derived from CellTypist models in cells from our dataset (fig. S1D).
PMC7612735	Cross-tissue immune cell analysis reveals tissue-specific features in humans.	In summary, we generated an in-depth map of immune cell populations across human tissues, and developed a framework for automated annotation of immune cell types and subtypes.
PMC7612735	Cross-tissue immune cell analysis reveals tissue-specific features in humans.	CellTypist produced fine-grained annotations on our multi-tissue and multi-lineage dataset, and its performance, as assessed on multiple metrics, was comparable or better relative to other label-transfer methods with minimal computational cost (figs. S13 and S14).
PMC7612735	Cross-tissue immune cell analysis reveals tissue-specific features in humans.	This approach allowed us to refine the description of many cell subtypes such as the progenitors and dendritic cell compartments at full transcriptomic breadth, resolving 43 cell states in total across our dataset.
PMC7612735	Cross-tissue immune cell analysis reveals tissue-specific features in humans.	This automated annotation forms the basis for further cross-tissue comparisons of cell compartments in the sections below.
PMC7612735	Cross-tissue immune cell analysis reveals tissue-specific features in humans.	Mononuclear phagocytes, including monocytes, macrophages and dendritic cells, are critical for immune surveillance and tissue homeostasis.
PMC7612735	Cross-tissue immune cell analysis reveals tissue-specific features in humans.	Automatic annotation by CellTypist identified eight populations in this compartment (fig. S15A).
PMC7612735	Cross-tissue immune cell analysis reveals tissue-specific features in humans.	To explore macrophage heterogeneity further, we built on CellTypist’s annotation by performing additional manual curation, which revealed further heterogeneity within the macrophages (Fig. 2A and fig. S15B).
PMC7612735	Cross-tissue immune cell analysis reveals tissue-specific features in humans.	The identities of these cells were supported by expression of well-established marker genes (Fig. 2B), and by markers independently identified from CellTypist models (fig. S15C).
PMC7612735	Cross-tissue immune cell analysis reveals tissue-specific features in humans.	Moreover, existence of these cell types was cross-validated, and thus consolidated, in the training datasets of CellTypist (fig. S15D), as well as in myeloid cells from two additional studies of the human intestinal tract (27) (fig. S15E) and lung (28) (fig. S15F).
PMC7612735	Cross-tissue immune cell analysis reveals tissue-specific features in humans.	Among macrophages, lung-resident cells constituted the majority, and were classified into two major clusters: (i) alveolar macrophages expressing GPNMB and TREM2, markers that have been related to alveolar macrophages (29) and disease-associated macrophages (30), respectively; and (ii) intermediate macrophages with unique expression of TNIP3 (Fig. 2, B to D).
PMC7612735	Cross-tissue immune cell analysis reveals tissue-specific features in humans.	TNIP3 (TNFAIP3-interacting protein 3) binds to A20, encoded by TNFAIP3, and inhibits TNF, IL-1 and LPS-induced NF-kB activation (31).
PMC7612735	Cross-tissue immune cell analysis reveals tissue-specific features in humans.	Its expression in lung macrophages may be related to underlying pathology as it was primarily detected in one donor (A29), a multitrauma donor with significant lung contusions.
PMC7612735	Cross-tissue immune cell analysis reveals tissue-specific features in humans.	Notably, this population also expressed the monocyte-recruiting chemokine CCL2 (Fig. 2B), providing a means of replenishing the lung macrophage pool.
PMC7612735	Cross-tissue immune cell analysis reveals tissue-specific features in humans.	Other macrophage subsets in our data also showed a high degree of tissue restriction (Fig. 2D).
PMC7612735	Cross-tissue immune cell analysis reveals tissue-specific features in humans.	Erythrophagocytic macrophages, including red pulp macrophages and Kupffer cells, mainly populated the spleen and liver, as expected, and shared high expression of CD5L, SCL40A1 and the transcription factor SPIC (32).
PMC7612735	Cross-tissue immune cell analysis reveals tissue-specific features in humans.	Notably, a number of macrophages from lymph nodes clustered together with erythrophagocytic macrophages, pointing to the presence of a small number of iron-recycling macrophages in lymph nodes (Fig. 2D).
PMC7612735	Cross-tissue immune cell analysis reveals tissue-specific features in humans.	Another macrophage population specifically present in the gut expressed CD209 (encoding DC-SIGN) and IGF1, markers that have been previously reported in mature intestinal macrophages and M2-like macrophages, respectively (33, 34).
PMC7612735	Cross-tissue immune cell analysis reveals tissue-specific features in humans.	Lastly, monocytes were clearly grouped in two major subgroups, classical and non-classical monocytes, which differed in the expression of CD14, FCGR3A and CX3CR1 as well as in their tissue distribution (Fig. 2, A to D).
PMC7612735	Cross-tissue immune cell analysis reveals tissue-specific features in humans.	Among dendritic cells, DC1 expressed XCR1 and CLEC9A, consistent with their identity as conventional DCs (DC1), specialised for cross-presentation of antigens (Fig. 2B).
PMC7612735	Cross-tissue immune cell analysis reveals tissue-specific features in humans.	Conventional DC2s expressed CD1C and CLEC10A, and migDCs were CCR7+ LAMP3+.
PMC7612735	Cross-tissue immune cell analysis reveals tissue-specific features in humans.	CCR7 is upregulated in tissue DCs following TLR or FcγR ligation (35, 36), enabling migration towards CCL19/21-expressing lymphatic endothelium and stromal cells in the T cell zone of lymph nodes (37, 38).
PMC7612735	Cross-tissue immune cell analysis reveals tissue-specific features in humans.	Consistent with this, we observed a marked enrichment of CCR7+ migDCs in lung-draining and mesenteric lymph nodes (Fig. 2D).
PMC7612735	Cross-tissue immune cell analysis reveals tissue-specific features in humans.	Interestingly, migDCs showed upregulation of AIRE, PDLIM4 and EBI3 in lymph nodes (Fig. 2E).
PMC7612735	Cross-tissue immune cell analysis reveals tissue-specific features in humans.	Extra-thymic expression of the autoimmune regulator AIRE has been reported in humans (39, 40), however, its functional role in secondary lymphoid organs remains poorly understood and is a matter of intense research (41–43).
PMC7612735	Cross-tissue immune cell analysis reveals tissue-specific features in humans.	We validated the presence of migDCs in lung-draining lymph nodes by immunofluorescence (fig. S16A) and AIRE expression by single-molecule FISH (smFISH) (Fig. 2F).
PMC7612735	Cross-tissue immune cell analysis reveals tissue-specific features in humans.	In addition, another subpopulation of migDCs found in lung and lung-draining lymph nodes upregulated CRLF2 (encoding TLSPR), chemokines (CCL22, CCL17), CSF2RA and GPR157 (Fig. 2E).
PMC7612735	Cross-tissue immune cell analysis reveals tissue-specific features in humans.	TLSPR is involved in the induction of Th2 responses in asthma (44).
PMC7612735	Cross-tissue immune cell analysis reveals tissue-specific features in humans.	Expression of these genes in lung DCs was also observed in published scRNA-seq datasets (45, 46) (fig. S16, B and C).
PMC7612735	Cross-tissue immune cell analysis reveals tissue-specific features in humans.	These observations suggest that dendritic cell activation coincides with the acquisition of tissue-specific markers that differ depending on the local microenvironment.
PMC7612735	Cross-tissue immune cell analysis reveals tissue-specific features in humans.	Overall, our analysis of the myeloid compartment has revealed shared and tissue-restricted features of mononuclear phagocytes, including alveolar macrophages in the lung, iron-recycling macrophages mostly localized in the spleen, and subtypes of migratory dendritic cells.
PMC7612735	Cross-tissue immune cell analysis reveals tissue-specific features in humans.	B cells comprise progenitors in the bone marrow, developmental states in lymphoid tissues and terminally differentiated memory and plasma cell states in lymphoid and non-lymphoid tissues.
PMC7612735	Cross-tissue immune cell analysis reveals tissue-specific features in humans.	They play a central role in humoral immunity via the production of antibodies tailored to specific body sites.
PMC7612735	Cross-tissue immune cell analysis reveals tissue-specific features in humans.	We first annotated the B cells using CellTypist and obtained six populations (fig. S17A).
PMC7612735	Cross-tissue immune cell analysis reveals tissue-specific features in humans.	Manual curation revealed further heterogeneity in memory B cells and plasma cells, identifying 11 cell types in total (Fig. 3A and fig. S17B).
PMC7612735	Cross-tissue immune cell analysis reveals tissue-specific features in humans.	As with the myeloid compartment, we cross-checked and verified these cell types in CellTypist training datasets (fig. S17, C and D) and in two independent immune datasets from gut (27) and lung (28) (fig. S17, E and F).
PMC7612735	Cross-tissue immune cell analysis reveals tissue-specific features in humans.	Naive B cells expressed TCL1A and were primarily found in lymphoid tissues (Fig. 3, B to D).
PMC7612735	Cross-tissue immune cell analysis reveals tissue-specific features in humans.	In addition, we identified two populations of germinal center B cells, expressing AICDA and BCL6, that differed in their proliferative states (marked by MKI67).
PMC7612735	Cross-tissue immune cell analysis reveals tissue-specific features in humans.	Of note, we did not find differential expression of dark zone and light zone marker genes in these two populations, probably reflecting limited germinal center activity in our adult donors.
PMC7612735	Cross-tissue immune cell analysis reveals tissue-specific features in humans.	Moreover, these germinal center populations were present in lymph nodes and diverse gut regions (Fig. 3, C and D), presumably representing Peyer’s patches.
PMC7612735	Cross-tissue immune cell analysis reveals tissue-specific features in humans.	Within memory B cells, which were characterized by expression of the B-cell lineage markers (MS4A1, CD19) and TNFRSF13B, we found a transcriptomically distinct cluster positive for ITGAX, TBX21 and FCRL2, encoding CD11c, T-bet and the Fc receptor-like protein 2, respectively (Fig. 3B).
PMC7612735	Cross-tissue immune cell analysis reveals tissue-specific features in humans.	CD11c+T-bet+ B cells, also known as age-associated B cells (ABCs), have been reported in autoimmunity and aging (47–49), and likely correspond to this ITGAX+ memory B cell population.
PMC7612735	Cross-tissue immune cell analysis reveals tissue-specific features in humans.	Notably, unlike conventional memory B cells, they showed relatively low expression of CR2 (encoding CD21) and CD27 (Fig. 3B).
PMC7612735	Cross-tissue immune cell analysis reveals tissue-specific features in humans.	Interestingly, this subset was mainly present in the liver and bone marrow, while in secondary lymphoid organs, it was primarily found in the spleen (confirmed by flow cytometry and immunofluorescence (Fig. 3, C and D, and fig. S18).
PMC7612735	Cross-tissue immune cell analysis reveals tissue-specific features in humans.	This data deepens our understanding of the phenotype of this non-classical subtype of memory B cells, and their tissue distribution.
PMC7612735	Cross-tissue immune cell analysis reveals tissue-specific features in humans.	We uncovered two populations of plasmablasts and plasma cells marked by expression of CD38, XBP1 and SDC1.
PMC7612735	Cross-tissue immune cell analysis reveals tissue-specific features in humans.	Whereas the former expressed MKI67 and were found in the spleen, liver, bone marrow and blood, the latter expressed the integrin alpha-8-encoding gene ITGA8 and the adhesion molecule CERCAM and were enriched in the jejunum and liver (Fig. 3, B to D).
PMC7612735	Cross-tissue immune cell analysis reveals tissue-specific features in humans.	ITGA8+ plasma cells have recently been reported in the context of an analysis of bone marrow plasma cells (50), and are likely a long-lived plasma cell population that is quiescent and tissue-resident.
PMC7612735	Cross-tissue immune cell analysis reveals tissue-specific features in humans.	Here we expand their tissue distribution to the liver and gut, and describe their specific clonal distribution pattern below.
PMC7612735	Cross-tissue immune cell analysis reveals tissue-specific features in humans.	B cells have an additional source of variability due to VDJ recombination, somatic hypermutation and class-switching, which can relate to cell phenotype.
PMC7612735	Cross-tissue immune cell analysis reveals tissue-specific features in humans.	Therefore, we performed targeted enrichment and sequencing of B-cell receptor (BCR) transcripts to assess isotypes, hypermutation levels and clonal architecture of the B cell populations identified above.
PMC7612735	Cross-tissue immune cell analysis reveals tissue-specific features in humans.	This analysis revealed an isotype and subclass usage pattern that related to cellular phenotype (fig. S19A).
PMC7612735	Cross-tissue immune cell analysis reveals tissue-specific features in humans.	As expected, naive B cells mainly showed a subclass preference for IgM and IgD. Interestingly, while evidence of class switching to IgA1 and IgG1 was seen within memory B cells (including ABCs), plasmablasts and plasma cells also showed class switching to IgA2 and IgG2.
PMC7612735	Cross-tissue immune cell analysis reveals tissue-specific features in humans.	To determine to what extent this isotype subclass bias correlated with the tissue of origin, we assessed each cell state independently (requiring a minimum cell count of 50).
PMC7612735	Cross-tissue immune cell analysis reveals tissue-specific features in humans.	Memory B cells showed a bias towards IgA1 in the mesenteric lymph nodes, and towards IgA2 in the ileum, where Peyer’s patches are found (Fig. 3E).
PMC7612735	Cross-tissue immune cell analysis reveals tissue-specific features in humans.	In the plasma cell compartment, we found an even more striking preference for IgA2 in the gut region (specifically in the jejunum lamina propria), consistent with the known dominance of this isotype at mucosal surfaces (Fig. 3E).
PMC7612735	Cross-tissue immune cell analysis reveals tissue-specific features in humans.	Of note, plasma cells in the bone marrow, liver and spleen were composed of over 20% IgG2 subclass.
PMC7612735	Cross-tissue immune cell analysis reveals tissue-specific features in humans.	With more limited numbers, we report isotype distributions across tissues for other B cell populations (fig. S19, B and C).
PMC7612735	Cross-tissue immune cell analysis reveals tissue-specific features in humans.	ABCs were dominated by IgM in both the spleen and lung-draining lymph nodes, consistent with previous reports (51).
PMC7612735	Cross-tissue immune cell analysis reveals tissue-specific features in humans.	Somatic hypermutation (SHM) levels were, as expected, lowest in naive B cells and highest in plasma cells (fig. S19D).
PMC7612735	Cross-tissue immune cell analysis reveals tissue-specific features in humans.	Between isotypes and subclasses, SHM did not differ significantly.
PMC7612735	Cross-tissue immune cell analysis reveals tissue-specific features in humans.	Nonetheless, there was a tendency towards higher mutation rates in the distal classes IgG2, IgG4 and IgA2, which are downstream from the IgH locus and can thus accumulate more mutations during sequential switching (52) (Fig. 3F).
PMC7612735	Cross-tissue immune cell analysis reveals tissue-specific features in humans.	We also explored the occurrence of sequential class switching events in our data by assessing the isotype frequency among expanded clonotypes (>10 cells).
PMC7612735	Cross-tissue immune cell analysis reveals tissue-specific features in humans.	Mixed isotype clones were rare in our data (fig. S19E).
PMC7612735	Cross-tissue immune cell analysis reveals tissue-specific features in humans.	Next, we evaluated the distribution of expanded clones across tissues and cell types, and found three major groups of clones - present in only two tissues, three to four tissues or five or more tissues, respectively (Fig. 3G), similar to previously reported patterns of B cell clonal tissue distribution (53).
PMC7612735	Cross-tissue immune cell analysis reveals tissue-specific features in humans.	While the clones restricted to two tissues, typically between the spleen and the liver or bone marrow, were enriched in plasma cells, those distributed across more than five tissues, including lymph nodes, were over-represented in memory B cells.
PMC7612735	Cross-tissue immune cell analysis reveals tissue-specific features in humans.	Together, these findings suggest that tissue-restricted clones may represent long-term immunological memory maintained by long-lived plasma cells resident in the bone marrow and spleen as well as liver in our data.
PMC7612735	Cross-tissue immune cell analysis reveals tissue-specific features in humans.	Overall, we characterized nine cell states in the B cell compartment, and gained insights from in-depth characterisation of both naive and memory B cell as well as plasma cell subsets.
PMC7612735	Cross-tissue immune cell analysis reveals tissue-specific features in humans.	We identified distinct clonal distribution patterns for the more tissue-restricted long-lived quiescent plasma cells versus the broad tissue distribution of classical memory B cell clones.
PMC7612735	Cross-tissue immune cell analysis reveals tissue-specific features in humans.	For annotation of the T cell/innate lymphocyte compartment, CellTypist identified 18 cell types (fig. S20A).
PMC7612735	Cross-tissue immune cell analysis reveals tissue-specific features in humans.	After manual inspection, these clusters were further divided into additional subtypes (e.g. for cytotoxic T cells) (Fig. 4A and fig. S20B).
PMC7612735	Cross-tissue immune cell analysis reveals tissue-specific features in humans.	As described above for the myeloid and B cell compartments, identities of the derived cell types were cross-validated in the immune compartment of the CellTypist training datasets (fig. S20, C and D) and the two independent studies of gut (27) and lung (28) (fig. S20, E and F).
PMC7612735	Cross-tissue immune cell analysis reveals tissue-specific features in humans.	Naive/central memory CD4+ T cells were transcriptionally close to naive CD8+ T cells as defined by high expression of CCR7 and SELL and were mainly found in lymphoid sites (Fig. 4B).
PMC7612735	Cross-tissue immune cell analysis reveals tissue-specific features in humans.	Other CD4+ T cells identified included follicular helper T cells (Tfh) expressing CXCR5, regulatory T cells (Tregs) expressing FOXP3 and CTLA4, effector memory CD4+ T cells, and tissue-resident memory Th1 and Th17 cells expressing CCR9, ITGAE and ITGA1 found largely in intestinal sites (jejunum and ileum) and lungs (Fig. 4, B to D).
PMC7612735	Cross-tissue immune cell analysis reveals tissue-specific features in humans.	Within the memory CD8+ T compartment, we found three major subsets: Trm_gut_CD8 (resident memory T cells, Trm), Tem/emra_CD8 (effector memory, Tem; effector memory re-expressing CD45RA, Temra) and Trm/em_CD8.
PMC7612735	Cross-tissue immune cell analysis reveals tissue-specific features in humans.	These subsets were characterized by differential expression of the chemokine receptors CCR9 and CX3CR1 and the activation marker CRTAM (Fig. 4B).
PMC7612735	Cross-tissue immune cell analysis reveals tissue-specific features in humans.	The Trm_gut_CD8 population (CCR9+) expressed the tissue-residency markers ITGAE and ITGA1, encoding CD103 and CD49a respectively and localized to intestinal sites (Fig. 4B).
PMC7612735	Cross-tissue immune cell analysis reveals tissue-specific features in humans.	By contrast, the Tem/Temra_CD8 population expressing CX3CR1 was found in blood-rich sites (blood, bone marrow, lung, and liver) and was excluded from lymph nodes and gut (Fig. 4, C and D), consistent with previous flow cytometry analysis of Temra cells (54), and results showing CX3CR1+CD8+ T cells as blood-confined and absent from thoracic duct lymph (55).
PMC7612735	Cross-tissue immune cell analysis reveals tissue-specific features in humans.	The Trm/em_CD8 population expressed high levels of CRTAM, a gene previously shown to be expressed by Trm (56) and was found in spleen, bone marrow, and to a lesser extent in lymph nodes and lungs.
PMC7612735	Cross-tissue immune cell analysis reveals tissue-specific features in humans.	This may be a resident population more prevalent in lymphoid sites (16).
PMC7612735	Cross-tissue immune cell analysis reveals tissue-specific features in humans.	We validated and mapped the Trm/em_CD8 population using smFISH in the liver (Fig. 4E) and lung-draining lymph nodes (Fig. 4F).
PMC7612735	Cross-tissue immune cell analysis reveals tissue-specific features in humans.	Furthermore, we validated all three memory CD8+ T cell populations at the protein level by flow cytometry of cells purified from human spleen (fig. S21).
PMC7612735	Cross-tissue immune cell analysis reveals tissue-specific features in humans.	Although we could validate CRTAM at the RNA level by smFISH, the protein could not be detected without stimulation, suggesting that CRTAM is subject to post-translational regulation upon T-cell receptor (TCR) activation.
PMC7612735	Cross-tissue immune cell analysis reveals tissue-specific features in humans.	These three distinct populations represent different states of tissue adaptation and maturation between effector memory and tissue-resident T cell memory states.
PMC7612735	Cross-tissue immune cell analysis reveals tissue-specific features in humans.	We also detected invariant T cell subsets such as MAIT cells, characterised by expression of TRAV1-2 and SLC4A10, and two populations of γδ T cells: Trm_Tgd and Tgd_CRTAM+.
PMC7612735	Cross-tissue immune cell analysis reveals tissue-specific features in humans.	The CCR9+ Trm_Tgd population populated the gut and expressed the tissue-residency markers ITGAE and ITGA1, whereas the Tgd_CRTAM+ population overexpressed CRTAM, IKZF2 (encoding HELIOS) and the integrin molecule ITGAD (encoding CD11d) and was found primarily in the spleen, bone marrow and liver (Fig. 4, B to D, and fig. S22, A and B).
PMC7612735	Cross-tissue immune cell analysis reveals tissue-specific features in humans.	We validated the latter population by quantitative PCR (qPCR) of flow sorted CD3+TCRγδ+ and CD3+TCRαβ+ cells from cryopreserved spleen samples from three donors (fig. S22C, D).
PMC7612735	Cross-tissue immune cell analysis reveals tissue-specific features in humans.	As a small fraction of ɑβ T cells, marked by low expression of CD52 and CD127, were also noted to express ITGAD, the CD3+TCRαβ population was split into CD52-CD127- and CD52+CD127+ subpopulations.
PMC7612735	Cross-tissue immune cell analysis reveals tissue-specific features in humans.	In keeping with our scRNA-seq data, ITGAD expression was high in CD3+TCRγδ and CD52-CD127-CD3+TCRαβ, providing additional evidence for the specific expression of this integrin alpha subunit in this subpopulation of γδ T cells.
PMC7612735	Cross-tissue immune cell analysis reveals tissue-specific features in humans.	Lastly, NK cells in our data were represented by two clusters with high expression of either FCGR3A (encoding CD16) or NCAM1 (encoding CD56).
PMC7612735	Cross-tissue immune cell analysis reveals tissue-specific features in humans.	We also defined an ILC3 population within a small cluster mixed with NK cells, via expression of markers including PCDH9 (Fig. 4, A and B).
PMC7612735	Cross-tissue immune cell analysis reveals tissue-specific features in humans.	Analyses of the tissue distribution of these populations revealed that, whereas the majority of CD4+ T and ILC3 cells were located in the lymph nodes and to some extent in the spleen, cytotoxic T and NK cells were more abundant in the bone marrow, spleen and non-lymphoid tissues (Fig. 4, C and D).
PMC7612735	Cross-tissue immune cell analysis reveals tissue-specific features in humans.	To understand T cell-mediated protection in more depth, we analysed T cell clonal distribution in a subset of the data within different tissues of a single individual and across different individuals.

PMC7612735

Cross-tissue immune cell analysis reveals tissue-specific features in humans.

Furthermore, CellTypist clearly resolved monocytes and macrophages, which often form a transcriptomic continuum in scRNA-seq datasets due to their functional plasticity.

PMC7612735

Cross-tissue immune cell analysis reveals tissue-specific features in humans.

Thus CellTypist was successfully able to identify major groups of cell populations with different abundances in our dataset (fig. S1C).

PMC7612735

Cross-tissue immune cell analysis reveals tissue-specific features in humans.

To automatically annotate fine-grained immune sub-populations, we next applied the low-hierarchy (high-resolution, 91 cell types and subtypes) classifier, which was able to classify cells into 43 specific subtypes including subsets of T cells, B cells, ILCs, and mononuclear phagocytes (Fig. 1E).

PMC7612735

Cross-tissue immune cell analysis reveals tissue-specific features in humans.

This revealed a high degree of heterogeneity within the T cell compartment, not only distinguishing between αβ and γδ T cells, but also between CD4+ and CD8+ T cell subtypes and their more detailed effector and functional phenotypes.

PMC7612735

Cross-tissue immune cell analysis reveals tissue-specific features in humans.

Specifically, the CD4+ T cell cluster was classified into helper, regulatory and cytotoxic subsets, and the CD8+ T cell clusters contained unconventional T cell subpopulations such as MAIT cells.

PMC7612735

Cross-tissue immune cell analysis reveals tissue-specific features in humans.

In the B cell compartment, a clear distinction was observed between naive and memory B cells.

PMC7612735

Cross-tissue immune cell analysis reveals tissue-specific features in humans.

Moreover, CellTypist revealed three distinct subsets of dendritic cells (DC) - DC1, DC2 and migratory DCs (migDCs) (25, 26), again highlighting the granularity CellTypist can achieve.

PMC7612735

Cross-tissue immune cell analysis reveals tissue-specific features in humans.

This fine-grained dissection of each compartment also allowed for the cross-validation and consolidation of cell types by examining the expression of marker genes derived from CellTypist models in cells from our dataset (fig. S1D).

PMC7612735

Cross-tissue immune cell analysis reveals tissue-specific features in humans.

In summary, we generated an in-depth map of immune cell populations across human tissues, and developed a framework for automated annotation of immune cell types and subtypes.

PMC7612735

Cross-tissue immune cell analysis reveals tissue-specific features in humans.

CellTypist produced fine-grained annotations on our multi-tissue and multi-lineage dataset, and its performance, as assessed on multiple metrics, was comparable or better relative to other label-transfer methods with minimal computational cost (figs. S13 and S14).

PMC7612735

Cross-tissue immune cell analysis reveals tissue-specific features in humans.

This approach allowed us to refine the description of many cell subtypes such as the progenitors and dendritic cell compartments at full transcriptomic breadth, resolving 43 cell states in total across our dataset.

PMC7612735

Cross-tissue immune cell analysis reveals tissue-specific features in humans.

This automated annotation forms the basis for further cross-tissue comparisons of cell compartments in the sections below.

PMC7612735

Cross-tissue immune cell analysis reveals tissue-specific features in humans.

Mononuclear phagocytes, including monocytes, macrophages and dendritic cells, are critical for immune surveillance and tissue homeostasis.

PMC7612735

Cross-tissue immune cell analysis reveals tissue-specific features in humans.

Automatic annotation by CellTypist identified eight populations in this compartment (fig. S15A).

PMC7612735

Cross-tissue immune cell analysis reveals tissue-specific features in humans.

To explore macrophage heterogeneity further, we built on CellTypist’s annotation by performing additional manual curation, which revealed further heterogeneity within the macrophages (Fig. 2A and fig. S15B).

PMC7612735

Cross-tissue immune cell analysis reveals tissue-specific features in humans.

The identities of these cells were supported by expression of well-established marker genes (Fig. 2B), and by markers independently identified from CellTypist models (fig. S15C).

PMC7612735

Cross-tissue immune cell analysis reveals tissue-specific features in humans.

Moreover, existence of these cell types was cross-validated, and thus consolidated, in the training datasets of CellTypist (fig. S15D), as well as in myeloid cells from two additional studies of the human intestinal tract (27) (fig. S15E) and lung (28) (fig. S15F).

PMC7612735

Cross-tissue immune cell analysis reveals tissue-specific features in humans.

Among macrophages, lung-resident cells constituted the majority, and were classified into two major clusters: (i) alveolar macrophages expressing GPNMB and TREM2, markers that have been related to alveolar macrophages (29) and disease-associated macrophages (30), respectively; and (ii) intermediate macrophages with unique expression of TNIP3 (Fig. 2, B to D).

PMC7612735

Cross-tissue immune cell analysis reveals tissue-specific features in humans.

TNIP3 (TNFAIP3-interacting protein 3) binds to A20, encoded by TNFAIP3, and inhibits TNF, IL-1 and LPS-induced NF-kB activation (31).

PMC7612735

Cross-tissue immune cell analysis reveals tissue-specific features in humans.

Its expression in lung macrophages may be related to underlying pathology as it was primarily detected in one donor (A29), a multitrauma donor with significant lung contusions.

PMC7612735

Cross-tissue immune cell analysis reveals tissue-specific features in humans.

Notably, this population also expressed the monocyte-recruiting chemokine CCL2 (Fig. 2B), providing a means of replenishing the lung macrophage pool.

PMC7612735

Cross-tissue immune cell analysis reveals tissue-specific features in humans.

Other macrophage subsets in our data also showed a high degree of tissue restriction (Fig. 2D).

PMC7612735

Cross-tissue immune cell analysis reveals tissue-specific features in humans.

Erythrophagocytic macrophages, including red pulp macrophages and Kupffer cells, mainly populated the spleen and liver, as expected, and shared high expression of CD5L, SCL40A1 and the transcription factor SPIC (32).

PMC7612735

Cross-tissue immune cell analysis reveals tissue-specific features in humans.

Notably, a number of macrophages from lymph nodes clustered together with erythrophagocytic macrophages, pointing to the presence of a small number of iron-recycling macrophages in lymph nodes (Fig. 2D).

PMC7612735

Cross-tissue immune cell analysis reveals tissue-specific features in humans.

Another macrophage population specifically present in the gut expressed CD209 (encoding DC-SIGN) and IGF1, markers that have been previously reported in mature intestinal macrophages and M2-like macrophages, respectively (33, 34).

PMC7612735

Cross-tissue immune cell analysis reveals tissue-specific features in humans.

Lastly, monocytes were clearly grouped in two major subgroups, classical and non-classical monocytes, which differed in the expression of CD14, FCGR3A and CX3CR1 as well as in their tissue distribution (Fig. 2, A to D).

PMC7612735

Cross-tissue immune cell analysis reveals tissue-specific features in humans.

Among dendritic cells, DC1 expressed XCR1 and CLEC9A, consistent with their identity as conventional DCs (DC1), specialised for cross-presentation of antigens (Fig. 2B).

PMC7612735

Cross-tissue immune cell analysis reveals tissue-specific features in humans.

Conventional DC2s expressed CD1C and CLEC10A, and migDCs were CCR7+ LAMP3+.

PMC7612735

Cross-tissue immune cell analysis reveals tissue-specific features in humans.

CCR7 is upregulated in tissue DCs following TLR or FcγR ligation (35, 36), enabling migration towards CCL19/21-expressing lymphatic endothelium and stromal cells in the T cell zone of lymph nodes (37, 38).

PMC7612735

Cross-tissue immune cell analysis reveals tissue-specific features in humans.

Consistent with this, we observed a marked enrichment of CCR7+ migDCs in lung-draining and mesenteric lymph nodes (Fig. 2D).

PMC7612735

Cross-tissue immune cell analysis reveals tissue-specific features in humans.

Interestingly, migDCs showed upregulation of AIRE, PDLIM4 and EBI3 in lymph nodes (Fig. 2E).

PMC7612735

Cross-tissue immune cell analysis reveals tissue-specific features in humans.

Extra-thymic expression of the autoimmune regulator AIRE has been reported in humans (39, 40), however, its functional role in secondary lymphoid organs remains poorly understood and is a matter of intense research (41–43).

PMC7612735

Cross-tissue immune cell analysis reveals tissue-specific features in humans.

We validated the presence of migDCs in lung-draining lymph nodes by immunofluorescence (fig. S16A) and AIRE expression by single-molecule FISH (smFISH) (Fig. 2F).

PMC7612735

Cross-tissue immune cell analysis reveals tissue-specific features in humans.

In addition, another subpopulation of migDCs found in lung and lung-draining lymph nodes upregulated CRLF2 (encoding TLSPR), chemokines (CCL22, CCL17), CSF2RA and GPR157 (Fig. 2E).

PMC7612735

Cross-tissue immune cell analysis reveals tissue-specific features in humans.

TLSPR is involved in the induction of Th2 responses in asthma (44).

PMC7612735

Cross-tissue immune cell analysis reveals tissue-specific features in humans.

Expression of these genes in lung DCs was also observed in published scRNA-seq datasets (45, 46) (fig. S16, B and C).

PMC7612735

Cross-tissue immune cell analysis reveals tissue-specific features in humans.

These observations suggest that dendritic cell activation coincides with the acquisition of tissue-specific markers that differ depending on the local microenvironment.

PMC7612735

Cross-tissue immune cell analysis reveals tissue-specific features in humans.

Overall, our analysis of the myeloid compartment has revealed shared and tissue-restricted features of mononuclear phagocytes, including alveolar macrophages in the lung, iron-recycling macrophages mostly localized in the spleen, and subtypes of migratory dendritic cells.

PMC7612735

Cross-tissue immune cell analysis reveals tissue-specific features in humans.

B cells comprise progenitors in the bone marrow, developmental states in lymphoid tissues and terminally differentiated memory and plasma cell states in lymphoid and non-lymphoid tissues.

PMC7612735

Cross-tissue immune cell analysis reveals tissue-specific features in humans.

They play a central role in humoral immunity via the production of antibodies tailored to specific body sites.

PMC7612735

Cross-tissue immune cell analysis reveals tissue-specific features in humans.

We first annotated the B cells using CellTypist and obtained six populations (fig. S17A).

PMC7612735

Cross-tissue immune cell analysis reveals tissue-specific features in humans.

Manual curation revealed further heterogeneity in memory B cells and plasma cells, identifying 11 cell types in total (Fig. 3A and fig. S17B).

PMC7612735

Cross-tissue immune cell analysis reveals tissue-specific features in humans.

As with the myeloid compartment, we cross-checked and verified these cell types in CellTypist training datasets (fig. S17, C and D) and in two independent immune datasets from gut (27) and lung (28) (fig. S17, E and F).

PMC7612735

Cross-tissue immune cell analysis reveals tissue-specific features in humans.

Naive B cells expressed TCL1A and were primarily found in lymphoid tissues (Fig. 3, B to D).

PMC7612735

Cross-tissue immune cell analysis reveals tissue-specific features in humans.

In addition, we identified two populations of germinal center B cells, expressing AICDA and BCL6, that differed in their proliferative states (marked by MKI67).

PMC7612735

Cross-tissue immune cell analysis reveals tissue-specific features in humans.

Of note, we did not find differential expression of dark zone and light zone marker genes in these two populations, probably reflecting limited germinal center activity in our adult donors.

PMC7612735

Cross-tissue immune cell analysis reveals tissue-specific features in humans.

Moreover, these germinal center populations were present in lymph nodes and diverse gut regions (Fig. 3, C and D), presumably representing Peyer’s patches.

PMC7612735

Cross-tissue immune cell analysis reveals tissue-specific features in humans.

Within memory B cells, which were characterized by expression of the B-cell lineage markers (MS4A1, CD19) and TNFRSF13B, we found a transcriptomically distinct cluster positive for ITGAX, TBX21 and FCRL2, encoding CD11c, T-bet and the Fc receptor-like protein 2, respectively (Fig. 3B).

PMC7612735

Cross-tissue immune cell analysis reveals tissue-specific features in humans.

CD11c+T-bet+ B cells, also known as age-associated B cells (ABCs), have been reported in autoimmunity and aging (47–49), and likely correspond to this ITGAX+ memory B cell population.

PMC7612735

Cross-tissue immune cell analysis reveals tissue-specific features in humans.

Notably, unlike conventional memory B cells, they showed relatively low expression of CR2 (encoding CD21) and CD27 (Fig. 3B).

PMC7612735

Cross-tissue immune cell analysis reveals tissue-specific features in humans.

Interestingly, this subset was mainly present in the liver and bone marrow, while in secondary lymphoid organs, it was primarily found in the spleen (confirmed by flow cytometry and immunofluorescence (Fig. 3, C and D, and fig. S18).

PMC7612735

Cross-tissue immune cell analysis reveals tissue-specific features in humans.

This data deepens our understanding of the phenotype of this non-classical subtype of memory B cells, and their tissue distribution.

PMC7612735

Cross-tissue immune cell analysis reveals tissue-specific features in humans.

We uncovered two populations of plasmablasts and plasma cells marked by expression of CD38, XBP1 and SDC1.

PMC7612735

Cross-tissue immune cell analysis reveals tissue-specific features in humans.

Whereas the former expressed MKI67 and were found in the spleen, liver, bone marrow and blood, the latter expressed the integrin alpha-8-encoding gene ITGA8 and the adhesion molecule CERCAM and were enriched in the jejunum and liver (Fig. 3, B to D).

PMC7612735

Cross-tissue immune cell analysis reveals tissue-specific features in humans.

ITGA8+ plasma cells have recently been reported in the context of an analysis of bone marrow plasma cells (50), and are likely a long-lived plasma cell population that is quiescent and tissue-resident.

PMC7612735

Cross-tissue immune cell analysis reveals tissue-specific features in humans.

Here we expand their tissue distribution to the liver and gut, and describe their specific clonal distribution pattern below.

PMC7612735

Cross-tissue immune cell analysis reveals tissue-specific features in humans.

B cells have an additional source of variability due to VDJ recombination, somatic hypermutation and class-switching, which can relate to cell phenotype.

PMC7612735

Cross-tissue immune cell analysis reveals tissue-specific features in humans.

Therefore, we performed targeted enrichment and sequencing of B-cell receptor (BCR) transcripts to assess isotypes, hypermutation levels and clonal architecture of the B cell populations identified above.

PMC7612735

Cross-tissue immune cell analysis reveals tissue-specific features in humans.

This analysis revealed an isotype and subclass usage pattern that related to cellular phenotype (fig. S19A).

PMC7612735

Cross-tissue immune cell analysis reveals tissue-specific features in humans.

As expected, naive B cells mainly showed a subclass preference for IgM and IgD. Interestingly, while evidence of class switching to IgA1 and IgG1 was seen within memory B cells (including ABCs), plasmablasts and plasma cells also showed class switching to IgA2 and IgG2.

PMC7612735

Cross-tissue immune cell analysis reveals tissue-specific features in humans.

To determine to what extent this isotype subclass bias correlated with the tissue of origin, we assessed each cell state independently (requiring a minimum cell count of 50).

PMC7612735

Cross-tissue immune cell analysis reveals tissue-specific features in humans.

Memory B cells showed a bias towards IgA1 in the mesenteric lymph nodes, and towards IgA2 in the ileum, where Peyer’s patches are found (Fig. 3E).

PMC7612735

Cross-tissue immune cell analysis reveals tissue-specific features in humans.

In the plasma cell compartment, we found an even more striking preference for IgA2 in the gut region (specifically in the jejunum lamina propria), consistent with the known dominance of this isotype at mucosal surfaces (Fig. 3E).

PMC7612735

Cross-tissue immune cell analysis reveals tissue-specific features in humans.

Of note, plasma cells in the bone marrow, liver and spleen were composed of over 20% IgG2 subclass.

PMC7612735

Cross-tissue immune cell analysis reveals tissue-specific features in humans.

With more limited numbers, we report isotype distributions across tissues for other B cell populations (fig. S19, B and C).

PMC7612735

Cross-tissue immune cell analysis reveals tissue-specific features in humans.

ABCs were dominated by IgM in both the spleen and lung-draining lymph nodes, consistent with previous reports (51).

PMC7612735

Cross-tissue immune cell analysis reveals tissue-specific features in humans.

Somatic hypermutation (SHM) levels were, as expected, lowest in naive B cells and highest in plasma cells (fig. S19D).

PMC7612735

Cross-tissue immune cell analysis reveals tissue-specific features in humans.

Between isotypes and subclasses, SHM did not differ significantly.

PMC7612735

Cross-tissue immune cell analysis reveals tissue-specific features in humans.

Nonetheless, there was a tendency towards higher mutation rates in the distal classes IgG2, IgG4 and IgA2, which are downstream from the IgH locus and can thus accumulate more mutations during sequential switching (52) (Fig. 3F).

PMC7612735

Cross-tissue immune cell analysis reveals tissue-specific features in humans.

We also explored the occurrence of sequential class switching events in our data by assessing the isotype frequency among expanded clonotypes (>10 cells).

PMC7612735

Cross-tissue immune cell analysis reveals tissue-specific features in humans.

Mixed isotype clones were rare in our data (fig. S19E).

PMC7612735

Cross-tissue immune cell analysis reveals tissue-specific features in humans.

Next, we evaluated the distribution of expanded clones across tissues and cell types, and found three major groups of clones - present in only two tissues, three to four tissues or five or more tissues, respectively (Fig. 3G), similar to previously reported patterns of B cell clonal tissue distribution (53).

PMC7612735

Cross-tissue immune cell analysis reveals tissue-specific features in humans.

While the clones restricted to two tissues, typically between the spleen and the liver or bone marrow, were enriched in plasma cells, those distributed across more than five tissues, including lymph nodes, were over-represented in memory B cells.

PMC7612735

Cross-tissue immune cell analysis reveals tissue-specific features in humans.

Together, these findings suggest that tissue-restricted clones may represent long-term immunological memory maintained by long-lived plasma cells resident in the bone marrow and spleen as well as liver in our data.

PMC7612735

Cross-tissue immune cell analysis reveals tissue-specific features in humans.

Overall, we characterized nine cell states in the B cell compartment, and gained insights from in-depth characterisation of both naive and memory B cell as well as plasma cell subsets.

PMC7612735

Cross-tissue immune cell analysis reveals tissue-specific features in humans.

We identified distinct clonal distribution patterns for the more tissue-restricted long-lived quiescent plasma cells versus the broad tissue distribution of classical memory B cell clones.

PMC7612735

Cross-tissue immune cell analysis reveals tissue-specific features in humans.

For annotation of the T cell/innate lymphocyte compartment, CellTypist identified 18 cell types (fig. S20A).

PMC7612735

Cross-tissue immune cell analysis reveals tissue-specific features in humans.

After manual inspection, these clusters were further divided into additional subtypes (e.g. for cytotoxic T cells) (Fig. 4A and fig. S20B).

PMC7612735

Cross-tissue immune cell analysis reveals tissue-specific features in humans.

As described above for the myeloid and B cell compartments, identities of the derived cell types were cross-validated in the immune compartment of the CellTypist training datasets (fig. S20, C and D) and the two independent studies of gut (27) and lung (28) (fig. S20, E and F).

PMC7612735

Cross-tissue immune cell analysis reveals tissue-specific features in humans.

Naive/central memory CD4+ T cells were transcriptionally close to naive CD8+ T cells as defined by high expression of CCR7 and SELL and were mainly found in lymphoid sites (Fig. 4B).

PMC7612735

Cross-tissue immune cell analysis reveals tissue-specific features in humans.

Other CD4+ T cells identified included follicular helper T cells (Tfh) expressing CXCR5, regulatory T cells (Tregs) expressing FOXP3 and CTLA4, effector memory CD4+ T cells, and tissue-resident memory Th1 and Th17 cells expressing CCR9, ITGAE and ITGA1 found largely in intestinal sites (jejunum and ileum) and lungs (Fig. 4, B to D).

PMC7612735

Cross-tissue immune cell analysis reveals tissue-specific features in humans.

Within the memory CD8+ T compartment, we found three major subsets: Trm_gut_CD8 (resident memory T cells, Trm), Tem/emra_CD8 (effector memory, Tem; effector memory re-expressing CD45RA, Temra) and Trm/em_CD8.

PMC7612735

Cross-tissue immune cell analysis reveals tissue-specific features in humans.

These subsets were characterized by differential expression of the chemokine receptors CCR9 and CX3CR1 and the activation marker CRTAM (Fig. 4B).

PMC7612735

Cross-tissue immune cell analysis reveals tissue-specific features in humans.

The Trm_gut_CD8 population (CCR9+) expressed the tissue-residency markers ITGAE and ITGA1, encoding CD103 and CD49a respectively and localized to intestinal sites (Fig. 4B).

PMC7612735

Cross-tissue immune cell analysis reveals tissue-specific features in humans.

By contrast, the Tem/Temra_CD8 population expressing CX3CR1 was found in blood-rich sites (blood, bone marrow, lung, and liver) and was excluded from lymph nodes and gut (Fig. 4, C and D), consistent with previous flow cytometry analysis of Temra cells (54), and results showing CX3CR1+CD8+ T cells as blood-confined and absent from thoracic duct lymph (55).

PMC7612735

Cross-tissue immune cell analysis reveals tissue-specific features in humans.

The Trm/em_CD8 population expressed high levels of CRTAM, a gene previously shown to be expressed by Trm (56) and was found in spleen, bone marrow, and to a lesser extent in lymph nodes and lungs.

PMC7612735

Cross-tissue immune cell analysis reveals tissue-specific features in humans.

This may be a resident population more prevalent in lymphoid sites (16).

PMC7612735

Cross-tissue immune cell analysis reveals tissue-specific features in humans.

We validated and mapped the Trm/em_CD8 population using smFISH in the liver (Fig. 4E) and lung-draining lymph nodes (Fig. 4F).

PMC7612735

Cross-tissue immune cell analysis reveals tissue-specific features in humans.

Furthermore, we validated all three memory CD8+ T cell populations at the protein level by flow cytometry of cells purified from human spleen (fig. S21).

PMC7612735

Cross-tissue immune cell analysis reveals tissue-specific features in humans.

Although we could validate CRTAM at the RNA level by smFISH, the protein could not be detected without stimulation, suggesting that CRTAM is subject to post-translational regulation upon T-cell receptor (TCR) activation.

PMC7612735

Cross-tissue immune cell analysis reveals tissue-specific features in humans.

These three distinct populations represent different states of tissue adaptation and maturation between effector memory and tissue-resident T cell memory states.

PMC7612735

Cross-tissue immune cell analysis reveals tissue-specific features in humans.

We also detected invariant T cell subsets such as MAIT cells, characterised by expression of TRAV1-2 and SLC4A10, and two populations of γδ T cells: Trm_Tgd and Tgd_CRTAM+.

PMC7612735

Cross-tissue immune cell analysis reveals tissue-specific features in humans.

The CCR9+ Trm_Tgd population populated the gut and expressed the tissue-residency markers ITGAE and ITGA1, whereas the Tgd_CRTAM+ population overexpressed CRTAM, IKZF2 (encoding HELIOS) and the integrin molecule ITGAD (encoding CD11d) and was found primarily in the spleen, bone marrow and liver (Fig. 4, B to D, and fig. S22, A and B).

PMC7612735

Cross-tissue immune cell analysis reveals tissue-specific features in humans.

We validated the latter population by quantitative PCR (qPCR) of flow sorted CD3+TCRγδ+ and CD3+TCRαβ+ cells from cryopreserved spleen samples from three donors (fig. S22C, D).

PMC7612735

Cross-tissue immune cell analysis reveals tissue-specific features in humans.

As a small fraction of ɑβ T cells, marked by low expression of CD52 and CD127, were also noted to express ITGAD, the CD3+TCRαβ population was split into CD52-CD127- and CD52+CD127+ subpopulations.

PMC7612735

Cross-tissue immune cell analysis reveals tissue-specific features in humans.

In keeping with our scRNA-seq data, ITGAD expression was high in CD3+TCRγδ and CD52-CD127-CD3+TCRαβ, providing additional evidence for the specific expression of this integrin alpha subunit in this subpopulation of γδ T cells.

PMC7612735

Cross-tissue immune cell analysis reveals tissue-specific features in humans.

Lastly, NK cells in our data were represented by two clusters with high expression of either FCGR3A (encoding CD16) or NCAM1 (encoding CD56).

PMC7612735

Cross-tissue immune cell analysis reveals tissue-specific features in humans.

We also defined an ILC3 population within a small cluster mixed with NK cells, via expression of markers including PCDH9 (Fig. 4, A and B).

PMC7612735

Cross-tissue immune cell analysis reveals tissue-specific features in humans.

Analyses of the tissue distribution of these populations revealed that, whereas the majority of CD4+ T and ILC3 cells were located in the lymph nodes and to some extent in the spleen, cytotoxic T and NK cells were more abundant in the bone marrow, spleen and non-lymphoid tissues (Fig. 4, C and D).

PMC7612735

Cross-tissue immune cell analysis reveals tissue-specific features in humans.

To understand T cell-mediated protection in more depth, we analysed T cell clonal distribution in a subset of the data within different tissues of a single individual and across different individuals.