ABSTRACT
Immune cells are characterized by diversity, specificity, plasticity, and adaptability-properties that enable them to contribute to homeostasis and respond specifically and dynamically to the many threats encountered by the body. Single-cell technologies, including the assessment of transcriptomics, genomics, and proteomics at the level of individual cells, are ideally suited to studying these properties of immune cells. In this review we discuss the benefits of adopting single-cell approaches in studying underappreciated qualities of immune cells and highlight examples where these technologies have been critical to advancing our understanding of the immune system in health and disease.
Subject(s)
Immune System/immunology , Immune System/metabolism , Immunity , Single-Cell Analysis , Animals , Biomarkers , Disease Susceptibility , Homeostasis , Humans , Immune System/cytology , Molecular Imaging , Single-Cell Analysis/methodsABSTRACT
Haematopoiesis in the bone marrow (BM) maintains blood and immune cell production throughout postnatal life. Haematopoiesis first emerges in human BM at 11-12 weeks after conception1,2, yet almost nothing is known about how fetal BM (FBM) evolves to meet the highly specialized needs of the fetus and newborn. Here we detail the development of FBM, including stroma, using multi-omic assessment of mRNA and multiplexed protein epitope expression. We find that the full blood and immune cell repertoire is established in FBM in a short time window of 6-7 weeks early in the second trimester. FBM promotes rapid and extensive diversification of myeloid cells, with granulocytes, eosinophils and dendritic cell subsets emerging for the first time. The substantial expansion of B lymphocytes in FBM contrasts with fetal liver at the same gestational age. Haematopoietic progenitors from fetal liver, FBM and cord blood exhibit transcriptional and functional differences that contribute to tissue-specific identity and cellular diversification. Endothelial cell types form distinct vascular structures that we show are regionally compartmentalized within FBM. Finally, we reveal selective disruption of B lymphocyte, erythroid and myeloid development owing to a cell-intrinsic differentiation bias as well as extrinsic regulation through an altered microenvironment in Down syndrome (trisomy 21).
Subject(s)
Bone Marrow Cells/cytology , Bone Marrow , Down Syndrome/blood , Down Syndrome/immunology , Fetus/cytology , Hematopoiesis , Immune System/cytology , B-Lymphocytes/cytology , Dendritic Cells/cytology , Down Syndrome/metabolism , Down Syndrome/pathology , Endothelial Cells/pathology , Eosinophils/cytology , Erythroid Cells/cytology , Granulocytes/cytology , Humans , Immunity , Myeloid Cells/cytology , Stromal Cells/cytologyABSTRACT
Definitive haematopoiesis in the fetal liver supports self-renewal and differentiation of haematopoietic stem cells and multipotent progenitors (HSC/MPPs) but remains poorly defined in humans. Here, using single-cell transcriptome profiling of approximately 140,000 liver and 74,000 skin, kidney and yolk sac cells, we identify the repertoire of human blood and immune cells during development. We infer differentiation trajectories from HSC/MPPs and evaluate the influence of the tissue microenvironment on blood and immune cell development. We reveal physiological erythropoiesis in fetal skin and the presence of mast cells, natural killer and innate lymphoid cell precursors in the yolk sac. We demonstrate a shift in the haemopoietic composition of fetal liver during gestation away from being predominantly erythroid, accompanied by a parallel change in differentiation potential of HSC/MPPs, which we functionally validate. Our integrated map of fetal liver haematopoiesis provides a blueprint for the study of paediatric blood and immune disorders, and a reference for harnessing the therapeutic potential of HSC/MPPs.
Subject(s)
Fetus/cytology , Hematopoiesis , Liver/cytology , Liver/embryology , Blood Cells/cytology , Cellular Microenvironment , Female , Fetus/metabolism , Flow Cytometry , Gene Expression Profiling , Humans , Liver/metabolism , Lymphoid Tissue/cytology , Single-Cell Analysis , Stem Cells/metabolismABSTRACT
During early human pregnancy the uterine mucosa transforms into the decidua, into which the fetal placenta implants and where placental trophoblast cells intermingle and communicate with maternal cells. Trophoblast-decidual interactions underlie common diseases of pregnancy, including pre-eclampsia and stillbirth. Here we profile the transcriptomes of about 70,000 single cells from first-trimester placentas with matched maternal blood and decidual cells. The cellular composition of human decidua reveals subsets of perivascular and stromal cells that are located in distinct decidual layers. There are three major subsets of decidual natural killer cells that have distinctive immunomodulatory and chemokine profiles. We develop a repository of ligand-receptor complexes and a statistical tool to predict the cell-type specificity of cell-cell communication via these molecular interactions. Our data identify many regulatory interactions that prevent harmful innate or adaptive immune responses in this environment. Our single-cell atlas of the maternal-fetal interface reveals the cellular organization of the decidua and placenta, and the interactions that are critical for placentation and reproductive success.
Subject(s)
Cell Communication , Fetus/cytology , Histocompatibility, Maternal-Fetal/immunology , Placenta/cytology , Placenta/metabolism , Pregnancy/immunology , Single-Cell Analysis , Cell Communication/immunology , Cell Differentiation/genetics , Decidua/cytology , Decidua/immunology , Decidua/metabolism , Female , Fetus/immunology , Fetus/metabolism , Humans , Killer Cells, Natural/cytology , Killer Cells, Natural/immunology , Ligands , Placenta/immunology , RNA, Small Cytoplasmic/genetics , Sequence Analysis, RNA , Stromal Cells/cytology , Stromal Cells/metabolism , Transcriptome , Trophoblasts/cytology , Trophoblasts/immunology , Trophoblasts/metabolismABSTRACT
Recent advances in genome sequencing technologies provide unprecedented opportunities to characterize individual genomic landscapes and identify mutations relevant for diagnosis and therapy. Specifically, whole-exome sequencing using next-generation sequencing (NGS) technologies is gaining popularity in the human genetics community due to the moderate costs, manageable data amounts and straightforward interpretation of analysis results. While whole-exome and, in the near future, whole-genome sequencing are becoming commodities, data analysis still poses significant challenges and led to the development of a plethora of tools supporting specific parts of the analysis workflow or providing a complete solution. Here, we surveyed 205 tools for whole-genome/whole-exome sequencing data analysis supporting five distinct analytical steps: quality assessment, alignment, variant identification, variant annotation and visualization. We report an overview of the functionality, features and specific requirements of the individual tools. We then selected 32 programs for variant identification, variant annotation and visualization, which were subjected to hands-on evaluation using four data sets: one set of exome data from two patients with a rare disease for testing identification of germline mutations, two cancer data sets for testing variant callers for somatic mutations, copy number variations and structural variations, and one semi-synthetic data set for testing identification of copy number variations. Our comprehensive survey and evaluation of NGS tools provides a valuable guideline for human geneticists working on Mendelian disorders, complex diseases and cancers.
Subject(s)
Computational Biology/methods , High-Throughput Nucleotide Sequencing/statistics & numerical data , Sequence Analysis, DNA/statistics & numerical data , DNA Copy Number Variations , Disease/genetics , Exome , Genetic Variation , Genome, Human , Humans , Molecular Sequence Annotation , Mutation , Sequence Alignment/statistics & numerical data , SoftwareABSTRACT
Single cell data integration methods aim to integrate cells across data batches and modalities, and data integration tasks can be categorized into horizontal, vertical, diagonal, and mosaic integration, where mosaic integration is the most general and challenging case with few methods developed. We propose scMoMaT, a method that is able to integrate single cell multi-omics data under the mosaic integration scenario using matrix tri-factorization. During integration, scMoMaT is also able to uncover the cluster specific bio-markers across modalities. These multi-modal bio-markers are used to interpret and annotate the clusters to cell types. Moreover, scMoMaT can integrate cell batches with unequal cell type compositions. Applying scMoMaT to multiple real and simulated datasets demonstrated these features of scMoMaT and showed that scMoMaT has superior performance compared to existing methods. Specifically, we show that integrated cell embedding combined with learned bio-markers lead to cell type annotations of higher quality or resolution compared to their original annotations.
Subject(s)
Multiomics , SoftwareABSTRACT
Recent mechanistic insights obtained from preclinical studies and the approval of the first immunotherapies has motivated increasing number of academic investigators and pharmaceutical/biotech companies to further elucidate the role of immunity in tumor pathogenesis and to reconsider the role of immunotherapy. Additionally, technological advances (e.g., next-generation sequencing) are providing unprecedented opportunities to draw a comprehensive picture of the tumor genomics landscape and ultimately enable individualized treatment. However, the increasing complexity of the generated data and the plethora of bioinformatics methods and tools pose considerable challenges to both tumor immunologists and clinical oncologists. In this review, we describe current concepts and future challenges for the management and analysis of data for cancer immunology and immunotherapy. We first highlight publicly available databases with specific focus on cancer immunology including databases for somatic mutations and epitope databases. We then give an overview of the bioinformatics methods for the analysis of next-generation sequencing data (whole-genome and exome sequencing), epitope prediction tools as well as methods for integrative data analysis and network modeling. Mathematical models are powerful tools that can predict and explain important patterns in the genetic and clinical progression of cancer. Therefore, a survey of mathematical models for tumor evolution and tumor-immune cell interaction is included. Finally, we discuss future challenges for individualized immunotherapy and suggest how a combined computational/experimental approaches can lead to new insights into the molecular mechanisms of cancer, improved diagnosis, and prognosis of the disease and pinpoint novel therapeutic targets.
Subject(s)
Computational Biology/methods , Immunotherapy , Neoplasms/immunology , Neoplasms/therapy , B-Lymphocytes/immunology , Base Sequence , Databases, Genetic , Epitopes/immunology , Humans , Models, Biological , Molecular Sequence Data , Neoplasms/genetics , Sequence Analysis, DNA , T-Lymphocytes/immunologyABSTRACT
Cell-cell communication is crucial for development and tissue homeostasis in multicellular organisms. Single-cell transcriptomics has emerged as a revolutionary technique for dissecting cellular compositions and potential cell-cell communication events via ligand-receptor pairs. To provide a systematic characterization of intercellular communication, we developed a framework to map cell-cell communication events mediated by ligand-receptor interactions across different cell types using single-cell transcriptomics data. Our repository of ligands, receptors and their interactions is integrated with a computational approach to identify cell-type specific and biologically relevant interactions. Here, we summarize the structure and content of our repository and present a practical guide for inferring cell-cell communication networks from single-cell RNA sequencing data.
Subject(s)
Receptors, Cell Surface/genetics , Single-Cell Analysis , Cell Communication/genetics , Humans , Ligands , Sequence Analysis, RNA , Software , TranscriptomeABSTRACT
Multimodal data is rapidly growing in many fields of science and engineering, including single-cell biology. We introduce MultiMAP, a novel algorithm for dimensionality reduction and integration. MultiMAP can integrate any number of datasets, leverages features not present in all datasets, is not restricted to a linear mapping, allows the user to specify the influence of each dataset, and is extremely scalable to large datasets. We apply MultiMAP to single-cell transcriptomics, chromatin accessibility, methylation, and spatial data and show that it outperforms current approaches. On a new thymus dataset, we use MultiMAP to integrate cells along a temporal trajectory. This enables quantitative comparison of transcription factor expression and binding site accessibility over the course of T cell differentiation, revealing patterns of expression versus binding site opening kinetics.
Subject(s)
Chromosome Mapping/methods , Single-Cell Analysis/methods , Transcriptome , Algorithms , Chromatin , Chromosomes, Human , Gene Expression Regulation , Genetic Markers , Genomics , Humans , Software , Transcription FactorsABSTRACT
The transcription factor Rora has been shown to be important for the development of ILC2 and the regulation of ILC3, macrophages and Treg cells. Here we investigate the role of Rora across CD4+ T cells in general, but with an emphasis on Th2 cells, both in vitro as well as in the context of several in vivo type 2 infection models. We dissect the function of Rora using overexpression and a CD4-conditional Rora-knockout mouse, as well as a RORA-reporter mouse. We establish the importance of Rora in CD4+ T cells for controlling lung inflammation induced by Nippostrongylus brasiliensis infection, and have measured the effect on downstream genes using RNA-seq. Using a systematic stimulation screen of CD4+ T cells, coupled with RNA-seq, we identify upstream regulators of Rora, most importantly IL-33 and CCL7. Our data suggest that Rora is a negative regulator of the immune system, possibly through several downstream pathways, and is under control of the local microenvironment.
Subject(s)
CD4-Positive T-Lymphocytes/immunology , Macrophages/immunology , Nuclear Receptor Subfamily 1, Group F, Member 1/immunology , Nuclear Receptor Subfamily 1, Group F, Member 1/metabolism , Pneumonia/immunology , Th2 Cells/immunology , Animals , Antigens, Helminth/immunology , Antigens, Helminth/metabolism , Cells, Cultured , Cytokines/metabolism , Disease Models, Animal , Female , Gene Expression Regulation/immunology , Lymphocyte Activation , Mice , Mice, Inbred C57BL , Mice, Knockout , Mice, Transgenic , Nippostrongylus/immunology , Pneumonia/parasitology , Pneumonia/pathology , Strongylida Infections/immunology , Strongylida Infections/parasitologyABSTRACT
BACKGROUND: Immunotherapy with checkpoint inhibitors has shown impressive results in patients with melanoma, but still many do not benefit from this line of treatment. A lack of tumor-infiltrating T cells is a common reason for therapy failure but also a loss of intratumoral dendritic cells (DCs) has been described. METHODS: We used the transgenic tg(Grm1)EPv melanoma mouse strain that develops spontaneous, slow-growing tumors to perform immunological analysis during tumor progression. With flow cytometry, the frequencies of DCs and T cells at different tumor stages and the expression of the inhibitory molecules programmed cell death protein-1 (PD-1) and T-cell immunoglobulin and mucin-domain containing-3 (TIM-3) on T cells were analyzed. This was complemented with RNA-sequencing (RNA-seq) and real-time quantitative PCR (RT-qPCR) analysis to investigate the immune status of the tumors. To boost DC numbers and function, we administered Fms-related tyrosine 3 ligand (Flt3L) plus an adjuvant mix of polyI:C and anti-CD40. To enhance T cell function, we tested several checkpoint blockade antibodies. Immunological alterations were characterized in tumor and tumor-draining lymph nodes (LNs) by flow cytometry, CyTOF, microarray and RT-qPCR to understand how immune cells can control tumor growth. The specific role of migratory skin DCs was investigated by coculture of sorted DC subsets with melanoma-specific CD8+ T cells. RESULTS: Our study revealed that tumor progression is characterized by upregulation of checkpoint molecules and a gradual loss of the dermal conventional DC (cDC) 2 subset. Monotherapy with checkpoint blockade could not restore antitumor immunity, whereas boosting DC numbers and activation increased tumor immunogenicity. This was reflected by higher numbers of activated cDC1 and cDC2 as well as CD4+ and CD8+ T cells in treated tumors. At the same time, the DC boost approach reinforced migratory dermal DC subsets to prime gp100-specific CD8+ T cells in tumor-draining LNs that expressed PD-1/TIM-3 and produced interferon γ (IFNγ)/tumor necrosis factor α (TNFα). As a consequence, the combination of the DC boost with antibodies against PD-1 and TIM-3 released the brake from T cells, leading to improved function within the tumors and delayed tumor growth. CONCLUSIONS: Our results set forth the importance of skin DC in cancer immunotherapy, and demonstrates that restoring DC function is key to enhancing tumor immunogenicity and subsequently responsiveness to checkpoint blockade therapy.
Subject(s)
Antibodies/administration & dosage , Hepatitis A Virus Cellular Receptor 2/metabolism , Immune Checkpoint Inhibitors/administration & dosage , Melanoma, Experimental/drug therapy , Poly I-C/administration & dosage , Programmed Cell Death 1 Receptor/metabolism , Skin/cytology , Animals , Antibodies/pharmacology , CD40 Antigens/antagonists & inhibitors , Cell Line, Tumor , Coculture Techniques , Dendritic Cells/drug effects , Dendritic Cells/immunology , Gene Expression Regulation, Neoplastic/drug effects , Hepatitis A Virus Cellular Receptor 2/genetics , Humans , Immune Checkpoint Inhibitors/pharmacology , Melanoma, Experimental/genetics , Melanoma, Experimental/immunology , Melanoma, Experimental/pathology , Mice , Neoplasm Staging , Poly I-C/pharmacology , Programmed Cell Death 1 Receptor/genetics , Sequence Analysis, RNA , Skin/drug effects , Skin/immunologyABSTRACT
The skin confers biophysical and immunological protection through a complex cellular network established early in embryonic development. We profiled the transcriptomes of more than 500,000 single cells from developing human fetal skin, healthy adult skin, and adult skin with atopic dermatitis and psoriasis. We leveraged these datasets to compare cell states across development, homeostasis, and disease. Our analysis revealed an enrichment of innate immune cells in skin during the first trimester and clonal expansion of disease-associated lymphocytes in atopic dermatitis and psoriasis. We uncovered and validated in situ a reemergence of prenatal vascular endothelial cell and macrophage cellular programs in atopic dermatitis and psoriasis lesional skin. These data illustrate the dynamism of cutaneous immunity and provide opportunities for targeting pathological developmental programs in inflammatory skin diseases.
Subject(s)
Dermatitis, Atopic/embryology , Dermatitis, Atopic/pathology , Psoriasis/embryology , Psoriasis/pathology , Skin/embryology , Animals , Atlases as Topic , Cell Movement , Datasets as Topic , Dendritic Cells/immunology , Dermatitis, Atopic/immunology , Dermatologic Agents/pharmacology , Humans , Immunity, Innate/genetics , Methotrexate/pharmacology , Mice , Phagocytes/immunology , Psoriasis/immunology , Single-Cell Analysis , Skin/cytology , Skin/immunology , T-Lymphocytes/immunology , TranscriptomeABSTRACT
Cell-cell communication mediated by ligand-receptor complexes is critical to coordinating diverse biological processes, such as development, differentiation and inflammation. To investigate how the context-dependent crosstalk of different cell types enables physiological processes to proceed, we developed CellPhoneDB, a novel repository of ligands, receptors and their interactions. In contrast to other repositories, our database takes into account the subunit architecture of both ligands and receptors, representing heteromeric complexes accurately. We integrated our resource with a statistical framework that predicts enriched cellular interactions between two cell types from single-cell transcriptomics data. Here, we outline the structure and content of our repository, provide procedures for inferring cell-cell communication networks from single-cell RNA sequencing data and present a practical step-by-step guide to help implement the protocol. CellPhoneDB v.2.0 is an updated version of our resource that incorporates additional functionalities to enable users to introduce new interacting molecules and reduces the time and resources needed to interrogate large datasets. CellPhoneDB v.2.0 is publicly available, both as code and as a user-friendly web interface; it can be used by both experts and researchers with little experience in computational genomics. In our protocol, we demonstrate how to evaluate meaningful biological interactions with CellPhoneDB v.2.0 using published datasets. This protocol typically takes ~2 h to complete, from installation to statistical analysis and visualization, for a dataset of ~10 GB, 10,000 cells and 19 cell types, and using five threads.
Subject(s)
Cell Communication/genetics , Gene Expression Profiling/methods , Software , Transcriptome/genetics , Animals , Humans , Ligands , Mice , Receptors, Cell Surface/genetics , Receptors, Cell Surface/metabolism , Sequence Analysis, RNA/methods , Signal Transduction , Single-Cell Analysis/methodsABSTRACT
Hemocytes limit the capacity of mosquitoes to transmit human pathogens. Here we profile the transcriptomes of 8506 hemocytes of Anopheles gambiae and Aedes aegypti mosquito vectors. Our data reveal the functional diversity of hemocytes, with different subtypes of granulocytes expressing distinct and evolutionarily conserved subsets of effector genes. A previously unidentified cell type in An. gambiae, which we term "megacyte," is defined by a specific transmembrane protein marker (TM7318) and high expression of lipopolysaccharide-induced tumor necrosis factor-α transcription factor 3 (LL3). Knockdown experiments indicate that LL3 mediates hemocyte differentiation during immune priming. We identify and validate two main hemocyte lineages and find evidence of proliferating granulocyte populations. This atlas of medically relevant invertebrate immune cells at single-cell resolution identifies cellular events that underpin mosquito immunity to malaria infection.
Subject(s)
Aedes/immunology , Anopheles/immunology , Hemocytes/immunology , Immunity, Cellular , Malaria/transmission , Mosquito Vectors/immunology , Aedes/genetics , Animals , Anopheles/genetics , Female , Gene Expression Profiling , Gene Knockdown Techniques , Granulocytes/immunology , Hemocytes/metabolism , Malaria/immunology , Malaria/parasitology , Mice , Mosquito Vectors/genetics , RNA-Seq , Single-Cell AnalysisABSTRACT
Here, using single-cell RNA sequencing, we examine the stromal compartment in murine melanoma and draining lymph nodes (LNs) at points across tumor development, providing data at http://www.teichlab.org/data/. Naive lymphocytes from LNs undergo activation and clonal expansion within the tumor, before PD1 and Lag3 expression, while tumor-associated myeloid cells promote the formation of a suppressive niche. We identify three temporally distinct stromal populations displaying unique functional signatures, conserved across mouse and human tumors. Whereas "immune" stromal cells are observed in early tumors, "contractile" cells become more prevalent at later time points. Complement component C3 is specifically expressed in the immune population. Its cleavage product C3a supports the recruitment of C3aR+ macrophages, and perturbation of C3a and C3aR disrupts immune infiltration, slowing tumor growth. Our results highlight the power of scRNA-seq to identify complex interplays and increase stromal diversity as a tumor develops, revealing that stromal cells acquire the capacity to modulate immune landscapes from early disease.
Subject(s)
Melanoma/immunology , Sequence Analysis, RNA/methods , Stromal Cells/metabolism , Tumor Microenvironment/immunology , Animals , Humans , MiceABSTRACT
Psoriatic arthritis (PsA) is a debilitating immune-mediated inflammatory arthritis of unknown pathogenesis commonly affecting patients with skin psoriasis. Here we use complementary single-cell approaches to study leukocytes from PsA joints. Mass cytometry demonstrates a 3-fold expansion of memory CD8 T cells in the joints of PsA patients compared to peripheral blood. Meanwhile, droplet-based and plate-based single-cell RNA sequencing of paired T cell receptor alpha and beta chain sequences show pronounced CD8 T cell clonal expansions within the joints. Transcriptome analyses find these expanded synovial CD8 T cells to express cycling, activation, tissue-homing and tissue residency markers. T cell receptor sequence comparison between patients identifies clonal convergence. Finally, chemokine receptor CXCR3 is upregulated in the expanded synovial CD8 T cells, while two CXCR3 ligands, CXCL9 and CXCL10, are elevated in PsA synovial fluid. Our data thus provide a quantitative molecular insight into the cellular immune landscape of psoriatic arthritis.
Subject(s)
Arthritis, Psoriatic/immunology , CD8-Positive T-Lymphocytes/immunology , Clonal Selection, Antigen-Mediated , Receptors, Lymphocyte Homing/metabolism , Synovial Fluid/immunology , Arthritis, Psoriatic/blood , CD8-Positive T-Lymphocytes/metabolism , Gene Expression Profiling , Humans , Immunologic Memory , Receptors, Antigen, T-Cell, alpha-beta/genetics , Receptors, Antigen, T-Cell, alpha-beta/metabolism , Receptors, Chemokine/metabolism , Receptors, Lymphocyte Homing/genetics , Single-Cell Analysis , Synovial Membrane/immunologyABSTRACT
Tissue-resident immune cells are important for organ homeostasis and defense. The epithelium may contribute to these functions directly or by cross-talk with immune cells. We used single-cell RNA sequencing to resolve the spatiotemporal immune topology of the human kidney. We reveal anatomically defined expression patterns of immune genes within the epithelial compartment, with antimicrobial peptide transcripts evident in pelvic epithelium in the mature, but not fetal, kidney. A network of tissue-resident myeloid and lymphoid immune cells was evident in both fetal and mature kidney, with postnatal acquisition of transcriptional programs that promote infection-defense capabilities. Epithelial-immune cross-talk orchestrated localization of antibacterial macrophages and neutrophils to the regions of the kidney most susceptible to infection. Overall, our study provides a global overview of how the immune landscape of the human kidney is zonated to counter the dominant immunological challenge.
Subject(s)
Kidney/immunology , Macrophages/cytology , Neutrophils/cytology , Adult , Animals , Epithelial Cells/cytology , Female , Fetus , Gene Expression Regulation, Developmental , Humans , Kidney/anatomy & histology , Kidney/cytology , Lymphocytes/cytology , Mice, Inbred C57BL , Mice, Transgenic , Myeloid Cells/cytology , RNA-Seq , Single-Cell Analysis , Urinary Tract Infections/immunologyABSTRACT
Human lungs enable efficient gas exchange and form an interface with the environment, which depends on mucosal immunity for protection against infectious agents. Tightly controlled interactions between structural and immune cells are required to maintain lung homeostasis. Here, we use single-cell transcriptomics to chart the cellular landscape of upper and lower airways and lung parenchyma in healthy lungs, and lower airways in asthmatic lungs. We report location-dependent airway epithelial cell states and a novel subset of tissue-resident memory T cells. In the lower airways of patients with asthma, mucous cell hyperplasia is shown to stem from a novel mucous ciliated cell state, as well as goblet cell hyperplasia. We report the presence of pathogenic effector type 2 helper T cells (TH2) in asthmatic lungs and find evidence for type 2 cytokines in maintaining the altered epithelial cell states. Unbiased analysis of cell-cell interactions identifies a shift from airway structural cell communication in healthy lungs to a TH2-dominated interactome in asthmatic lungs.
Subject(s)
Asthma/pathology , Lung/cytology , Adult , Aged , CD4-Positive T-Lymphocytes/physiology , Cell Communication , Epithelial Cells/immunology , Epithelial Cells/physiology , Female , Genome-Wide Association Study , Goblet Cells/metabolism , Humans , Lung/immunology , Lung/pathology , Male , Metaplasia , Middle Aged , Th2 Cells/physiology , TranscriptomeABSTRACT
The cancer immunoediting hypothesis postulates a dual role of the immune system: protecting the host by eliminating tumor cells, and shaping the tumor by editing its genome. Here, we elucidate the impact of evolutionary and immune-related forces on editing the tumor in a mouse model for hypermutated and microsatellite-instable colorectal cancer. Analyses of wild-type and immunodeficient RAG1 knockout mice transplanted with MC38 cells reveal that upregulation of checkpoint molecules and infiltration by Tregs are the major tumor escape mechanisms. Our results show that the effects of immunoediting are weak and that neutral accumulation of mutations dominates. Targeting the PD-1/PD-L1 pathway using immune checkpoint blocker effectively potentiates immunoediting. The immunoediting effects are less pronounced in the CT26 cell line, a non-hypermutated/microsatellite-instable model. Our study demonstrates that neutral evolution is another force that contributes to sculpting the tumor and that checkpoint blockade effectively enforces T-cell-dependent immunoselective pressure.