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1.
Nat Immunol ; 21(3): 343-353, 2020 03.
Article in English | MEDLINE | ID: mdl-32066951

ABSTRACT

Gastrointestinal microbiota and immune cells interact closely and display regional specificity; however, little is known about how these communities differ with location. Here, we simultaneously assess microbiota and single immune cells across the healthy, adult human colon, with paired characterization of immune cells in the mesenteric lymph nodes, to delineate colonic immune niches at steady state. We describe distinct helper T cell activation and migration profiles along the colon and characterize the transcriptional adaptation trajectory of regulatory T cells between lymphoid tissue and colon. Finally, we show increasing B cell accumulation, clonal expansion and mutational frequency from the cecum to the sigmoid colon and link this to the increasing number of reactive bacterial species.


Subject(s)
Colon/immunology , Colon/microbiology , Gastrointestinal Microbiome/immunology , Adult , B-Lymphocytes/immunology , Colon/cytology , Humans , Intestinal Mucosa/cytology , Intestinal Mucosa/immunology , Intestinal Mucosa/microbiology , Lymph Nodes/cytology , Lymph Nodes/immunology , Lymphocyte Activation , Organ Specificity , RNA-Seq , T-Lymphocytes, Helper-Inducer/immunology , T-Lymphocytes, Regulatory/immunology , Transcriptome
2.
Nature ; 630(8015): 166-173, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38778114

ABSTRACT

For many adult human organs, tissue regeneration during chronic disease remains a controversial subject. Regenerative processes are easily observed in animal models, and their underlying mechanisms are becoming well characterized1-4, but technical challenges and ethical aspects are limiting the validation of these results in humans. We decided to address this difficulty with respect to the liver. This organ displays the remarkable ability to regenerate after acute injury, although liver regeneration in the context of recurring injury remains to be fully demonstrated. Here we performed single-nucleus RNA sequencing (snRNA-seq) on 47 liver biopsies from patients with different stages of metabolic dysfunction-associated steatotic liver disease to establish a cellular map of the liver during disease progression. We then combined these single-cell-level data with advanced 3D imaging to reveal profound changes in the liver architecture. Hepatocytes lose their zonation and considerable reorganization of the biliary tree takes place. More importantly, our study uncovers transdifferentiation events that occur between hepatocytes and cholangiocytes without the presence of adult stem cells or developmental progenitor activation. Detailed analyses and functional validations using cholangiocyte organoids confirm the importance of the PI3K-AKT-mTOR pathway in this process, thereby connecting this acquisition of plasticity to insulin signalling. Together, our data indicate that chronic injury creates an environment that induces cellular plasticity in human organs, and understanding the underlying mechanisms of this process could open new therapeutic avenues in the management of chronic diseases.


Subject(s)
Cell Transdifferentiation , Hepatocytes , Liver Diseases , Liver , Humans , Biliary Tract/cytology , Biliary Tract/metabolism , Biliary Tract/pathology , Biopsy , Cell Plasticity , Chronic Disease , Disease Progression , Epithelial Cells/metabolism , Epithelial Cells/cytology , Epithelial Cells/pathology , Hepatocytes/metabolism , Hepatocytes/cytology , Hepatocytes/pathology , Insulin/metabolism , Liver/pathology , Liver/metabolism , Liver/cytology , Liver Diseases/pathology , Liver Diseases/metabolism , Liver Regeneration , Organoids/metabolism , Organoids/pathology , Phosphatidylinositol 3-Kinases/metabolism , Proto-Oncogene Proteins c-akt/metabolism , RNA-Seq , Signal Transduction , Single-Cell Analysis , TOR Serine-Threonine Kinases/metabolism
3.
Nature ; 619(7971): 801-810, 2023 Jul.
Article in English | MEDLINE | ID: mdl-37438528

ABSTRACT

The function of a cell is defined by its intrinsic characteristics and its niche: the tissue microenvironment in which it dwells. Here we combine single-cell and spatial transcriptomics data to discover cellular niches within eight regions of the human heart. We map cells to microanatomical locations and integrate knowledge-based and unsupervised structural annotations. We also profile the cells of the human cardiac conduction system1. The results revealed their distinctive repertoire of ion channels, G-protein-coupled receptors (GPCRs) and regulatory networks, and implicated FOXP2 in the pacemaker phenotype. We show that the sinoatrial node is compartmentalized, with a core of pacemaker cells, fibroblasts and glial cells supporting glutamatergic signalling. Using a custom CellPhoneDB.org module, we identify trans-synaptic pacemaker cell interactions with glia. We introduce a druggable target prediction tool, drug2cell, which leverages single-cell profiles and drug-target interactions to provide mechanistic insights into the chronotropic effects of drugs, including GLP-1 analogues. In the epicardium, we show enrichment of both IgG+ and IgA+ plasma cells forming immune niches that may contribute to infection defence. Overall, we provide new clarity to cardiac electro-anatomy and immunology, and our suite of computational approaches can be applied to other tissues and organs.


Subject(s)
Cellular Microenvironment , Heart , Multiomics , Myocardium , Humans , Cell Communication , Fibroblasts/cytology , Glutamic Acid/metabolism , Heart/anatomy & histology , Heart/innervation , Ion Channels/metabolism , Myocardium/cytology , Myocardium/immunology , Myocardium/metabolism , Myocytes, Cardiac/cytology , Neuroglia/cytology , Pericardium/cytology , Pericardium/immunology , Plasma Cells/immunology , Receptors, G-Protein-Coupled/metabolism , Sinoatrial Node/anatomy & histology , Sinoatrial Node/cytology , Sinoatrial Node/physiology , Heart Conduction System/anatomy & histology , Heart Conduction System/cytology , Heart Conduction System/metabolism
4.
Nature ; 615(7950): 134-142, 2023 03.
Article in English | MEDLINE | ID: mdl-36470304

ABSTRACT

Preventing SARS-CoV-2 infection by modulating viral host receptors, such as angiotensin-converting enzyme 2 (ACE2)1, could represent a new chemoprophylactic approach for COVID-19 that complements vaccination2,3. However, the mechanisms that control the expression of ACE2 remain unclear. Here we show that the farnesoid X receptor (FXR) is a direct regulator of ACE2 transcription in several tissues affected by COVID-19, including the gastrointestinal and respiratory systems. We then use the over-the-counter compound z-guggulsterone and the off-patent drug ursodeoxycholic acid (UDCA) to reduce FXR signalling and downregulate ACE2 in human lung, cholangiocyte and intestinal organoids and in the corresponding tissues in mice and hamsters. We show that the UDCA-mediated downregulation of ACE2 reduces susceptibility to SARS-CoV-2 infection in vitro, in vivo and in human lungs and livers perfused ex situ. Furthermore, we reveal that UDCA reduces the expression of ACE2 in the nasal epithelium in humans. Finally, we identify a correlation between UDCA treatment and positive clinical outcomes after SARS-CoV-2 infection using retrospective registry data, and confirm these findings in an independent validation cohort of recipients of liver transplants. In conclusion, we show that FXR has a role in controlling ACE2 expression and provide evidence that modulation of this pathway could be beneficial for reducing SARS-CoV-2 infection, paving the way for future clinical trials.


Subject(s)
Angiotensin-Converting Enzyme 2 , COVID-19 , Receptors, Virus , Ursodeoxycholic Acid , Animals , Humans , Mice , Angiotensin-Converting Enzyme 2/genetics , Angiotensin-Converting Enzyme 2/metabolism , COVID-19/metabolism , COVID-19/prevention & control , Receptors, Virus/genetics , Receptors, Virus/metabolism , Retrospective Studies , SARS-CoV-2/metabolism , COVID-19 Drug Treatment , Cricetinae , Transcription, Genetic , Ursodeoxycholic Acid/pharmacology , Lung/drug effects , Lung/metabolism , Organoids/drug effects , Organoids/metabolism , Liver/drug effects , Liver/metabolism , Nasal Mucosa/drug effects , Nasal Mucosa/metabolism , Registries , Reproducibility of Results , Liver Transplantation
5.
Immunity ; 50(4): 1099-1114.e10, 2019 04 16.
Article in English | MEDLINE | ID: mdl-30876876

ABSTRACT

Inflammatory bowel disease is a chronic, relapsing condition with two subtypes, Crohn's disease (CD) and ulcerative colitis (UC). Genome-wide association studies (GWASs) in UC implicate a FCGR2A variant that alters the binding affinity of the antibody receptor it encodes, FcγRIIA, for immunoglobulin G (IgG). Here, we aimed to understand the mechanisms whereby changes in FcγRIIA affinity would affect inflammation in an IgA-dominated organ. We found a profound induction of anti-commensal IgG and a concomitant increase in activating FcγR signaling in the colonic mucosa of UC patients. Commensal-IgG immune complexes engaged gut-resident FcγR-expressing macrophages, inducing NLRP3- and reactive-oxygen-species-dependent production of interleukin-1ß (IL-1ß) and neutrophil-recruiting chemokines. These responses were modulated by the FCGR2A genotype. In vivo manipulation of macrophage FcγR signal strength in a mouse model of UC determined the magnitude of intestinal inflammation and IL-1ß-dependent type 17 immunity. The identification of an important contribution of IgG-FcγR-dependent inflammation to UC has therapeutic implications.


Subject(s)
Antibodies, Bacterial/immunology , Colitis, Ulcerative/immunology , Gastrointestinal Microbiome/immunology , Immunoglobulin G/immunology , Interleukin-1beta/immunology , Th17 Cells/immunology , Animals , Colitis/chemically induced , Colitis/immunology , Colitis/microbiology , Colitis/pathology , Colitis, Ulcerative/microbiology , Colitis, Ulcerative/pathology , Dextran Sulfate/toxicity , Gene Expression Regulation , Genotype , Humans , Inflammation , Interleukin-8/biosynthesis , Interleukin-8/genetics , Intestinal Mucosa/immunology , Intestinal Mucosa/microbiology , Macrophages/immunology , Mice , Phagocytes/immunology , RNA, Messenger/biosynthesis , Reactive Oxygen Species , Receptors, IgG/biosynthesis , Receptors, IgG/genetics , Receptors, IgG/immunology
6.
Nature ; 608(7924): 724-732, 2022 08.
Article in English | MEDLINE | ID: mdl-35948631

ABSTRACT

The lymphocyte genome is prone to many threats, including programmed mutation during differentiation1, antigen-driven proliferation and residency in diverse microenvironments. Here, after developing protocols for expansion of single-cell lymphocyte cultures, we sequenced whole genomes from 717 normal naive and memory B and T cells and haematopoietic stem cells. All lymphocyte subsets carried more point mutations and structural variants than haematopoietic stem cells, with higher burdens in memory cells than in naive cells, and with T cells accumulating mutations at a higher rate throughout life. Off-target effects of immunological diversification accounted for approximately half of the additional differentiation-associated mutations in lymphocytes. Memory B cells acquired, on average, 18 off-target mutations genome-wide for every on-target IGHV mutation during the germinal centre reaction. Structural variation was 16-fold higher in lymphocytes than in stem cells, with around 15% of deletions being attributable to off-target recombinase-activating gene activity. DNA damage from ultraviolet light exposure and other sporadic mutational processes generated hundreds to thousands of mutations in some memory cells. The mutation burden and signatures of normal B cells were broadly similar to those seen in many B-cell cancers, suggesting that malignant transformation of lymphocytes arises from the same mutational processes that are active across normal ontogeny. The mutational landscape of normal lymphocytes chronicles the off-target effects of programmed genome engineering during immunological diversification and the consequences of differentiation, proliferation and residency in diverse microenvironments.


Subject(s)
Lymphocytes , Mutation , B-Lymphocytes/cytology , B-Lymphocytes/immunology , B-Lymphocytes/metabolism , B-Lymphocytes/pathology , Cell Differentiation , Cell Proliferation , Cellular Microenvironment , DNA Damage/genetics , DNA Damage/radiation effects , Germinal Center/cytology , Germinal Center/immunology , Humans , Immunologic Memory/genetics , Lymphocytes/cytology , Lymphocytes/immunology , Lymphocytes/metabolism , Lymphocytes/pathology , Neoplasms/genetics , Neoplasms/pathology
7.
Nature ; 597(7875): 250-255, 2021 09.
Article in English | MEDLINE | ID: mdl-34497389

ABSTRACT

The cellular landscape of the human intestinal tract is dynamic throughout life, developing in utero and changing in response to functional requirements and environmental exposures. Here, to comprehensively map cell lineages, we use single-cell RNA sequencing and antigen receptor analysis of almost half a million cells from up to 5 anatomical regions in the developing and up to 11 distinct anatomical regions in the healthy paediatric and adult human gut. This reveals the existence of transcriptionally distinct BEST4 epithelial cells throughout the human intestinal tract. Furthermore, we implicate IgG sensing as a function of intestinal tuft cells. We describe neural cell populations in the developing enteric nervous system, and predict cell-type-specific expression of genes associated with Hirschsprung's disease. Finally, using a systems approach, we identify key cell players that drive the formation of secondary lymphoid tissue in early human development. We show that these programs are adopted in inflammatory bowel disease to recruit and retain immune cells at the site of inflammation. This catalogue of intestinal cells will provide new insights into cellular programs in development, homeostasis and disease.


Subject(s)
Aging , Enteric Nervous System/cytology , Fetus/cytology , Health , Intestines/cytology , Intestines/growth & development , Lymph Nodes/cytology , Lymph Nodes/growth & development , Adult , Animals , Child , Crohn Disease/pathology , Datasets as Topic , Enteric Nervous System/anatomy & histology , Enteric Nervous System/embryology , Enteric Nervous System/growth & development , Epithelial Cells/cytology , Female , Fetus/anatomy & histology , Fetus/embryology , Humans , Intestines/embryology , Intestines/innervation , Lymph Nodes/embryology , Lymph Nodes/pathology , Mice , Mice, Inbred C57BL , Organogenesis , Receptors, IgG/metabolism , Signal Transduction , Spatio-Temporal Analysis , Time Factors
8.
Nature ; 593(7859): 405-410, 2021 05.
Article in English | MEDLINE | ID: mdl-33911282

ABSTRACT

Somatic mutations drive the development of cancer and may contribute to ageing and other diseases1,2. Despite their importance, the difficulty of detecting mutations that are only present in single cells or small clones has limited our knowledge of somatic mutagenesis to a minority of tissues. Here, to overcome these limitations, we developed nanorate sequencing (NanoSeq), a duplex sequencing protocol with error rates of less than five errors per billion base pairs in single DNA molecules from cell populations. This rate is two orders of magnitude lower than typical somatic mutation loads, enabling the study of somatic mutations in any tissue independently of clonality. We used this single-molecule sensitivity to study somatic mutations in non-dividing cells across several tissues, comparing stem cells to differentiated cells and studying mutagenesis in the absence of cell division. Differentiated cells in blood and colon displayed remarkably similar mutation loads and signatures to their corresponding stem cells, despite mature blood cells having undergone considerably more divisions. We then characterized the mutational landscape of post-mitotic neurons and polyclonal smooth muscle, confirming that neurons accumulate somatic mutations at a constant rate throughout life without cell division, with similar rates to mitotically active tissues. Together, our results suggest that mutational processes that are independent of cell division are important contributors to somatic mutagenesis. We anticipate that the ability to reliably detect mutations in single DNA molecules could transform our understanding of somatic mutagenesis and enable non-invasive studies on large-scale cohorts.


Subject(s)
Blood Cells/metabolism , Cell Differentiation/genetics , DNA Mutational Analysis/methods , Muscle, Smooth/metabolism , Mutation , Neurons/metabolism , Single Molecule Imaging/methods , Stem Cells/metabolism , Alzheimer Disease/genetics , Blood Cells/cytology , Cell Division , Cohort Studies , Colon/cytology , Epithelium/metabolism , Granulocytes/cytology , Granulocytes/metabolism , Healthy Volunteers , Humans , Male , Middle Aged , Muscle, Smooth/cytology , Mutagenesis , Mutation Rate , Neurons/cytology , Stem Cells/cytology
9.
Nature ; 580(7805): 640-646, 2020 04.
Article in English | MEDLINE | ID: mdl-32350471

ABSTRACT

All normal somatic cells are thought to acquire mutations, but understanding of the rates, patterns, causes and consequences of somatic mutations in normal cells is limited. The uterine endometrium adopts multiple physiological states over a lifetime and is lined by a gland-forming epithelium1,2. Here, using whole-genome sequencing, we show that normal human endometrial glands are clonal cell populations with total mutation burdens that increase at about 29 base substitutions per year and that are many-fold lower than those of endometrial cancers. Normal endometrial glands frequently carry 'driver' mutations in cancer genes, the burden of which increases with age and decreases with parity. Cell clones with drivers often originate during the first decades of life and subsequently progressively colonize the epithelial lining of the endometrium. Our results show that mutational landscapes differ markedly between normal tissues-perhaps shaped by differences in their structure and physiology-and indicate that the procession of neoplastic change that leads to endometrial cancer is initiated early in life.


Subject(s)
DNA Mutational Analysis , Endometrium/cytology , Endometrium/metabolism , Epithelium/metabolism , Health , Mutation , Adult , Age of Onset , Aged , Aged, 80 and over , Aging/genetics , Carcinogenesis/genetics , Clone Cells/cytology , Endometrial Neoplasms/genetics , Endometrium/pathology , Epithelial Cells/cytology , Epithelial Cells/metabolism , Epithelial Cells/pathology , Epithelium/pathology , Female , Humans , Middle Aged , Parity/genetics , Time Factors , Young Adult
10.
Nature ; 588(7838): 466-472, 2020 12.
Article in English | MEDLINE | ID: mdl-32971526

ABSTRACT

Cardiovascular disease is the leading cause of death worldwide. Advanced insights into disease mechanisms and therapeutic strategies require a deeper understanding of the molecular processes involved in the healthy heart. Knowledge of the full repertoire of cardiac cells and their gene expression profiles is a fundamental first step in this endeavour. Here, using state-of-the-art analyses of large-scale single-cell and single-nucleus transcriptomes, we characterize six anatomical adult heart regions. Our results highlight the cellular heterogeneity of cardiomyocytes, pericytes and fibroblasts, and reveal distinct atrial and ventricular subsets of cells with diverse developmental origins and specialized properties. We define the complexity of the cardiac vasculature and its changes along the arterio-venous axis. In the immune compartment, we identify cardiac-resident macrophages with inflammatory and protective transcriptional signatures. Furthermore, analyses of cell-to-cell interactions highlight different networks of macrophages, fibroblasts and cardiomyocytes between atria and ventricles that are distinct from those of skeletal muscle. Our human cardiac cell atlas improves our understanding of the human heart and provides a valuable reference for future studies.


Subject(s)
Myocardium/cytology , Single-Cell Analysis , Transcriptome , Adipocytes/classification , Adipocytes/metabolism , Adult , Angiotensin-Converting Enzyme 2/analysis , Angiotensin-Converting Enzyme 2/genetics , Angiotensin-Converting Enzyme 2/metabolism , Epithelial Cells/classification , Epithelial Cells/metabolism , Epithelium , Female , Fibroblasts/classification , Fibroblasts/metabolism , Gene Expression Profiling , Genome-Wide Association Study , Heart Atria/anatomy & histology , Heart Atria/cytology , Heart Atria/innervation , Heart Ventricles/anatomy & histology , Heart Ventricles/cytology , Heart Ventricles/innervation , Homeostasis/immunology , Humans , Macrophages/immunology , Macrophages/metabolism , Male , Muscle, Skeletal/cytology , Muscle, Skeletal/metabolism , Myocytes, Cardiac/classification , Myocytes, Cardiac/metabolism , Neurons/classification , Neurons/metabolism , Pericytes/classification , Pericytes/metabolism , Receptors, Coronavirus/analysis , Receptors, Coronavirus/genetics , Receptors, Coronavirus/metabolism , SARS-CoV-2/metabolism , SARS-CoV-2/pathogenicity , Stromal Cells/classification , Stromal Cells/metabolism
11.
Blood ; 141(19): 2343-2358, 2023 05 11.
Article in English | MEDLINE | ID: mdl-36758207

ABSTRACT

Classic Hodgkin lymphoma (cHL) has a rich immune infiltrate, which is an intrinsic component of the neoplastic process. Malignant Hodgkin Reed-Sternberg cells (HRSCs) create an immunosuppressive microenvironment by the expression of regulatory molecules, preventing T-cell activation. It has also been demonstrated that mononuclear phagocytes (MNPs) in the vicinity of HRSCs express similar regulatory mechanisms in parallel, and their presence in tissue is associated with inferior patient outcomes. MNPs in cHL have hitherto been identified by a small number of canonical markers and are usually described as tumor-associated macrophages. The organization of MNP networks and interactions with HRSCs remains unexplored at high resolution. Here, we defined the global immune-cell composition of cHL and nonlymphoma lymph nodes, integrating data across single-cell RNA sequencing, spatial transcriptomics, and multiplexed immunofluorescence. We observed that MNPs comprise multiple subsets of monocytes, macrophages, and dendritic cells (DCs). Classical monocytes, macrophages and conventional DC2s were enriched in the vicinity of HRSCs, but plasmacytoid DCs and activated DCs were excluded. Unexpectedly, cDCs and monocytes expressed immunoregulatory checkpoints PD-L1, TIM-3, and the tryptophan-catabolizing protein IDO, at the same level as macrophages. Expression of these molecules increased with age. We also found that classical monocytes are important signaling hubs, potentially controlling the retention of cDC2 and ThExh via CCR1-, CCR4-, CCR5-, and CXCR3-dependent signaling. Enrichment of the cDC2-monocyte-macrophage network in diagnostic biopsies is associated with early treatment failure. These results reveal unanticipated complexity and spatial polarization within the MNP compartment, further demonstrating their potential roles in immune evasion by cHL.


Subject(s)
Hodgkin Disease , Humans , Hodgkin Disease/diagnosis , Reed-Sternberg Cells/metabolism , Macrophages/metabolism , Monocytes/metabolism , Immunosuppressive Agents , Tumor Microenvironment
12.
Nature ; 574(7779): 532-537, 2019 10.
Article in English | MEDLINE | ID: mdl-31645730

ABSTRACT

The colorectal adenoma-carcinoma sequence has provided a paradigmatic framework for understanding the successive somatic genetic changes and consequent clonal expansions that lead to cancer1. However, our understanding of the earliest phases of colorectal neoplastic changes-which may occur in morphologically normal tissue-is comparatively limited, as for most cancer types. Here we use whole-genome sequencing to analyse hundreds of normal crypts from 42 individuals. Signatures of multiple mutational processes were revealed; some of these were ubiquitous and continuous, whereas others were only found in some individuals, in some crypts or during certain periods of life. Probable driver mutations were present in around 1% of normal colorectal crypts in middle-aged individuals, indicating that adenomas and carcinomas are rare outcomes of a pervasive process of neoplastic change across morphologically normal colorectal epithelium. Colorectal cancers exhibit substantially increased mutational burdens relative to normal cells. Sequencing normal colorectal cells provides quantitative insights into the genomic and clonal evolution of cancer.


Subject(s)
Colon/cytology , Epithelial Cells/cytology , Epithelial Cells/metabolism , Mutation , Prodromal Symptoms , Rectum/cytology , Adenoma/genetics , Adenoma/pathology , Aged , Axin Protein/genetics , Carcinoma/genetics , Carcinoma/pathology , Cell Transformation, Neoplastic , Clone Cells/cytology , Clone Cells/metabolism , Colorectal Neoplasms/genetics , Colorectal Neoplasms/pathology , DNA Copy Number Variations , DNA Mutational Analysis , Female , Humans , Intestinal Mucosa/cytology , Intestinal Mucosa/metabolism , Intestinal Mucosa/pathology , Male , Middle Aged , Stem Cells/cytology , Stem Cells/metabolism
13.
Kidney Int ; 106(1): 85-97, 2024 Jul.
Article in English | MEDLINE | ID: mdl-38431215

ABSTRACT

Despite the recent advances in our understanding of the role of lipids, metabolites, and related enzymes in mediating kidney injury, there is limited integrated multi-omics data identifying potential metabolic pathways driving impaired kidney function. The limited availability of kidney biopsies from living donors with acute kidney injury has remained a major constraint. Here, we validated the use of deceased transplant donor kidneys as a good model to study acute kidney injury in humans and characterized these kidneys using imaging and multi-omics approaches. We noted consistent changes in kidney injury and inflammatory markers in donors with reduced kidney function. Neighborhood and correlation analyses of imaging mass cytometry data showed that subsets of kidney cells (proximal tubular cells and fibroblasts) are associated with the expression profile of kidney immune cells, potentially linking these cells to kidney inflammation. Integrated transcriptomic and metabolomic analysis of human kidneys showed that kidney arachidonic acid metabolism and seven other metabolic pathways were upregulated following diminished kidney function. To validate the arachidonic acid pathway in impaired kidney function we demonstrated increased levels of cytosolic phospholipase A2 protein and related lipid mediators (prostaglandin E2) in the injured kidneys. Further, inhibition of cytosolic phospholipase A2 reduced injury and inflammation in human kidney proximal tubular epithelial cells in vitro. Thus, our study identified cell types and metabolic pathways that may be critical for controlling inflammation associated with impaired kidney function in humans.


Subject(s)
Acute Kidney Injury , Phenotype , Humans , Acute Kidney Injury/metabolism , Acute Kidney Injury/pathology , Acute Kidney Injury/etiology , Male , Middle Aged , Metabolomics/methods , Female , Kidney Transplantation/adverse effects , Adult , Image Cytometry/methods , Kidney/pathology , Kidney/metabolism , Phospholipases A2/metabolism , Arachidonic Acid/metabolism , Kidney Tubules, Proximal/metabolism , Kidney Tubules, Proximal/pathology , Transcriptome , Dinoprostone/metabolism , Dinoprostone/analysis , Fibroblasts/metabolism , Gene Expression Profiling , Epithelial Cells/metabolism , Epithelial Cells/pathology , Biopsy , Multiomics
14.
Blood ; 139(23): 3387-3401, 2022 06 09.
Article in English | MEDLINE | ID: mdl-35073399

ABSTRACT

Rare hematopoietic stem and progenitor cell (HSPC) pools outside the bone marrow (BM) contribute to blood production in stress and disease but remain ill-defined. Although nonmobilized peripheral blood (PB) is routinely sampled for clinical management, the diagnosis and monitoring potential of PB HSPCs remain untapped, as no healthy PB HSPC baseline has been reported. Here we comprehensively delineate human extramedullary HSPC compartments comparing spleen, PB, and mobilized PB to BM using single-cell RNA-sequencing and/or functional assays. We uncovered HSPC features shared by extramedullary tissues and others unique to PB. First, in contrast to actively dividing BM HSPCs, we found no evidence of substantial ongoing hematopoiesis in extramedullary tissues at steady state but report increased splenic HSPC proliferative output during stress erythropoiesis. Second, extramedullary hematopoietic stem cells/multipotent progenitors (HSCs/MPPs) from spleen, PB, and mobilized PB share a common transcriptional signature and increased abundance of lineage-primed subsets compared with BM. Third, healthy PB HSPCs display a unique bias toward erythroid-megakaryocytic differentiation. At the HSC/MPP level, this is functionally imparted by a subset of phenotypic CD71+ HSCs/MPPs, exclusively producing erythrocytes and megakaryocytes, highly abundant in PB but rare in other adult tissues. Finally, the unique erythroid-megakaryocytic-skewing of PB is perturbed with age in essential thrombocythemia and ß-thalassemia. Collectively, we identify extramedullary lineage-primed HSPC reservoirs that are nonproliferative in situ and report involvement of splenic HSPCs during demand-adapted hematopoiesis. Our data also establish aberrant composition and function of circulating HSPCs as potential clinical indicators of BM dysfunction.


Subject(s)
Hematopoiesis , Hematopoietic Stem Cells , Adult , Bone Marrow , Bone Marrow Cells/physiology , Erythropoiesis , Humans , Megakaryocytes
15.
Blood ; 139(14): 2227-2239, 2022 04 07.
Article in English | MEDLINE | ID: mdl-35051265

ABSTRACT

The process of platelet production has so far been understood to be a 2-stage process: megakaryocyte maturation from hematopoietic stem cells followed by proplatelet formation, with each phase regulating the peripheral blood platelet count. Proplatelet formation releases into the bloodstream beads-on-a-string preplatelets, which undergo fission into mature platelets. For the first time, we show that preplatelet maturation is a third, tightly regulated, critical process akin to cytokinesis that regulates platelet count. We show that deficiency in cytokine receptor-like factor 3 (CRLF3) in mice leads to an isolated and sustained 25% to 48% reduction in the platelet count without any effect on other blood cell lineages. We show that Crlf3-/- preplatelets have increased microtubule stability, possibly because of increased microtubule glutamylation via the interaction of CRLF3 with key members of the Hippo pathway. Using a mouse model of JAK2 V617F essential thrombocythemia, we show that a lack of CRLF3 leads to long-term lineage-specific normalization of the platelet count. We thereby postulate that targeting CRLF3 has therapeutic potential for treatment of thrombocythemia.


Subject(s)
Blood Platelets , Thrombocythemia, Essential , Blood Platelets/metabolism , Humans , Megakaryocytes/metabolism , Microtubules , Platelet Count , Receptors, Cytokine , Thrombocythemia, Essential/drug therapy , Thrombopoiesis/genetics
16.
Am J Transplant ; 23(2): 165-170, 2023 02.
Article in English | MEDLINE | ID: mdl-36695696

ABSTRACT

For decades, transplantation has been a life-saving treatment for those fortunate enough to gain access. Nevertheless, many patients die waiting for an organ and countless more never make it onto the waitlist because of a shortage of donor organs. Concurrently, thousands of donated organs are declined for transplant each year because of concerns about poor outcomes post-transplant. The decline of any donated organ-even if medically justified-is tragic for both the donor family and potential recipients. In this Personal Viewpoint, we discuss the need for a new mindset in how we honor the gift of organ donation. We believe that the use of transplant-declined human organs in translational research has the potential to hasten breakthrough discoveries in a multitude of scientific and medical areas. More importantly, such breakthroughs will allow us to properly value every donated organ. We further discuss the many practical challenges that such research presents and offer some possible solutions based on experiences in our own research laboratories. Finally, we share our perspective on what we believe are the necessary next steps to ensure a future where every donated organ realizes its full potential to impact the lives of current and future patients.


Subject(s)
Organ Transplantation , Tissue and Organ Procurement , Humans , Tissue Donors , Waiting Lists
17.
Eur Respir J ; 60(2)2022 08.
Article in English | MEDLINE | ID: mdl-35086829

ABSTRACT

The Human Cell Atlas (HCA) consortium aims to establish an atlas of all organs in the healthy human body at single-cell resolution to increase our understanding of basic biological processes that govern development, physiology and anatomy, and to accelerate diagnosis and treatment of disease. The Lung Biological Network of the HCA aims to generate the Human Lung Cell Atlas as a reference for the cellular repertoire, molecular cell states and phenotypes, and cell-cell interactions that characterise normal lung homeostasis in healthy lung tissue. Such a reference atlas of the healthy human lung will facilitate mapping the changes in the cellular landscape in disease. The discovAIR project is one of six pilot actions for the HCA funded by the European Commission in the context of the H2020 framework programme. discovAIR aims to establish the first draft of an integrated Human Lung Cell Atlas, combining single-cell transcriptional and epigenetic profiling with spatially resolving techniques on matched tissue samples, as well as including a number of chronic and infectious diseases of the lung. The integrated Human Lung Cell Atlas will be available as a resource for the wider respiratory community, including basic and translational scientists, clinical medicine, and the private sector, as well as for patients with lung disease and the interested lay public. We anticipate that the Human Lung Cell Atlas will be the founding stone for a more detailed understanding of the pathogenesis of lung diseases, guiding the design of novel diagnostics and preventive or curative interventions.


Subject(s)
Lung Diseases , Lung , Humans , Proteomics , Thorax
18.
Hepatology ; 73(1): 247-267, 2021 01.
Article in English | MEDLINE | ID: mdl-32222998

ABSTRACT

BACKGROUND AND AIMS: Organoids provide a powerful system to study epithelia in vitro. Recently, this approach was applied successfully to the biliary tree, a series of ductular tissues responsible for the drainage of bile and pancreatic secretions. More precisely, organoids have been derived from ductal tissue located outside (extrahepatic bile ducts; EHBDs) or inside the liver (intrahepatic bile ducts; IHBDs). These organoids share many characteristics, including expression of cholangiocyte markers such as keratin (KRT) 19. However, the relationship between these organoids and their tissues of origin, and to each other, is largely unknown. APPROACH AND RESULTS: Organoids were derived from human gallbladder, common bile duct, pancreatic duct, and IHBDs using culture conditions promoting WNT signaling. The resulting IHBD and EHBD organoids expressed stem/progenitor markers leucine-rich repeat-containing G-protein-coupled receptor 5/prominin 1 and ductal markers KRT19/KRT7. However, RNA sequencing revealed that organoids conserve only a limited number of regional-specific markers corresponding to their location of origin. Of particular interest, down-regulation of biliary markers and up-regulation of cell-cycle genes were observed in organoids. IHBD and EHBD organoids diverged in their response to WNT signaling, and only IHBDs were able to express a low level of hepatocyte markers under differentiation conditions. CONCLUSIONS: Taken together, our results demonstrate that differences exist not only between extrahepatic biliary organoids and their tissue of origin, but also between IHBD and EHBD organoids. This information may help to understand the tissue specificity of cholangiopathies and also to identify targets for therapeutic development.


Subject(s)
Bile Ducts, Extrahepatic/cytology , Bile Ducts, Intrahepatic/cytology , Epithelial Cells/cytology , Organoids/physiology , Animals , Bile , Bile Ducts, Extrahepatic/physiology , Bile Ducts, Intrahepatic/physiology , Cell Differentiation , Common Bile Duct/cytology , Epithelial Cells/physiology , Gallbladder/cytology , Gene Expression Regulation , Humans , Keratin-19/analysis , Liver/physiology , Mice , RNA-Seq , Tissue and Organ Procurement
19.
BJU Int ; 130(4): 408-419, 2022 10.
Article in English | MEDLINE | ID: mdl-35388587

ABSTRACT

OBJECTIVES: To summarise the causes of ureteric damage and the current standard of care, discussing the risks and benefits of available therapeutic options. We then focus on the current and future solutions that can be provided by ureteric bioengineering and provide a description of the ideal characteristics of a bioengineered product. METHODS: We performed a literature search in February 2021 in: Google Scholar, Medline, and Web of Science. Three searches were conducted, investigating: (a) the epidemiology of ureteric pathology, (b) the current standard of care, and (c) the state of the art in ureteric bioengineering. RESULTS: The most-common causes of ureteric damage are iatrogenic injury and external trauma. Current approaches to treatment include stent placement or surgical reconstruction. Reconstruction can be done using either urological tissue or segments of the gastrointestinal tract. Limitations include scarring, strictures, and infections. Several bioengineered alternatives have been explored in animal studies, with variations in the choice of scaffold material, cellular seeding populations, and pre-implantation processing. Natural grafts and hybrid material appear to be associated with superior outcomes. Furthermore, seeding of the scaffold material with stem cells or differentiated urothelial cells allows for better function compared to acellular scaffolds. Some studies have attempted to pre-implant the graft in the omentum prior to reconstruction, but this has yet to prove any definitive benefits. CONCLUSION: There is an unmet clinical need for safer and more effective treatment for ureteric injuries. Urological bioengineering is a promising solution in preclinical studies. However, substantial scientific, logistic, and economic challenges must be addressed to harness its transformative potential in improving outcomes.


Subject(s)
Ureter , Urologic Diseases , Animals , Bioengineering , Constriction, Pathologic , Treatment Outcome , Ureter/surgery
20.
J Immunol ; 205(5): 1376-1384, 2020 09 01.
Article in English | MEDLINE | ID: mdl-32737150

ABSTRACT

Acute kidney injury (AKI) is a serious condition affecting one fifth of hospital inpatients. B lymphocytes have immunological functions beyond Ab production and may produce cytokines and chemokines that modulate inflammation. In this study, we investigated leukocyte responses in a mouse model of AKI and observed an increase in circulating and kidney B cells, particularly a B220low subset, following AKI. We found that B cells produce the chemokine CCL7, with the potential to facilitate neutrophil and monocyte recruitment to the injured kidney. Siglec-G-deficient mice, which have increased numbers of B220low innate B cells and a lower B cell activation threshold, had increased Ccl7 transcripts, increased neutrophil and monocyte numbers in the kidney, and more severe AKI. CCL7 blockade in mice reduced myeloid cell infiltration into the kidney and ameliorated AKI. In two independent cohorts of human patients with AKI, we observed significantly higher CCL7 transcripts compared with controls, and in a third cohort, we observed an increase in urinary CCL7 levels in AKI, supporting the clinical importance of this pathway. Together, our data suggest that B cells contribute to early sterile inflammation in AKI via the production of leukocyte-recruiting chemokines.


Subject(s)
Acute Kidney Injury/immunology , B-Lymphocytes/immunology , Chemokine CCL7/immunology , Monocytes/immunology , Neutrophils/immunology , Animals , Cytokines/immunology , Disease Models, Animal , Female , Humans , Inflammation/immunology , Kidney/immunology , Leukocytes/immunology , Male , Mice , Mice, Inbred BALB C , Mice, Inbred C57BL
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