Tissue Niches Research Articles

Molecular and immune signatures, and pathological trajectories of fatal COVID-19 lungs defined by in situ spatial single-cell transcriptome analysis.

Despite intensive studies during the last 3 years, the pathology and underlying molecular mechanism of coronavirus disease 2019 (COVID-19) remain poorly defined. In this study, we investigated the spatial single-cell molecular and cellular features of postmortem COVID-19 lung tissues using in situ sequencing (ISS). We detected 10 414 863 transcripts of 221 genes in whole-slide tissues and segmented them into 1 719 459 cells that were mapped to 18 major parenchymal and immune cell types, all of which were infected by SARS-CoV-2. Compared with the non-COVID-19 control, COVID-19 lungs exhibited reduced alveolar cells (ACs) and increased innate and adaptive immune cells. We also identified 19 differentially expressed genes in both infected and uninfected cells across the tissues, which reflected the altered cellular compositions. Spatial analysis of local infection rates revealed regions with high infection rates that were correlated with high cell densities (HIHD). The HIHD regions expressed high levels of SARS-CoV-2 entry-related factors including ACE2, FURIN, TMPRSS2 and NRP1, and co-localized with organizing pneumonia (OP) and lymphocytic and immune infiltration, which exhibited increased ACs and fibroblasts but decreased vascular endothelial cells and epithelial cells, mirroring the tissue damage and wound healing processes. Sparse nonnegative matrix factorization (SNMF) analysis of niche features identified seven signatures that captured structure and immune niches in COVID-19 tissues. Trajectory inference based on immune niche signatures defined two pathological routes. Trajectory A primarily progressed with increased NK cells and granulocytes, likely reflecting the complication of microbial infections. Trajectory B was marked by increased HIHD and OP, possibly accounting for the increased immune infiltration. The OP regions were marked by high numbers of fibroblasts expressing extremely high levels of COL1A1 and COL1A2. Examination of single-cell RNA-seq data (scRNA-seq) from COVID-19 lung tissues and idiopathic pulmonary fibrosis (IPF) identified similar cell populations consisting mainly of myofibroblasts. Immunofluorescence staining revealed the activation of IL6-STAT3 and TGF-β-SMAD2/3 pathways in these cells, likely mediating the upregulation of COL1A1 and COL1A2 and excessive fibrosis in the lung tissues. Together, this study provides a spatial single-cell atlas of cellular and molecular signatures of fatal COVID-19 lungs, which reveals the complex spatial cellular heterogeneity, organization, and interactions that characterized the COVID-19 lung pathology.

Effects of an aged tissue niche on the immune potency of dendritic cells using simulated microgravity

Microgravity accelerates the aging of various physiological systems, and it is well acknowledged that aged individuals and astronauts both have increased susceptibility to infections and poor response to vaccination. Immunologically, dendritic cells (DCs) are the key players in linking innate and adaptive immune responses. Their distinct and optimized differentiation and maturation phases play a critical role in presenting antigens and mounting effective lymphocyte responses for long-term immunity. Despite their importance, no studies to date have effectively investigated the effects of microgravity on DCs in their native microenvironment, which is primarily located within tissues. Here, we address a significantly outstanding research gap by examining the effects of simulated microgravity via a random positioning machine on both immature and mature DCs cultured in biomimetic collagen hydrogels, a surrogate for tissue matrices. Furthermore, we explored the effects of loose and dense tissues via differences in collagen concentration. Under these various environmental conditions, the DC phenotype was characterized using surface markers, cytokines, function, and transcriptomic profiles. Our data indicate that aged or loose tissue and exposure to RPM-induced simulated microgravity both independently alter the immunogenicity of immature and mature DCs. Interestingly, cells cultured in denser matrices experience fewer effects of simulated microgravity at the transcriptome level. Our findings are a step forward to better facilitate healthier future space travel and enhance our understanding of the aging immune system on Earth.

Grafting Low-Temperature Micronized Adipose Tissue Niche to Treat Diabetic Foot Ulcers: A Pilot Study

Background: In a previous study, we suggested that micronized adipose tissue (MAT) niche could be an effective and safe treatment for diabetic foot ulcers. Fibrin glue was used to solidify the MAT niches. However, it took 40 to 50 minutes for the MAT niche to be ready for application. We have devised an alternate method in which the MAT niche is created at a low temperature to reduce the solidification time. This pilot study aimed to investigate the possibility and safety of grafting a low-temperature MAT niche for treating diabetic foot ulcers.Methods: Patients with diabetic foot ulcers who were treated with low-temperature MAT or conventional methods between March 2020 and December 2021 were included in this study. We evaluated the efficacy of the treatment by measuring the wound size reduction rate. All adverse events were recorded.Results: The MAT niche treatment group showed a statistically significant wound reduction rate during the entire study period of 4 weeks (P<0.005). The wound reduction rates in the 4th week after the treatment were 75.7%±16.9% in the treatment group and 33.5%±19.0% in the control group (P=0.001). No serious adverse events related to low-temperature MAT niche treatment were observed.Conclusion: This pilot study demonstrated the potential of low-temperature MAT niche as an effective and safe method for the treatment of diabetic foot ulcers.

Elucidating and characterizing the dynamic biological processes that account for the sustainability of Leishmania populations

To attempt resolving this issue accurately, it was necessary to anchor our experimental approaches in the observations and pioneering work of our predecessors, notably Alphonse Laveran, Louis Parrot, Edmond and Étienne Sergent. The latter, among other things, had identified as natural hosts of leishmaniasis, rodent populations with which hematophagous telmophagous sand fly populations cohabited closely.When human populations emerged in these natural ecosystems, after the sedentarization of Homo sapiens, more or less important disturbances would have led to a transition of sand fly hematophagy, from zoophilia, to zoo-anthropophilia and anthropophilia.The creation of infrastructures that allow the breeding and integration into experimental groups of both holobiont sand flies and holobiont laboratory rodents (rats, mice, hamsters, etc.) remains crucial. With such infrastructures, it becomes possible to grasp and characterize the multilateral dynamic processes - mostly clinically silent - that account for the biogenesis of tissue and/or cellular niches protecting populations of Leishmania developmental morphotypes, including those ensuring host-to-host transmission, albeit in small numbers.

Systematic dissection of coordinated stromal remodeling identifies Sox10+ glial cells as a therapeutic target in myelofibrosis

Remodeling of the tissue niche is often evident in diseases, yet, the stromal alterations and their contribution to pathogenesis are poorly characterized. Bone marrow fibrosis is a maladaptive feature of primary myelofibrosis (PMF). We performed lineage tracing and found that most collagen-expressing myofibroblasts were derived from leptin-receptor-positive (LepR+) mesenchymal cells, whereas a minority were from Gli1-lineage cells. Deletion of Gli1 did not impact PMF. Unbiased single-cell RNA sequencing (scRNA-seq) confirmed that virtually all myofibroblasts originated from LepR-lineage cells, with reduced expression of hematopoietic niche factors and increased expression of fibrogenic factors. Concurrently, endothelial cells upregulated arteriolar-signature genes. Pericytes and Sox10+ glial cells expanded drastically with heightened cell-cell signaling, suggesting important functional roles in PMF. Chemical or genetic ablation of bone marrow glial cells ameliorated fibrosis and improved other pathology in PMF. Thus, PMF involves complex remodeling of the bone marrow microenvironment, and glial cells represent a promising therapeutic target.

Organoids are not organs: Sources of variation and misinformation inorganoid biology.

In the past decade, the term organoid has moved from obscurity to common use to describe a 3D invitro cellular model of a tissue that recapitulates structural and functional elements of the invivo organ it models. The term organoid is now applied to structures formed as a result of two distinct processes: the capacity for adult epithelial stem cells to re-create a tissue niche invitro and the ability to direct the differentiation of pluripotent stem cells to a 3D self-organizing multicellular model of organogenesis. While these two organoid fields rely upon different stem cell types and recapitulate different processes, both share common challenges around robustness, accuracy, and reproducibility. Critically, organoids are not organs. This commentary serves to discuss these challenges, how they impact genuine utility, and shine a light onthe need to improve the standards applied to all organoid approaches.

Lymph node location and retention properties of DC‐SIGN engagement with the Immunoglobulin Oligomannoses of Follicular Lymphoma

Introduction: The oligomannose-type glycans occupying the surface immunoglobulin antigen-binding site (sIg-Mann) are a tumor-founding post-translational requirement of classic follicular lymphoma (FL). These are universally acquired and a clonal necessity during the entire natural history of FL from the early stages throughout transformation into EZB-DLBCL (Chiodin G, Blood 2021, Odabashian M, Blood 2020). The low-affinity interaction of sIg-Mann with its specific ligand DC-SIGN distinguishes from conventional high-affinity antigen:Ig protein interactions for promoting prolonged low-level growth and prosurvival signals via PI3K/AKT and not endocytosis (Linley A, Blood 2015). However, the location and function of DC-SIGN remains to be further elucidated. Here, we investigated the hypothesis that the specific DC-SIGN:Ig-Mann interaction functions to promote retention of FL cells in tissue niches maintaining selective survival advantage. Methods: Immunofluorescence imaging was used to determine DC-SIGN histological location in primary FL lymph nodes. In WSU-FSCCL cells, DC-SIGN effects on sIg redistribution were measured by dSTORM; adhesion to VCAM-1 in presence/absence of inhibitors was measured by flow cytometry. Results: Immunofluorescence of lymph nodes from FL patients revealed that DC-SIGN was expressed on interfollicular CD163+ macrophages and, remarkably, on CD23+ follicular dendritic cells (FDC), claiming an influence on FL cell retention and survival. dSTORM revealed that DC-SIGN induced less dense and more diffuse surface Ig clusters compared to anti-Ig, reflecting an immature sIg redistribution unable to promote endocytosis and death. However, DC-SIGN efficiently induced adhesion of sIg-Mann+ve lymphoma cells to VCAM-1, known to be expressed on both lymph node macrophages and FDC, and inhibited migration towards SDF-1 in vitro. Blocking of DC-SIGN carbohydrate-recognition domain completely abrogated DC-SIGN-induced adhesion. Although intracellular signals were significantly lower, DC-SIGN induced levels of adhesion similar to those induced by anti-Ig. Adhesion to VCAM-1 was observed at concentrations from 20 µg/ml down to 20 ng/ml, even when AKT and ERK phosphorylation was not detectable. Either proximal inhibition of the PI3K/AKT pathway, or distal inhibition of ARP2/3, formin, and Cdc42 for lamellipodium formation at the surface membrane, suppressed adhesion. Conclusions: These results reveal an important mechanism of the DC-SIGN:sIg-Mann interaction that fine-tunes signals for membrane adaptation towards tumor cell adhesion, without promotion of cell death. This possibly facilitates FL cell retention in the lymph node protected tumor niche where selective growth and survival signals are maintained. Interrupting this interaction will be a novel way towards tumour-specific targeted therapy in FL patients. The research was funded by: This research was funded by Blood Cancer UK (grant 18009), Cancer Research UK (ECRIN-M3 accelerator award C42023/A29370, program C2750/A23669, and BTERP project C36811/A29101). D.T. was funded by the Eyles Cancer Immunology PhD scholarship, G.C. was funded by the Eyles Cancer Immunology Fellowship and the Southampton Cancer Immunology Centre Pump-priming award 2021). Keywords: Indolent non-Hodgkin lymphoma, Microenvironment, Targeting the Tumor Microenvironment Conflicts of interests pertinent to the abstract. F. Forconi Employment or leadership position: University of Siena Consultant or advisory role: Beigene Honoraria: Abbvie, Janssen-cilag, Beigene, Astra-Zeneca Research funding: Cancer Research UK Educational grants: Beigene, Abbvie Other remuneration: BC Platform

Metabolic enzyme Suclg2 maintains tolerogenicity of regulatory dendritic cells diffDCs by suppressing Lactb succinylation

Metabolic reprogramming plays a pivotal role in the differentiation and function of immune cells including dendritic cells (DCs). Regulatory DCs can be generated in regional tissue niches like splenic stroma and act as an important part of stromal control of immune response for the maintenance of immune tolerance. However, the metabolic alterations during splenic stroma-driven regulatory DCs differentiation and the metabolic enzyme involved in regulatory DCs function remain poorly understood. By combining metabolomic, transcriptomic, and functional investigations of mature DCs (maDCs) and diffDCs (regulatory DCs differentiated from activated mature DCs through coculturing with splenic stroma), here we identified succinate-CoA ligase subunit beta Suclg2 as a key metabolic enzyme that reprograms the proinflammatory status of mature DCs into a tolerogenic phenotype via preventing NF-κB signaling activation. diffDCs downregulate succinic acid levels and increase the Suclg2 expression along with their differentiation from mature DCs. Suclg2-interference impaired the tolerogenic function of diffDCs in inducing T cell apoptosis and enhanced activation of NF-κB signaling and expression of inflammatory genes CD40, Ccl5, and Il12b in diffDCs. Furthermore, we identified Lactb as a new positive regulator of NF-κB signaling in diffDCs whose succinylation at the lysine 288 residue was inhibited by Suclg2. Our study reveals that the metabolic enzyme Suclg2 is required to maintain the immunoregulatory function of diffDCs, adding mechanistic insights into the metabolic regulation of DC-based immunity and tolerance.

Foxp3+ regulatory T cells in the central nervous system and other nonlymphoid tissues.

Foxp3+ regulatory T (Treg) cells are indispensable for the maintenance of immunologic self-tolerance as well as for the confinement of autoimmune inflammation after the breach of self-tolerance. In order to fulfill these tasks, Treg cells operate in secondary lymphoid tissues and nonlymphoid tissues. The conditions for Treg cell stability and for their modes of action are different according to their compartment of residence. In addition, Treg cells initiate residency programs to inhabit niches in nonlympoid tissues (NLT) in steady state and after re-establishment of previously deflected homeostasis for extended periods of time. These NLT Treg cells are different from lymphoid tissue residing Treg cells and are functionally specialized to subserve not only immune functions but support intrinsic functions of their tissue of residence. This review will highlight current ideas about the functional specialization of NLT Treg cells in particular in the central nervous system (CNS) and discuss challenges that we are facing in an effort to exploit the power of NLT Treg cells for maintenance of tissue homeostasis and perhaps also tissue regeneration.

The transcriptional repressor HIC1 is required for the maintenance of tissue-resident ILC1

Abstract The group 1 innate lymphoid cell compartment is comprised of conventional natural killer (cNK) and type 1 innate lymphoid cells (ILC1). Within the innate lymphoid cell pool, these cells are delineated by expression of the transcription factor TBET, and both subtypes express cell surface receptors NK1.1 and NKp46. Functionally, ILC1 and cNK cells have been shown to mediate pathogen clearance and tumour control through release of type 1 cytokines, particularly IFN-□. While being closely related, a key feature distinguishing ILC1 from cNK cells is their propensity to reside within a tissue niche rather than enter the circulation. However, the precise mechanisms that regulate tissue residency of ILC1s remain unknown. Here, we show that the transcription factor Hypermethylated in Cancer 1 (HIC1) is a critical control point in the development and maintenance of ILC1. In the liver, HIC1 expression is restricted to the ILC1 compartment. Deletion of HIC1 in NKp46 +cells (Hic1 ΔNcr1mice) resulted in a specific and significant reduction in liver-resident ILC1, while cNK cells were unaffected. Additionally, we show that cNK cells isolated from Hic1 ΔNcr1mice are incapable of restoring the ILC1 compartment in lymphocyte-deficient hosts, unlike wild type donors. Thus, our results identify an important role for HIC1 in the development and maintenance of peripheral ILC1.

PASK links cellular energy metabolism with a mitotic self-renewal network to establish differentiation competence.

Quiescent stem cells are activated in response to a mechanical or chemical injury to their tissue niche. Activated cells rapidly generate a heterogeneous progenitor population that regenerates the damaged tissues. While the transcriptional cadence that generates heterogeneity is known, the metabolic pathways influencing the transcriptional machinery to establish a heterogeneous progenitor population remains unclear. Here, we describe a novel pathway downstream of mitochondrial glutamine metabolism that confers stem cell heterogeneity and establishes differentiation competence by countering post-mitotic self-renewal machinery. We discovered that mitochondrial glutamine metabolism induces CBP/EP300-dependent acetylation of stem cell-specific kinase, PAS domain-containing kinase (PASK), resulting in its release from cytoplasmic granules and subsequent nuclear migration. In the nucleus, PASK catalytically outcompetes mitotic WDR5-anaphase-promoting complex/cyclosome (APC/C) interaction resulting in the loss of post-mitotic Pax7 expression and exit from self-renewal. In concordance with these findings, genetic or pharmacological inhibition of PASK or glutamine metabolism upregulated Pax7 expression, reduced stem cell heterogeneity, and blocked myogenesis in vitro and muscle regeneration in mice. These results explain a mechanism whereby stem cells co-opt the proliferative functions of glutamine metabolism to generate transcriptional heterogeneity and establish differentiation competence by countering the mitotic self-renewal network via nuclear PASK.

Expression of RANKL in breast cancer tissue in patients with fibrous dysplasia/McCune-Albright syndrome.

In fibrous dysplasia/McCune-Albright syndrome (FD/MAS), mosaic mutations in the GNAS gene lead to locally abnormal bone turnover. Additionally, patients with FD/MAS, particularly with thoracic lesions, have an increased risk for breast cancer. Development and progression of breast cancer has been associated with expression of Receptor Activator of NF-κB ligand (RANKL) in mammary tissue, and due to the GNAS mutation, RANKL is systemically increased in patients with FD/MAS. Yet it is unknown whether breast cancer in FD/MAS is also dependent on RANKL. We hypothesized that the GNAS mutation might induce RANKL overproduction and an oncogenic niche in mammary tissue, and examined RANKL expression in breast cancer tissue of patients with FD/MAS compared to controls. Nine patients with FD/MAS and breast cancer were included and clinical data were retrieved. Patients were matched to controls with breast cancer without FD/MAS based on age and tumor type. Three pregnant breast cancer patients were included as positive controls. Immunohistochemical detection of RANKL was performed on formalin-fixed paraffin-embedded breast cancer specimens. Staining intensity was classified as weak, moderate or intense. The area of positive RANKL staining divided by the total ductal-lobular area was assessed (positive area percentage, PAP). Number of patients with RANKL expression was compared between FD/MAS and control group by chi-square (χ2) test, the PAP by Mann-Whitney U test (MWU). RANKL expression was observed in 3 patients with FD/MAS (38%), mainly in healthy tissue, and none of the control patients (χ2p=0.055). The FD/MAS group demonstrated considerably more intense staining than the control group, comparable to positive controls. The median PAP was 0.64% (range 0.14-2.04%) in the 3 FD/MAS patients with RANKL expression, 0.01% (Q1-Q3: 0.0003-0.514%) in the entire FD/MAS group, 0.006% (Q1-Q3: 0.001-0.012%) in the control group (MWU=0.574), and 0.19% (0.08-0.32%) in the pregnant patients. All patients with FD/MAS and RANKL expression had thoracic bone lesions, but no correlation was observed between RANKL expression and presence of the GNAS mutation or FD disease burden. The triad of a higher number of patients, higher positive area percentage and stronger intensity in the FD/MAS compared to the control group indicates that RANKL may be upregulated in mammary tissue in a subset of patients with FD/MAS, which may explain the increased risk for breast cancer, although the clinical significance remains unclear. Further research is needed to establish risk profiles for the development of RANKL-positive breast cancer and to improve early screening and treatment.

MP01-03 XENO-FREE PEPTIDE-FUNCTIONALIZED BIOINKS IMPROVE EX VIVO CULTURE OF HUMAN TESTICULAR TISSUES

You have accessJournal of UrologyCME1 Apr 2023MP01-03 XENO-FREE PEPTIDE-FUNCTIONALIZED BIOINKS IMPROVE EX VIVO CULTURE OF HUMAN TESTICULAR TISSUES Meghan Robinson and Ryan Flannigan Meghan RobinsonMeghan Robinson More articles by this author and Ryan FlanniganRyan Flannigan More articles by this author View All Author Informationhttps://doi.org/10.1097/JU.0000000000003212.03AboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail Abstract INTRODUCTION AND OBJECTIVE: The development of human in vitro spermatogenesis (IVS) is a promising regenerative platform for the treatment of male factor infertility. IVS has been demonstrated in rodent models, but despite decades of research remains a challenge in the human sphere. A promising strategy may be to culture fragments of testis tissues in hydrogels. Hydrogels can be functionalized to sequester matrix and signaling peptides in a local manner mimicking tissue niche function. In this study we investigated the use of xeno-free hydrogels functionalized with biomimetic peptide motifs for their ability to improve ex vivo culture of human testicular tissues. METHODS: Human testicular tissues were obtained from hormone-treated gender affirmation patients following informed consent, gently teased apart, cut into small fragments and mixed into bioinks (VitroInk) containing either YIGSR (laminin), COL (collagen), or MMPs (matrix metalloproteinases) peptide motifs, then printed into ∼1 cm3 droplets using a BioX6 extrusion bioprinter (Figure 1A). 1 mL of media was placed on each and they were cultured in 34°C at 5% CO2 and ambient oxygen (21%) for 12 days, with 50% media changes every other day. The media consisted of Human Plasma-Like Medium (HPLM) with 15% CTS™ KnockOut™ SR XenoFree Medium, vitamins, metabolites, antioxidants, growth factors and hormones known to be present in the testis niche. Tissues were analyzed after 12 days by quantitative real-time polymerase chain reaction (qPCR) for gene expression associated with apoptosis, somatic cell function, spermatogonial stem cell maintenance, and spermatogenesis. RESULTS: After 12 days gene expression associated with somatic cell function and spermatogenesis was higher than suspension culture controls in all hydrogel groups (Figure 1B). Compared to freshly harvested testicular tissues, COL- and YIGSR-functionalized hydrogels exhibited similar expression levels of genes associated with somatic cell function, and the highest increased levels of genes associated with early spermatogenesis (Figure 1B). CONCLUSIONS: COL- or YIGSR peptide-functionalized hydrogels sustain testicular tissue function ex vivo in short-term cultures, whereas suspension culture exhibited tissue function loss, suggesting the utility of functionalized hydrogels for human IVS. Source of Funding: None © 2023 by American Urological Association Education and Research, Inc.FiguresReferencesRelatedDetails Volume 209Issue Supplement 4April 2023Page: e1 Advertisement Copyright & Permissions© 2023 by American Urological Association Education and Research, Inc.MetricsAuthor Information Meghan Robinson More articles by this author Ryan Flannigan More articles by this author Expand All Advertisement PDF downloadLoading ...

T helper cell subsets: diversification of the field.

Polarized T helper cell (Th cell) responses are important determinants of host protection. Th cell subsets tailor their functional repertoire of cytokines to their cognate antigens to efficiently contribute to their clearance. In contrast, in settings of immune abrogation, these polarized cytokine patterns of Th cells can mediate tissue damage and pathology resulting in allergy or autoimmunity. Recent technological developments in single-cell genomics and proteomics as well as advances in the high-dimensional bioinformatic analysis of complex datasets have challenged the prevailing Th cell subset classification into Th1, Th2, Th17, and other subsets. Additionally, systems immunology approaches have revealed that instructive input from the peripheral tissue microenvironment can have differential effects on the overall phenotype and molecular wiring of Th cells depending on their spatial distribution. Th cells from the blood or secondary lymphoid organs are therefore expected to follow distinct rules of regulation. In this review, the functional heterogeneity of Th cell subsets will be reviewed in the context of new technological developments and T-cell compartmentalization in tissue niches. This work will especially focus on challenges to the traditional boundaries of Th cell subsets and will discuss the underlying regulatory checkpoints, which could reveal new therapeutic strategies for various immune-mediated diseases.

Activation of Endogenous Mesenchymal Stromal Cells as an Approach to Tissue Regeneration

Mesenchymal stromal cells (MSCs) which have a complex pro-regenerative effect on damaged tissues represent a promising resource for cell therapy for a wide range of diseases. However, transplantation of autologous or donor MSCs to a patient is associated with a number of problems, such as variability of cell properties depending on their source and cultivation conditions, a decrease in their therapeutic potential and the possibility of acquiring immunogenicity or tumorigenicity during in vitro expansion, and the invasiveness of the isolation procedure. One of the ways to avoid these problems can be the impact on endogenous MSCs by stimulating their directed migration into tissue defects, without the need for extraction from the body, in vitro cultivation and reintroduction to the patient. This review discusses approaches to activating the mobilization of MSCs from tissue niches and/or stimulating their migration to the target area, which can be considered as a safer, and possibly more effective alternative to MSC transplantation.

Fibroblast heterogeneity: Keystone of tissue homeostasis and pathology in inflammation and ageing.

Fibroblasts, derived from the embryonic mesenchyme, are a diverse array of cells with roles in development, homeostasis, repair, and disease across tissues. In doing so, fibroblasts maintain micro-environmental homeostasis and create tissue niches by producing a complex extracellular matrix (ECM) including various structural proteins. Although long considered phenotypically homogenous and functionally identical, the emergence of novel technologies such as single cell transcriptomics has allowed the identification of different phenotypic and cellular states to be attributed to fibroblasts, highlighting their role in tissue regulation and inflammation. Therefore, fibroblasts are now recognised as central actors in many diseases, increasing the need to discover new therapies targeting those cells. Herein, we review the phenotypic heterogeneity and functionality of these cells and their roles in health and disease.

Molecular Mechanisms Responsible for Mesenchymal Stem Cell-Based Modulation of Obstructive Sleep Apnea.

Mesenchymal stem cells (MSCs) are adult stem cells that reside in almost all postnatal tissues where, due to the potent regenerative, pro-angiogenic and immunomodulatory properties, regulate tissue homeostasis. Obstructive sleep apnea (OSA) induces oxidative stress, inflammation and ischemia which recruit MSCs from their niches in inflamed and injured tissues. Through the activity of MSC-sourced anti-inflammatory and pro-angiogenic factors, MSCs reduce hypoxia, suppress inflammation, prevent fibrosis and enhance regeneration of damaged cells in OSA-injured tissues. The results obtained in large number of animal studies demonstrated therapeutic efficacy of MSCs in the attenuation of OSA-induced tissue injury and inflammation. Herewith, in this review article, we emphasized molecular mechanisms which are involved in MSC-based neo-vascularization and immunoregulation and we summarized current knowledge about MSC-dependent modulation of OSA-related pathologies.

Distinct tissue niches direct lung immunopathology via CCL18 and CCL21 in severe COVID-19

Prolonged lung pathology has been associated with COVID-19, yet the cellular and molecular mechanisms behind this chronic inflammatory disease are poorly understood. In this study, we combine advanced imaging and spatial transcriptomics to shed light on the local immune response in severe COVID-19. We show that activated adventitial niches are crucial microenvironments contributing to the orchestration of prolonged lung immunopathology. Up-regulation of the chemokines CCL21 and CCL18 associates to endothelial-to-mesenchymal transition and tissue fibrosis within these niches. CCL21 over-expression additionally links to the local accumulation of T cells expressing the cognate receptor CCR7. These T cells are imprinted with an exhausted phenotype and form lymphoid aggregates that can organize in ectopic lymphoid structures. Our work proposes immune-stromal interaction mechanisms promoting a self-sustained and non-resolving local immune response that extends beyond active viral infection and perpetuates tissue remodeling.

Large-scale proteomic analysis of T. spiralis muscle-stage ESPs identifies a novel upstream motif for in silico prediction of secreted products

The Trichinella genus contains parasitic nematodes capable of infecting a wide range of hosts including mammals, birds and reptiles. Like other helminths, T. spiralis secretes a complex mixture of bioactive molecules capable of modulating its immediate surroundings and creating a hospitable environment for growth, survival and ultimately transmission. The constitution of these excretory-secretory products (ESPs) changes depending on the tissue niche and the specific stage of parasite development. Unique to T. spiralis is a true intracellular stage wherein larvae develop inside striated myotubes. Remarkably, the parasite larvae do not destroy the host cell but rather reprogram it to support their presence and growth. This transformation is largely mediated through stage-specific secretions released into the host cell cytoplasm. In this study, we apply state of the art proteomics and computational approaches to elucidate the composition and functions of muscle-stage T. spiralis ESPs. Moreover, we define a recurring, upstream motif associated with the stichosome, the main secretory organ of this worm, and can be used to predict secreted proteins across experimentally less tractable T. spiralis life cycle stages.

A topographic atlas defines developmental origins of cell heterogeneity in the human embryonic lung

The lung contains numerous specialized cell types with distinct roles in tissue function and integrity. To clarify the origins and mechanisms generating cell heterogeneity, we created a comprehensive topographic atlas of early human lung development. Here we report 83 cell states and several spatially resolved developmental trajectories and predict cell interactions within defined tissue niches. We integrated single-cell RNA sequencing and spatially resolved transcriptomics into a web-based, open platform for interactive exploration. We show distinct gene expression programmes, accompanying sequential events of cell differentiation and maturation of the secretory and neuroendocrine cell types in proximal epithelium. We define the origin of airway fibroblasts associated with airway smooth muscle in bronchovascular bundles and describe a trajectory of Schwann cell progenitors to intrinsic parasympathetic neurons controlling bronchoconstriction. Our atlas provides a rich resource for further research and a reference for defining deviations from homeostatic and repair mechanisms leading to pulmonary diseases.