Single Cell Transcriptomics Implicate Novel Monocyte and T Cell Immune Dysregulation in Sarcoidosis (original) (raw)
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RNA-sequencing Identifies Novel Pathways in Sarcoidosis Monocytes
Scientific reports, 2017
Sarcoidosis is a complex systemic granulomatous disorder of unknown etiology. Genome-wide association studies have not been able to explain a causative role for nucleotide variation in its pathogenesis. The goal of the present study was to identify the gene expression profile and the cellular pathways altered in sarcoidosis monocytes via RNA-sequencing. Peripheral blood monocytes play a role in sarcoidosis inflammation. Therefore, we determined and compared the transcriptional signature of monocytes from peripheral blood from sarcoidosis patients and healthy controls via RNA-sequencing. We found 2,446 differentially expressed (DE) genes between sarcoidosis and healthy control monocytes. Analysis of these DE genes showed enrichment for ribosome, phagocytosis, lysosome, proteasome, oxidative phosphorylation and metabolic pathways. RNA-sequencing identified upregulation of genes involved in phagocytosis and lysosomal pathway in sarcoidosis monocytes, whereas genes involved in proteasom...
Monocytes in sarcoidosis are potent TNF producers and predict disease outcome
European Respiratory Journal, 2021
BackgroundPulmonary sarcoidosis is an inflammatory disease characterised by granuloma formation and heterogeneous clinical outcome. TNF is a proinflammatory cytokine contributing to granuloma formation and high levels of TNF have been shown to associate with progressive disease. Mononuclear phagocytes (MNPs) are potent producers of TNF and highly responsive to inflammation. In sarcoidosis, alveolar macrophages (AMs) have been well studied. However, MNPs also include monocytes/monocyte-derived cells and dendritic cells (DCs) that despite their central role in inflammation are poorly studied in sarcoidosis.ObjectiveTo determine the role of pulmonary monocyte-derived cells and DCs during sarcoidosis.MethodsWe performed in-depth phenotypic, functional and transcriptomic analysis of MNPs subsets from blood and bronchoalveolar lavage (BAL) fluid from 108 sarcoidosis patients and 30 healthy controls. We followed the clinical development of patients and assessed how the repertoire and funct...
Longitudinal analysis of sarcoidosis blood transcriptomic signatures and disease outcomes
The European respiratory journal, 2014
Previously, we demonstrated concordance in differentially expressed genes in sarcoidosis blood and lung, implicating shared dysfunction of specific immune pathways. In the present study, we hypothesised that expression levels of candidate genes in sarcoidosis blood could predict and track with disease outcomes longitudinally. We applied Ingenuity Pathway Analysis to a cross-sectional derivation microarray dataset (n=38) to identify canonical pathways and candidate genes associated with sarcoidosis. In a separate longitudinal sarcoidosis cohort (n=103), we serially measured 48 candidate gene transcripts, and assessed their relation to disease chronicity and severity. In the cross-sectional derivation study, pathway analysis showed upregulation of genes related to interferon signalling and the role of pattern recognition receptors, and downregulation of T-cell receptor (TCR) signalling pathways in sarcoidosis. In the longitudinal cohort, factor analysis confirmed coregulation of genes...
Gain-of-function mutations inSTING1, which encodes the Stimulator of Interferon Gene (STING), result in a severe autoinflammatory disease termed STING-associated vasculopathy with onset in infancy (SAVI). Although elevated type I interferon (IFN) production is thought to be the leading cause of the symptoms observed in patients, STING can induce a set of pathways, which roles in the onset and severity of SAVI, remain to be elucidated. To address this point, we compared a single-cell RNA sequencing (scRNA-seq) dataset of peripheral blood mononuclear cells (PBMCs) from SAVI patients to a dataset of healthy PBMCs treated with recombinant IFN-β. We revealed a loss of mucosal associated invariant T cells and CD56brightnatural killer cells in SAVI patients, not observed in IFN-β-treated PBMC. Patients’ T cells present markers of early activation, associated with markers of senescence and apoptosis. Inferring cell-to-cell communication from scRNA-seq predicted monocytes as potential driver...
Nature Communications
Human T cells coordinate adaptive immunity in diverse anatomic compartments through production of cytokines and effector molecules, but it is unclear how tissue site influences T cell persistence and function. Here, we use single cell RNA-sequencing (scRNA-seq) to define the heterogeneity of human T cells isolated from lungs, lymph nodes, bone marrow and blood, and their functional responses following stimulation. Through analysis of >50,000 resting and activated T cells, we reveal tissue T cell signatures in mucosal and lymphoid sites, and lineage-specific activation states across all sites including distinct effector states for CD8+ T cells and an interferon-response state for CD4+ T cells. Comparing scRNA-seq profiles of tumor-associated T cells to our dataset reveals predominant activated CD8+ compared to CD4+ T cell states within multiple tumor types. Our results therefore establish a high dimensional reference map of human T cell activation in health for analyzing T cells i...
2020
Rationale: Despite the availability of multi-“omics” strategies, insights into the etiology and pathogenesis of sarcoidosis have been elusive. This is partly due to the lack of reliable preclinical models and a paucity of validated biomarkers. As granulomas are a key feature of sarcoidosis, we speculate that direct genomic interrogation of sarcoid tissues, may lead to identification of dysregulated gene pathways or biomarker signatures.Objective: To facilitate the development sarcoidosis genomic biomarkers by gene expression profiling of sarcoidosis granulomas in lung and lymph node tissues (most commonly affected organs) and comparison to infectious granulomas (coccidiodomycosis and tuberculosis). Methods: Transcriptomic profiles of immune-related gene from micro-dissected lungs and mediastinal lymph nodes sarcoidosis granulomas was compared to infectious granulomas. Differentially-expressed genes (DEGs) were profiled, compared among the three granulomatous diseases and analyzed fo...
ObjectiveSingle cell profiling of synovial tissue has previously identified gene signatures associated with rheumatoid arthritis (RA) pathophysiology, but synovial tissue is difficult to obtain. This study leverages single cell sequencing of peripheral blood mononuclear cells (PBMCs) from patients with RA and matched healthy controls to identify disease relevant cell subsets and cell type specific signatures of disease.MethodsSingle-cell RNA sequencing (scRNAseq) was performed on peripheral blood mononuclear cells (PBMCs) from 18 RA patients and 18 matched controls, accounting for age, gender, race, and ethnicity). Samples were processed using standard CellRanger and Scanpy pipelines, pseudobulk differential gene expression analysis was performed using DESeq2, and cell-cell communication analysis using CellChat.ResultsWe identified 18 distinct PBMC subsets, including a novel IFITM3+ monocyte subset. CD4+ T effector memory cells were increased in patients with moderate to high diseas...
Mapping mononuclear phagocytes in blood, lungs, and lymph nodes of sarcoidosis patients
Journal of Leukocyte Biology, 2019
Sarcoidosis is a T-cell driven inflammatory disease characterized by granuloma formation. Mononuclear phagocytes (MNPs)—macrophages, monocytes, and dendritic cells (DCs)—are likely critical in sarcoidosis as they initiate and maintain T cell activation and contribute to granuloma formation by cytokine production. Granulomas manifest primarily in lungs and lung-draining lymph nodes (LLNs) but these compartments are less studied compared to blood and bronchoalveolar lavage (BAL). Sarcoidosis can present with an acute onset (usually Löfgren’s syndrome (LS)) or a gradual onset (non-LS). LS patients typically recover within 2 years while 60% of non-LS patients maintain granulomas for up to 5 years. Here, four LS and seven non-LS patients underwent bronchoscopy with endobronchial ultrasound-guided transbronchial needle aspiration (EBUS-TBNA). From each patient, blood, BAL, endobronchial biopsies (EBBs), and LLN samples obtained by EBUS-TBNA were collected and MNPs characterized using mult...
Proceedings of the National Academy of Sciences, 2015
Despite recent advances in single-cell genomic, transcriptional, and mass-cytometric profiling, it remains a challenge to collect highly multiplexed measurements of secreted proteins from single cells for comprehensive analysis of functional states. Herein, we combine spatial and spectral encoding with polydimethylsiloxane (PDMS) microchambers for codetection of 42 immune effector proteins secreted from single cells, representing the highest multiplexing recorded to date for a single-cell secretion assay. Using this platform to profile differentiated macrophages stimulated with lipopolysaccharide (LPS), the ligand of Toll-like receptor 4 (TLR4), reveals previously unobserved deep functional heterogeneity and varying levels of pathogenic activation. Uniquely protein profiling on the same single cells before and after LPS stimulation identified a role for macrophage inhibitory factor (MIF) to potentiate the activation of LPS-induced cytokine production. Advanced clustering analysis identified functional subsets including quiescent, polyfunctional fully activated, partially activated populations with different cytokine profiles. This population architecture is conserved throughout the cell activation process and prevails as it is extended to other TLR ligands and to primary macrophages derived from a healthy donor. This work demonstrates that the phenotypically similar cell population still exhibits a large degree of intrinsic heterogeneity at the functional and cell behavior level. This technology enables fullspectrum dissection of immune functional states in response to pathogenic or environmental stimulation, and opens opportunities to quantify deep functional heterogeneity for more comprehensive and accurate immune monitoring.
Identification of key regulators in Sarcoidosis through multidimensional systems biological approach
Scientific Reports, 2022
Sarcoidosis is a multi-organ disorder where immunology, genetic and environmental factors play a key role in causing Sarcoidosis, but its molecular mechanism remains unclear. Identification of its genetics profiling that regulates the Sarcoidosis network will be one of the main challenges to understand its aetiology. We have identified differentially expressed genes (DEGs) by analyzing the gene expression profiling of Sarcoidosis and compared it with healthy control. Gene set enrichment analysis showed that these DEGs were mainly enriched in the inflammatory response, immune system, and pathways in cancer. Sarcoidosis protein interaction network was constructed by a total of 877 DEGs (up-down) and calculated its network topological properties, which follow hierarchical scale-free fractal nature up to six levels of the organization. We identified a large number of leading hubs that contain six key regulators (KRs) including ICOS, CTLA4, FLT3LG, CD33, GPR29 and ITGA4 are deeply rooted in the network from top to bottom, considering a backbone of the network. We identified the transcriptional factors (TFs) which are closely interacted with KRs. These genes and their TFs regulating the Sarcoidosis network are expected to be the main target for the therapeutic approaches and potential biomarkers. However, experimental validations of KRs needed to confirm their efficacy. Sarcoidosis (SARC) is an inflammatory disease (multiple organ inflammation) that causes abnormal granulomas consisting of inflamed tissue that is usually observed in the lungs and lymph glands. These granulomas may alter the normal structure and function of the affected organs. SARC affects people of all ages, genders, and ethnic backgrounds. It usually affects adults less than 40 years of age, and the incidence peaks in the third decade of life and is less common in children. Many studies reported a slightly higher rate of incidence in women across racial/ethnic groups 1. The worldwide prevalence varies from 2 to 80 per 100,000 2. In India, the prevalence is estimated to be 10-12 per 1000 3. However, in 30-60% of the cases the prevalence may be underestimated by the asymptomatic signs of the disease. In Afro-Americans, the incidence is three times higher as compared to Caucasians and it is also more likely to be fatal 4. The understanding of SARC has been challenging because of the multiple issues. Clinically, SARC is extremely complex because patients do not typically exhibit clear signs and symptoms; it varies depending on the organ affected. In the present era, the research on SARC has been focused on its pathological mechanism.It is believed that when a genetically susceptible individual is exposed to one or more extrinsic antigens, inflammatory pathways are over-activated, favoring the formation of sarcoidal granulomas. It has been suggested that there is an increased risk of SARC in individuals exposed to environmental entities such as microbial agents etc. 4. Susceptibility to the disease can be genetically determined and many genes have been identified that affect the prevalence and course of SARC. In particular, HLA genes have been shown to affect the progression of SARC and its development 5 .