scholarly journals A Novel Single Cell RNA-seq Analysis of Non-Myeloid Circulating Cells in Late Sepsis

2021 ◽  
Vol 12 ◽  
Author(s):  
Dijoia B. Darden ◽  
Xiaoru Dong ◽  
Maigan A. Brusko ◽  
Lauren Kelly ◽  
Brittany Fenner ◽  
...  

BackgroundWith the successful implementation of the Surviving Sepsis Campaign guidelines, post-sepsis in-hospital mortality to sepsis continues to decrease. Those who acutely survive surgical sepsis will either rapidly recover or develop a chronic critical illness (CCI). CCI is associated with adverse long-term outcomes and 1-year mortality. Although the pathobiology of CCI remains undefined, emerging evidence suggests a post-sepsis state of pathologic myeloid activation, inducing suboptimal lymphopoiesis and erythropoiesis, as well as downstream leukocyte dysfunction. Our goal was to use single-cell RNA sequencing (scRNA-seq) to perform a detailed transcriptomic analysis of lymphoid-derived leukocytes to better understand the pathology of late sepsis.MethodsA mixture of whole blood myeloid-enriched and Ficoll-enriched peripheral blood mononuclear cells from four late septic patients (post-sepsis day 14-21) and five healthy subjects underwent Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-seq).ResultsWe identified unique transcriptomic patterns for multiple circulating immune cell subtypes, including B- and CD4+, CD8+, activated CD4+ and activated CD8+ T-lymphocytes, as well as natural killer (NK), NKT, and plasmacytoid dendritic cells in late sepsis patients. Analysis demonstrated that the circulating lymphoid cells maintained a transcriptome reflecting immunosuppression and low-grade inflammation. We also identified transcriptomic differences between patients with bacterial versus fungal sepsis, such as greater expression of cytotoxic genes among CD8+ T-lymphocytes in late bacterial sepsis.ConclusionCirculating non-myeloid cells display a unique transcriptomic pattern late after sepsis. Non-myeloid leukocytes in particular reveal a host endotype of inflammation, immunosuppression, and dysfunction, suggesting a role for precision medicine-guided immunomodulatory therapy.

2021 ◽  
Author(s):  
Zhibin Li ◽  
chengcheng Sun ◽  
Fei Wang ◽  
Xiran Wang ◽  
Jiacheng Zhu ◽  
...  

Background: Immune cells play important roles in mediating immune response and host defense against invading pathogens. However, insights into the molecular mechanisms governing circulating immune cell diversity among multiple species are limited. Methods: In this study, we compared the single-cell transcriptomes of 77 957 immune cells from 12 species using single-cell RNA-sequencing (scRNA-seq). Distinct molecular profiles were characterized for different immune cell types, including T cells, B cells, natural killer cells, monocytes, and dendritic cells. Results: The results revealed the heterogeneity and compositions of circulating immune cells among 12 different species. Additionally, we explored the conserved and divergent cellular cross-talks and genetic regulatory networks among vertebrate immune cells. Notably, the ligand and receptor pair VIM-CD44 was highly conserved among the immune cells. Conclusions: This study is the first to provide a comprehensive analysis of the cross-species single-cell atlas for peripheral blood mononuclear cells (PBMCs). This research should advance our understanding of the cellular taxonomy and fundamental functions of PBMCs, with important implications in evolutionary biology, developmental biology, and immune system disorders


2021 ◽  
Author(s):  
Xinru Qiu ◽  
Jiang Li ◽  
Jeff Bonenfant ◽  
Lukasz Jaroszewski ◽  
Walter Klein ◽  
...  

AbstractSystemic infections, especially in patients with chronic diseases, result in sepsis: an explosive, uncoordinated immune response that can lead to multisystem organ failure with a high mortality rate. Sepsis survivors and non-survivors oftentimes have similar clinical phenotypes or sepsis biomarker expression upon diagnosis, suggesting that the dynamics of sepsis in the critical early stage may have an impact on these opposite outcomes. To investigate this, we designed a within-subject study of patients with systemic gram-negative bacterial sepsis with surviving and fatal outcomes and performed single-cell transcriptomic analyses of peripheral blood mononuclear cells (PBMC) collected during the critical period between sepsis recognition and 6 hours. We observed that the largest sepsis-induced expression changes over time in surviving versus fatal sepsis were in CD14+ monocytes, including gene signatures previously reported for sepsis outcomes. We further identify changes in the metabolic pathways of both monocytes and platelets, the emergence of erythroid precursors, and T cell exhaustion signatures, with the most extreme differences occurring between the non-sepsis control and the sepsis non-survivor. Our single-cell observations are consistent with trends from public datasets but also reveal specific effects in individual immune cell populations, which change within hours. In conclusion, this pilot study provides the first single-cell results with a repeated measures design in sepsis to analyze the temporal changes in the immune cell population behavior in surviving or fatal sepsis. These findings indicate that tracking temporal expression changes in specific cell-types could lead to more accurate predictions of sepsis outcomes. We also identify molecular pathways that could be therapeutically controlled to improve the sepsis trajectory toward better outcomes.Summary sentenceSingle cell transcriptomics of peripheral blood mononuclear cells in surviving and fatal sepsis reveal inflammatory and metabolic pathways that change within hours of sepsis recognition.


2020 ◽  
Author(s):  
Gang Xu ◽  
Furong Qi ◽  
Hanjie Li ◽  
Qianting Yang ◽  
Haiyan Wang ◽  
...  

Understanding the mechanism that leads to immune dysfunction induced by SARS-CoV2 virus is crucial to develop treatment for severe COVID-19. Here, using single cell RNA-seq, we characterized the peripheral blood mononuclear cells (PBMC) from uninfected controls and COVID-19 patients, and cells in paired broncho-alveolar lavage fluid (BALF). We found a close association of decreased dendritic cells (DC) and increased monocytes resembling myeloid-derived suppressor cells (MDSC) which correlated with lymphopenia and inflammation in the blood of severe COVID-19 patients. Those MDSC-like monocytes were immune-paralyzed. In contrast, monocyte-macrophages in BALFs of COVID-19 patients produced massive amounts of cytokines and chemokines, but secreted little interferons. The frequencies of peripheral T cells and NK cells were significantly decreased in severe COVID-19 patients, especially for innate-like T and various CD8+ T cell subsets, compared to health controls. In contrast, the proportions of various activated CD4+ T cell subsets, including Th1, Th2 and Th17-like cells were increased and more clonally expanded in severe COVID-19 patients. Patients' peripheral T cells showed no sign of exhaustion or augmented cell death, whereas T cells in BALFs produced higher levels of IFNG, TNF, CCL4 and CCL5 etc. Paired TCR tracking indicated abundant recruitment of peripheral T cells to the patients' lung. Together, this study comprehensively depicts how the immune cell landscape is perturbed in severe COVID-19.


Blood ◽  
2018 ◽  
Vol 132 (Supplement 1) ◽  
pp. 2406-2406 ◽  
Author(s):  
Ruth-Anne Langan ◽  
Dustin Shilling ◽  
Michael Gonzalez ◽  
Charlly Kao ◽  
Hakon Hakonarson ◽  
...  

Abstract Idiopathic multicentric Castleman disease (iMCD) is a rare and deadly hematologic illness involving episodic disease flares with polyclonal lymphoproliferation, systemic inflammation, and multiple organ system dysfunction. A cytokine storm involving interleukin(IL)-6 is believed to drive disease pathogenesis in some patients. However, only 34% of patients were found to respond to anti-IL-6 therapy with siltuximab in its registrational clinical trial; no other FDA approved treatments exist for iMCD. With the 5- and 10-year mortality rates reported as 35% and 60%, respectively, there is a clear need for additional treatment options. However, the development of next generation therapeutics is challenging as the etiology, pathological cell types, and signaling pathways involved in iMCD are largely unknown. To identify pathophysiological mechanisms and cellular drivers of iMCD, we applied cutting edge single-cell RNA-sequencing (scRNA-seq) technology to investigate bulk peripheral blood mononuclear cells (PBMCs) isolated from an iMCD patient at two distinct stages of disease activity. The first sample was collected during a short remission period following the patient's first disease flare (partial remission) (clinical symptom: fatigue; laboratory tests: hemoglobin 11.2 g/dL, platelets: 225,000/µL; albumin 4.2 g/dL, creatinine 0.73 mg/dL) and a second sample was collected at the start of his second flare (flare 2) (clinical symptoms: fatigue, fever, night sweats and fluid accumulation; laboratory tests: hemoglobin 12.9 g/dL, platelets: 122,000/µL; albumin 2.3 g/dL, creatinine 1.48 mg/dL). We utilized the Cellranger pipeline (10x Genomics, v.2.1.0) for aggregation of single-cell transcriptomes and Loupe Cell Browser (10x Genomics, v.2.1.0) for initial analysis of 20,135 recovered cells from partial remission (16,283 means reads/cell, 799 median genes/cell) and 19,322 recovered cells in flare 2 (17,327 reads/cell, 823 median genes/cell). Initial analyses of clusters revealed changes in the composition and frequency of immune cell subsets between the two samples. Plasmablasts (identified as expressing CD19, CD27, CD38, CD79a, CD79b) increased 7-fold in number during flare 2 with 28 cells in partial remission and 216 cells in flare 2. Similarly, monocyte and macrophage cell populations increased in frequency from 9% of all PBMCs in the partial remission sample to 15% of all PBMCs in the flare 2 sample. Conversely, CD8+ T cell frequency in the dataset decreased from 22% of the partial remission sample to 13% in flare 2. Interrogation of gene expression profiles of immune cell clusters identified highly activated CD8+ T cells which increased in frequency during flare 2 and are characterized by an inflammatory gene signature including expression of perforin and granzyme. Additionally, inflammatory gene signatures within the myeloid cell compartment during flare were identified, including elevated expression of S100 family members. S100 proteins are implicated in the pathogenesis of a number of autoimmune diseases and contribute to immune cell migration, chemotaxis, and leukocyte invasion. To our knowledge this is the first application of cutting edge single-cell sequencing technology to PBMCs obtained from an iMCD patient in flare and remission. Our observations support a role for both T and B cell activation in iMCD flare and lead us to hypothesize that CD8+ T cells may have left circulation and migrated to sites of active inflammation during this patient's disease flare. This dataset demonstrates involvement of multiple immune cell populations and inflammatory gene programs during disease flare in this patient and provides a novel resource for understanding gene expression and cell population changes in Castleman disease. Disclosures Fajgenbaum: Janssen Pharmaceuticals, Inc.: Research Funding.


2019 ◽  
Author(s):  
Tanya T. Karagiannis ◽  
John P. Cleary ◽  
Busra Gok ◽  
Nicholas G. Martin ◽  
Elliot C. Nelson ◽  
...  

AbstractChronic opioid usage not only causes addiction behavior through the central nervous system (CNS), but it also modulates the peripheral immune system. However, whether opioid usage positively or negatively impacts the immune system is still controversial. In order to understand the immune modulatory effect of opioids in a systematic and unbiased way, we performed single cell RNA sequencing (scRNA-seq) of peripheral blood mononuclear cells (PBMCs) from opioid-dependent individuals and non-dependent controls. We show that chronic opioid usage evokes widespread suppression of interferon-stimulated genes (ISGs) and antiviral gene program in naive monocytes and upon ex vivo stimulation with the pathogen component lipopolysaccharide (LPS) in multiple innate and adaptive immune cell types. Furthermore, scRNA-seq revealed the same phenomenon with in vitro morphine treatment; after just a short exposure to morphine stimulation, we observed the same suppression of antiviral genes in multiple immune cell types. These findings indicate that both acute and chronic opioid exposure may be harmful to our immune system by suppressing the antiviral gene program, our body’s defense response to potential infection. Our results suggest that further characterization of the immune modulatory effects of opioid use is critical to ensure the safety of clinical opioid usage.


Author(s):  
Jonas Schulte-Schrepping ◽  
Nico Reusch ◽  
Daniela Paclik ◽  
Kevin Baßler ◽  
Stephan Schlickeiser ◽  
...  

Abstract‘Severe Acute Respiratory Syndrome - Coronavirus-2’ (SARS-CoV-2) infection causes Coronavirus Disease 2019 (COVID-19), a mild to moderate respiratory tract infection in the majority of patients. A subset of patients, however, progresses to severe disease and respiratory failure with acute respiratory distress syndrome (ARDS). Severe COVID-19 has been associated with increased neutrophil counts and dysregulated immune responses. The mechanisms of protective immunity in mild forms and the pathogenesis of dysregulated inflammation in severe courses of COVID-19 remain largely unclear. Here, we combined two single-cell RNA-sequencing technologies and single-cell proteomics in whole blood and peripheral blood mononuclear cells (PBMC) to determine changes in immune cell composition and activation in two independent dual-center patient cohorts (n=46+n=54 COVID-19 samples), each with mild and severe cases of COVID-19. We observed a specific increase of HLA-DRhiCD11chi inflammatory monocytes that displayed a strong interferon (IFN)-stimulated gene signature in patients with mild COVID-19, which was absent in severe disease. Instead, we found evidence of emergency myelopoiesis, marked by the occurrence of immunosuppressive pre-neutrophils and immature neutrophils and populations of dysfunctional and suppressive mature neutrophils, as well as suppressive HLA-DRto monocytes in severe COVID-19. Our study provides detailed insights into systemic immune response to SARS-CoV-2 infection and it reveals profound alterations in the peripheral myeloid cell compartment associated with severe courses of COVID-19.


2019 ◽  
Vol 6 (Supplement_2) ◽  
pp. S42-S42
Author(s):  
Miguel Reyes ◽  
Roby P Bhattacharyya ◽  
Michael Filbin ◽  
Kianna Billman ◽  
Thomas Eisenhaure ◽  
...  

Abstract Background Despite intense efforts to understand the immunopathology of sepsis, no clinically reliable diagnostic biomarkers exist. Multiple whole-blood gene expression studies have sought sepsis-associated molecular signatures, but these have not yet resolved immune phenomena at the cellular level. Using single-cell RNA sequencing (scRNA-Seq) to profile peripheral blood mononuclear cells (PBMCs), we identified a novel cellular state enriched in patients with sepsis. Methods We performed scRNA-Seq on PBMCs from 26 patients with sepsis and 47 controls at two hospitals (mean age 57.5 years, SD 16.6; 54% male; 82% white), analyzing >200,000 single cells in total on a 10× Genomics platform. We identified immune cell states by stepwise clustering, first to identify the major immune cell types, then clustering each cell type into substates. Substate abundances were compared between cases and controls using the Wilcoxon rank-sum test. Results We identified 18 immune cell substates (Figure 1a), including a novel CD14+ monocyte substate (MS1) that is enriched in patients with sepsis (Figure 1b). The fractional abundance of the MS1 substate alone (ROC AUC 0.88) outperformed published bulk transcriptional signatures in identifying sepsis (AUC 0.68–0.82) across our clinical cohorts. Deconvolution of publicly available bulk transcriptional data to infer the abundance of the MS1 substate externally validated its accuracy in predicting sepsis of various etiologies across diverse geographic locations (Figure 1c), matching the best previously identified bulk signatures. Flow cytometry using cell surface markers unique to MS1 confirmed its marked expansion in sepsis, facilitating quantitation and isolation of this substate for further study. Conclusion This study demonstrates the utility of scRNA-Seq in discovering disease-associated cytologic signatures in blood and identifies a cell state signature for sepsis in patients with bacterial infections. This novel monocyte substate matched the performance of the best bulk transcriptional signatures in classifying patients as septic, and pointed to a specific cell state for further molecular and functional characterization of sepsis immunopathogenesis. Disclosures All Authors: No reported Disclosures.


2021 ◽  
Vol 12 ◽  
Author(s):  
Banafshe Hosseini ◽  
Bronwyn S. Berthon ◽  
Malcolm R. Starkey ◽  
Adam Collison ◽  
Rebecca F. McLoughlin ◽  
...  

BackgroundAsthma is the most frequent cause of hospitalisation among children; however, little is known regarding the effects of asthma on immune responses in children.ObjectiveThe present study aimed to evaluate cytokine responses of peripheral blood mononuclear cells (PBMCs), PBMC composition and lung function in children with and without asthma.MethodsUsing a case-control design, we compared 48 children with asthma aged 3-11 years with 14 age-matched healthy controls. PBMC composition and cytokine production including interferon (IFN)-γ, interleukin (IL)-1β, IL-5 and lL-6 following stimulation with rhinovirus-1B (RV1B), house dust mite (HDM) and lipopolysaccharide (LPS) were measured. Lung function was assessed using impulse oscillometry and nitrogen multiple breath washout.ResultsThe frequency of group 2 innate lymphoid cells were significantly higher in asthmatics and PBMCs from asthmatics had deficient IFN-γ production in response to both RV1B and LPS compared with controls (P<0.01). RV1B-induced IL-1β response and HDM-stimulated IL-5 production was higher in asthmatics than controls (P<0.05). In contrast, IL-1β and IL-6 were significantly reduced in response to HDM and LPS in asthmatics compared to controls (P<0.05). Children with asthma also had reduced pulmonary function, indicated by lower respiratory reactance as well as higher area of-reactance and lung clearance index values compared with controls (P<0.05).ConclusionOur study indicates that children with asthma have a reduced lung function in concert with impaired immune responses and altered immune cell subsets. Improving our understanding of immune responses to viral and bacterial infection in childhood asthma can help to tailor management of the disease.


2021 ◽  
Vol 6 (1) ◽  
Author(s):  
Yuan Hou ◽  
Yadi Zhou ◽  
Michaela U. Gack ◽  
Justin D. Lathia ◽  
Asha Kallianpur ◽  
...  

AbstractSex differences in the susceptibility of SARS-CoV-2 infection and severity have been controversial, and the underlying mechanisms of COVID-19 in a sex-specific manner remain understudied. Here we inspected sex differences in SARS-CoV-2 infection, hospitalization, admission to the intensive care unit (ICU), sera inflammatory biomarker profiling, and single-cell RNA-sequencing (scRNA-seq) profiles across nasal, bronchoalveolar lavage fluid (BALF), and peripheral blood mononuclear cells (PBMCs) from COVID-19 patients with varying degrees of disease severities. Our propensity score-matching observations revealed that male individuals have a 29% elevated likelihood of SARS-CoV-2 positivity, with a hazard ratio (HR) 1.32 (95% confidence interval [CI] 1.18–1.48) for hospitalization and HR 1.51 (95% CI 1.24–1.84) for admission to ICU. Sera from male patients at hospital admission had elevated neutrophil–lymphocyte ratio and elevated expression of inflammatory markers (C-reactive protein and procalcitonin). We found that SARS-CoV-2 entry factors, including ACE2, TMPRSS2, FURIN, and NRP1, have elevated expression in nasal squamous cells from male individuals with moderate and severe COVID-19. We observed male-biased transcriptional activation in SARS-CoV-2-infected macrophages from BALF and sputum samples, which offers potential molecular mechanism for sex-biased susceptibility to viral infection. Cell–cell interaction network analysis reveals potential epithelium–immune cell interactions and immune vulnerability underlying male-elevated disease severity and mortality in COVID-19. Mechanistically, monocyte-elevated expression of Toll-like receptor 7 (TLR7) and Bruton tyrosine kinase (BTK) is associated with severe outcomes in males with COVID-19. In summary, these findings provide basis to decipher immune responses underlying sex differences and designing sex-specific targeted interventions and patient care for COVID-19.


Author(s):  
Giulia Puliani ◽  
Valeria Hasenmajer ◽  
Francesca Sciarra ◽  
Federica Barbagallo ◽  
Emilia Sbardella ◽  
...  

Abstract Context Despite the pivotal role of calcium signaling in immune response, little is known about immune function in patients affected by hypoparathyroidism. Objective This work aimed to evaluate immune function in hypoparathyroidism. Methods The Evaluation of iMmune function in Postsurgical and AuToimmune HYpoparathyroidism (NCT04059380) is a case-control, cross-sectional study set in an Italian referral center. Participants included 20 patients with postsurgical hypoparathyroidism (12 females) and 20 age- and sex-matched controls. Main outcome measures included calcium metabolism assessment, peripheral blood mononuclear cells (PBMC) profiling via flow cytometry, parathyroid hormone receptor 1 (PTHr1) expression analysis using immunofluorescence and PrimeFlow RNA assay, gene expression analysis via real-time polymerase chain reaction, cytokine measurement, and evaluation of infectious disease frequency and severity. Results Immune cell profiling revealed decreased monocytes, regulatory, naive, and total CD4+ T lymphocytes, which correlated with total calcium, ionized calcium, and PTH levels, in patients with hypoparathyroidism. Patients with hypoparathyroidism had a higher CD3−CD56+ natural killer (NK) cell count, which inversely correlated with calcium, PTH, and vitamin D levels. Furthermore, they exhibited decreased tumor necrosis factor (TNF) and granulocyte-macrophage colony-stimulating factor gene expression and decreased circulating TNF levels. Gene expression and immunofluorescence analysis confirmed PTHr1 expression in all PBMC lineages; however, the percentage of cells expressing PTHr1 was lower, whereas the intensity of PTHr1 expression in monocytes, total T lymphocytes, CD8+CD4+ and CD4+ T lymphocytes, and total NK cells was higher in patients with hypoparathyroidism. Conclusions This study describes for the first time the immune alterations in patients with hypoparathyroidism receiving conventional therapies, supporting the immunoregulatory role of PTH and proposing an explanation for the increased susceptibility to infections observed in epidemiological studies.


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