scholarly journals Enabling out-of-clinic human immunity studies via single-cell profiling of capillary blood

2020 ◽  
Author(s):  
Tatyana Dobreva ◽  
David Brown ◽  
Jong Hwee Park ◽  
Matt Thomson
Keyword(s):  
Gene Expression ◽  
Immune System ◽  
Environmental Factors ◽  
Single Cell ◽  
Immune Cell ◽  
Cell Types ◽  
Capillary Blood ◽  
Specific Gene ◽  
Human Immune ◽  
Over Time

AbstractAn individual’s immune system is driven by both genetic and environmental factors that vary over time. To better understand the temporal and inter-individual variability of gene expression within distinct immune cell types, we developed a platform that leverages multiplexed single-cell sequencing and out-of-clinic capillary blood extraction to enable simplified, cost-effective profiling of the human immune system across people and time at single-cell resolution. Using the platform, we detect widespread differences in cell type-specific gene expression between subjects that are stable over multiple days.SummaryIncreasing evidence implicates the immune system in an overwhelming number of diseases, and distinct cell types play specific roles in their pathogenesis.1,2 Studies of peripheral blood have uncovered a wealth of associations between gene expression, environmental factors, disease risk, and therapeutic efficacy.4 For example, in rheumatoid arthritis, multiple mechanistic paths have been found that lead to disease, and gene expression of specific immune cell types can be used as a predictor of therapeutic non-response.12 Furthermore, vaccines, drugs, and chemotherapy have been shown to yield different efficacy based on time of administration, and such findings have been linked to the time-dependence of gene expression in downstream pathways.21,22,23 However, human immune studies of gene expression between individuals and across time remain limited to a few cell types or time points per subject, constraining our understanding of how networks of heterogeneous cells making up each individual’s immune system respond to adverse events and change over time.

scholarly journals Single cell profiling of capillary blood enables out of clinic human immunity studies

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Tatyana Dobreva ◽  
David Brown ◽  
Jong Hwee Park ◽  
Matt Thomson
Keyword(s):  
Gene Expression ◽  
Immune System ◽  
Single Cell ◽  
Immune Cell ◽  
Cost Effective ◽  
Cell Types ◽  
Individual Variability ◽  
Capillary Blood ◽  
Specific Gene ◽  
Human Immune System

AbstractAn individual’s immune system is driven by both genetic and environmental factors that vary over time. To better understand the temporal and inter-individual variability of gene expression within distinct immune cell types, we developed a platform that leverages multiplexed single-cell sequencing and out-of-clinic capillary blood extraction to enable simplified, cost-effective profiling of the human immune system across people and time at single-cell resolution. Using the platform, we detect widespread differences in cell type-specific gene expression between subjects that are stable over multiple days.

scholarly journals Comprehensive multi-omics single-cell data integration reveals greater heterogeneity in the human immune system

2021 ◽  
Author(s):  
Congmin Xu ◽  
Junkai Yang ◽  
Astrid Kosters ◽  
Benjamin R Babcock ◽  
Peng Qiu ◽  
...  
Keyword(s):  
Immune System ◽  
Single Cell ◽  
Immune Cell ◽  
Cell Types ◽  
Cell Receptor ◽  
Surface Proteins ◽  
Cell Type ◽  
Human Immune System ◽  
Receptor Repertoire ◽  
Human Immune

Single-cell transcriptomics enables the definition of diverse human immune cell types across multiple tissue and disease contexts. Still, deeper biological understanding requires comprehensive integration of multiple single-cell omics (transcriptomic, proteomic, and cell receptor repertoire). To improve the identification of diverse cell types and the accuracy of cell-type classification in our multi-omics single-cell datasets, we developed SuPERR-seq, a novel analysis workflow to increase the resolution and accuracy of clustering and allow for the discovery and characterization of previously hidden cell subsets. We show that by incorporating information from cell-surface proteins and immunoglobulin transcript counts, we accurately remove cell doublets and prevent widespread cell-type misclassification. This approach uniquely improves the identification of heterogeneous cell types in the human immune system, including a novel subset of antibody-secreting cells in the bone marrow.

scholarly journals A molecular cell atlas of the human lung from single cell RNA sequencing

2019 ◽  
Author(s):  
Kyle J. Travaglini ◽  
Ahmad N. Nabhan ◽  
Lolita Penland ◽  
Rahul Sinha ◽  
Astrid Gillich ◽  
...  
Keyword(s):  
Gene Expression ◽  
Single Cell ◽  
Rna Sequencing ◽  
Immune Cell ◽  
Human Lung ◽  
Expression Profiles ◽  
Cell Types ◽  
Specific Gene ◽  
Cell Trafficking ◽  
Single Cell Rna Sequencing

AbstractAlthough single cell RNA sequencing studies have begun providing compendia of cell expression profiles, it has proven more difficult to systematically identify and localize all molecular cell types in individual organs to create a full molecular cell atlas. Here we describe droplet- and plate-based single cell RNA sequencing applied to ∼75,000 human lung and blood cells, combined with a multi-pronged cell annotation approach, which have allowed us to define the gene expression profiles and anatomical locations of 58 cell populations in the human lung, including 41 of 45 previously known cell types or subtypes and 14 new ones. This comprehensive molecular atlas elucidates the biochemical functions of lung cell types and the cell-selective transcription factors and optimal markers for making and monitoring them; defines the cell targets of circulating hormones and predicts local signaling interactions including sources and targets of chemokines in immune cell trafficking and expression changes on lung homing; and identifies the cell types directly affected by lung disease genes and respiratory viruses. Comparison to mouse identified 17 molecular types that appear to have been gained or lost during lung evolution and others whose expression profiles have been substantially altered, revealing extensive plasticity of cell types and cell-type-specific gene expression during organ evolution including expression switches between cell types. This atlas provides the molecular foundation for investigating how lung cell identities, functions, and interactions are achieved in development and tissue engineering and altered in disease and evolution.

scholarly journals Human immune system variation during one year

2020 ◽  
Author(s):  
Tadepally Lakshmikanth ◽  
Sayyed Auwn Muhammad ◽  
Axel Olin ◽  
Yang Chen ◽  
Jaromir Mikes ◽  
...  
Keyword(s):  
Immune System ◽  
Individual Variation ◽  
Immune Cell ◽  
Metabolic Health ◽  
Individual Feature ◽  
Human Immune System ◽  
Principal Curve ◽  
Human Immune ◽  
One Year ◽  
Over Time

SUMMARYThe human immune system varies extensively between individuals, but variation within individuals over time has not been well characterized. Systems-level analyses allow for simultaneous quantification of many interacting immune system components, and the inference of global regulatory principles. Here we present a longitudinal, systems-level analysis in 99 healthy adults, 50 to 65 years of age and sampled every 3rd month during one year. We describe the structure of inter-individual variation and characterize extreme phenotypes along a principal curve. From coordinated measurement fluctuations, we infer relationships between 115 immune cell populations and 750 plasma proteins constituting the blood immune system. While most individuals have stable immune systems, the degree of longitudinal variability is an individual feature. The most variable individuals, in the absence of overt infections, exhibited markers of poor metabolic health suggestive of a functional link between metabolic and immunologic homeostatic regulation.HIGHLIGHTSLongitudinal variation in immune cell composition during one yearInter-individual variation can be described along a principal curveImmune cell and protein relationships are inferredVariability over time is an individual feature correlating with markers of poor metabolic health

PATH-26. EVALUATING THE DISTRIBUTION AND PROGNOSIS OF IMMUNE CELL SIGNATURES OF THE TUMOR MICRO-ENVIRONMENT IN DIFFUSE GLIOMAS

2021 ◽  
Vol 23 (Supplement_6) ◽  
pp. vi120-vi120
Author(s):  
Bharati Mehani ◽  
Saleembhasha Asanigari ◽  
Hye-Jung Chung ◽  
Kenneth Aldape
Keyword(s):  
Gene Expression ◽  
Single Cell ◽  
Immune Cell ◽  
Tumor Grade ◽  
Cell Types ◽  
Idh Mutation ◽  
Mutation Status ◽  
Cluster Analyses ◽  
Diffuse Gliomas ◽  
Cell Expression

Abstract The tumor micro-environment (TME) plays an important role in the biology of cancer, including gliomas. Single cell studies have highlighted the role of specific TME components in gliomas, and the methods to deconvolve bulk profiling data may serve to complement these studies on clinically annotated tumors. In this study, we estimated cell type proportions in 3 large glioma datasets (TCGA, CGGA-325, CGGA-693) using CIBERSORTx. Using a signature matrix comprising 22 immune cell types, we identified IDH mutation status-specific immune cell distributions and found that the proportions of 10 cell types were significantly different between IDHmut and IDHwt tumors across the 3 datasets. Looking further within IDHmut tumors, we found that monocytes were enriched in 1p/19q non-co-deleted tumors across the 3 glioma datasets, consistent with prior single cell studies. We then examined estimated gene expression among immune cell types relative to IDH mutation status and found clear separation of gene expression in 15 of 22 cell types in all 3 datasets. When we applied these 22 gene expression signatures in each tumor sample onto cluster-of-cluster analyses to identify tumor groups with distinct immune signature patterns, we found that samples were distributed largely according to the IDH status in all 3 datasets, confirming that immune cell expression is distinct based on IDH status. Among IDH-specific groups, cluster-of-cluster analyses showed that immune cell-based cluster groups had distinct survival outcomes, and that IDHwt samples were distributed significantly based on tumor grades as well as based on EGFR overexpression. Among IDHmut tumors, the distributions of tumor grade and 1p/19q co-deletion status were significantly different in the immune-based clusters in 2 of the 3 datasets examined. Overall, these results highlight the biological and clinical significance of the immune cell environment in gliomas, including distinctions based on IDH mutation status as well as prognosis within IDH-specific groups.

scholarly journals Single-cell RNA sequencing reveals micro-evolution of the stickleback immune system

2021 ◽  
Author(s):  
Lauren E Fuess ◽  
Daniel I Bolnick
Keyword(s):  
Immune System ◽  
Single Cell ◽  
Immune Cells ◽  
Gasterosteus Aculeatus ◽  
Immune Cell ◽  
Expression Profiles ◽  
Cell Types ◽  
Model Systems ◽  
System Structure ◽  
Ecological Processes

Pathogenic infection is an important driver of many ecological processes. Furthermore, variability in immune function is an important driver of differential infection outcomes. New evidence would suggest that immune variation extends to broad cellular structure of immune systems. However, variability at such broad levels is traditionally difficult to detect in non-model systems. Here we leverage single cell transcriptomic approaches to document signatures of microevolution of immune system structure in a natural system, the three-spined stickleback (Gasterosteus aculeatus). We sampled nine adult fish from three populations with variability in resistance to a cestode parasite, Schistocephalus solidus, to create the first comprehensive immune cell atlas for G. aculeatus. Eight major immune cell types, corresponding to major vertebrate immune cells, were identified. We were also able to document significant variation in both abundance and expression profiles of the individual immune cell types, among the three populations of fish. This variability may contribute to observed variability in parasite susceptibility. Finally, we demonstrate that identified cell type markers can be used to reinterpret traditional transcriptomic data. Combined our study demonstrates the power of single cell sequencing to not only document evolutionary phenomena (i.e. microevolution of immune cells), but also increase the power of traditional transcriptomic datasets.

scholarly journals Single cell transcriptomics reveals opioid usage evokes widespread suppression of antiviral gene program

2019 ◽  
Author(s):  
Tanya T. Karagiannis ◽  
John P. Cleary ◽  
Busra Gok ◽  
Nicholas G. Martin ◽  
Elliot C. Nelson ◽  
...  
Keyword(s):  
Immune System ◽  
Single Cell ◽  
Mononuclear Cells ◽  
Immune Cell ◽  
Ex Vivo ◽  
Cell Types ◽  
Short Exposure ◽  
Opioid Use ◽  
Peripheral Blood Mononuclear ◽  
Antiviral Gene

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.

scholarly journals Gene Expression Analysis Reveals Age and Ethnicity Signatures Between Young and Old Adults in Human PBMC

2021 ◽  
Author(s):  
Yang Hu ◽  
Yudai Xu ◽  
Lipeng Mao ◽  
Wen Lei ◽  
Jan Jian Xiang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Immune System ◽  
Large Scale ◽  
Mononuclear Cells ◽  
Immune Cell ◽  
Human Immune System ◽  
Immune Systems ◽  
Network Analyses ◽  
Age Related ◽  
Human Immune

Abstract Background: Human immune system functions over an entire lifetime, yet how and why the immune system becomes less effective with age are not well understood. Therefore, the aim of this study is to exploit a large-scale population-based strategy to systematically identify genes and pathways differentially expressed as a function of chronological age. Despite the importance of age and race in shaping immune cell numbers and functions, it is unclear whether Asian and Caucasian immune systems go through similar gene expression changes throughout their lifespan, and to what extent these aging-associated variations are shared among ethnicities. Results: Here, we characterize peripheral blood mononuclear cells transcriptome from 19 healthy adults of RNA-seq data and 153 healthy subjects of micoarray data with 21~90 years of age using the weighted gene correlation network analyses (WGCNA). These data reveal a set of insightful gene expression modules and representative gene biomarkers for human immune system aging from Asian and Caucasian ancestry, respectively. Among them, the aging-specific modules may show an age-related gene expression variation spike around early-seventies. In addition, we find the top hub genes including NUDT7, CLPB, OXNAD1 and MLLT3 are shared between Asian and Caucasian aging related modules and further validated in human PBMCs from different age groups. Conclusion: Overall, our findings reveal how age and race differentially affect the immune systems between Asian and Caucasian, as well as discovered a common genetic variant that greatly impacts normal PBMC aging between Asian and Caucasian.

scholarly journals The Power of ONE: Immunology in the Age of Single Cell Genomics

Blood ◽  
2019 ◽  
Vol 134 (Supplement_1) ◽  
pp. SCI-30-SCI-30
Author(s):  
Ido Amit
Keyword(s):  
Immune System ◽  
Single Cell ◽  
Spatial Organization ◽  
Immune Cell ◽  
Conflicts Of Interest ◽  
Cell Types ◽  
Single Cell Genomics ◽  
Clonal Distribution ◽  
Genomic Studies ◽  
Potential Impact

The immune system is a complex, dynamic and plastic network composed of various interacting cell types that are constantly sensing and responding to environmental cues. From very early on, the immunology field has invested great efforts and ingenuity to characterize the various immune cell types and elucidate their functions. However, accumulating evidence indicates that current technologies and classification schemes are limited in their ability to account for the functional heterogeneity of immune processes. Single cell genomics hold the potential to revolutionize the way we characterize complex immune cell assemblies and study their spatial organization, dynamics, clonal distribution, pathways, and crosstalk. This emerging field can greatly affect basic and translational research of the immune system. I will discuss how recent single cell genomic studies are changing our perspective of various immune related pathologies from cancer to neurodegeneration. Finally, I will consider recent and forthcoming technological and analytical advances in single cell genomics and their potential impact on the future of immunology research and immunotherapy. Disclosures No relevant conflicts of interest to declare.

scholarly journals NFIL3 mutations alter immune homeostasis and sensitise for arthritis pathology

2018 ◽  
Vol 78 (3) ◽  
pp. 342-349 ◽  
Author(s):  
Susan Schlenner ◽  
Emanuela Pasciuto ◽  
Vasiliki Lagou ◽  
Oliver Burton ◽  
Teresa Prezzemolo ◽  
...  
Keyword(s):  
Immune System ◽  
Single Cell ◽  
Immune Cell ◽  
Cell Types ◽  
Monozygotic Twin ◽  
Preclinical Model ◽  
Potential Contribution ◽  
Mutant Form ◽  
Single Cell Sequencing

ObjectivesNFIL3 is a key immunological transcription factor, with knockout mice studies identifying functional roles in multiple immune cell types. Despite the importance of NFIL3, little is known about its function in humans.MethodsHere, we characterised a kindred of two monozygotic twin girls with juvenile idiopathic arthritis at the genetic and immunological level, using whole exome sequencing, single cell sequencing and flow cytometry. Parallel studies were performed in a mouse model.ResultsThe patients inherited a novel p.M170I in NFIL3 from each of the parents. The mutant form of NFIL3 demonstrated reduced stability in vitro. The potential contribution of this mutation to arthritis susceptibility was demonstrated through a preclinical model, where Nfil3-deficient mice upregulated IL-1β production, with more severe arthritis symptoms on disease induction. Single cell sequencing of patient blood quantified the transcriptional dysfunctions present across the peripheral immune system, converging on IL-1β as a pivotal cytokine.ConclusionsNFIL3 mutation can sensitise for arthritis development, in mice and humans, and rewires the innate immune system for IL-1β over-production.

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