scholarly journals Virus-inclusive single-cell RNA sequencing reveals the molecular signature of progression to severe dengue

2018 ◽  
Vol 115 (52) ◽  
pp. E12363-E12369 ◽  
Author(s):  
Fabio Zanini ◽  
Makeda L. Robinson ◽  
Derek Croote ◽  
Malaya Kumar Sahoo ◽  
Ana Maria Sanz ◽  
...  
Keyword(s):  
B Cells ◽  
Single Cell ◽  
Mononuclear Cells ◽  
Dengue Infection ◽  
Cell Types ◽  
Denv Infection ◽  
Molecular Signature ◽  
Severe Dengue ◽  
Peripheral Blood Mononuclear

Dengue virus (DENV) infection can result in severe complications. However, the understanding of the molecular correlates of severity is limited, partly due to difficulties in defining the peripheral blood mononuclear cells (PBMCs) that contain DENV RNA in vivo. Accordingly, there are currently no biomarkers predictive of progression to severe dengue (SD). Bulk transcriptomics data are difficult to interpret because blood consists of multiple cell types that may react differently to infection. Here, we applied virus-inclusive single-cell RNA-seq approach (viscRNA-Seq) to profile transcriptomes of thousands of single PBMCs derived early in the course of disease from six dengue patients and four healthy controls and to characterize distinct leukocyte subtypes that harbor viral RNA (vRNA). Multiple IFN response genes, particularly MX2 in naive B cells and CD163 in CD14+ CD16+ monocytes, were up-regulated in a cell-specific manner before progression to SD. The majority of vRNA-containing cells in the blood of two patients who progressed to SD were naive IgM B cells expressing the CD69 and CXCR4 receptors and various antiviral genes, followed by monocytes. Bystander, non-vRNA–containing B cells also demonstrated immune activation, and IgG1 plasmablasts from two patients exhibited clonal expansions. Lastly, assembly of the DENV genome sequence revealed diversity at unexpected sites. This study presents a multifaceted molecular elucidation of natural dengue infection in humans with implications for any tissue and viral infection and proposes candidate biomarkers for prediction of SD.

scholarly journals Oncogene expression in autoimmune and normal peripheral blood mononuclear cells.

1986 ◽  
Vol 163 (5) ◽  
pp. 1292-1307 ◽  
Author(s):  
D M Klinman ◽  
J F Mushinski ◽  
M Honda ◽  
Y Ishigatsubo ◽  
J D Mountz ◽  
...  
Keyword(s):  
B Cells ◽  
Mononuclear Cells ◽  
Cell Types ◽  
Isolated Cells ◽  
Peripheral Blood Mononuclear ◽  
Normal Peripheral Blood ◽  
Additional Cell ◽  
Normal Controls

PBMC from patients with autoimmune diseases and from normal controls were studied for the expression of several cellular oncogenes. Gene expression was assessed by Northern blot analysis of poly(A)+ RNA obtained from leukapheresis samples. Patients with SLE expressed significantly more c-myc protooncogene RNA than did normal controls. Increased expression of the N-ras protooncogene was found in that subset of patients whose autoimmune disease was very active. Cells from individuals with SLE, but not from those with other autoimmune illnesses, showed significantly decreased levels of the c-myb and c-fos protooncogenes. To examine the implications of these findings, B and T cells were purified from apheresis samples donated by normal volunteers. When mitogen was used to activate the B cells in vitro, their pattern of protooncogene expression changed to resemble that found in freshly isolated cells from lupus patients. These results suggest that the differences detected in the expression of protooncogenes by patients with SLE may be due to the abnormal activation of their B cells in vivo. The pattern of protooncogene expression found in patients with other autoimmune illnesses is consistent with the activation of additional cell types in those diseases.

scholarly journals Virus-inclusive single cell RNA sequencing reveals molecular signature predictive of progression to severe dengue infection

2018 ◽  
Author(s):  
Fabio Zanini ◽  
Makeda L. Robinson ◽  
Derek Croote ◽  
Malaya Kumar Sahoo ◽  
Ana Maria Sanz ◽  
...  
Keyword(s):  
B Cells ◽  
Viral Infection ◽  
Single Cell ◽  
Immune Activation ◽  
Dengue Infection ◽  
Predictive Biomarkers ◽  
Molecular Signature ◽  
Interferon Response ◽  
Severe Dengue ◽  
Specific Cell

AbstractDengue virus (DENV) infection can result in severe complications. Yet, the understanding of the molecular correlates of severity is limited, partly due to difficulties in defining the peripheral blood mononuclear cells (PBMCs) that are associated with DENV in vivo. Additionally, there are currently no biomarkers predictive of progression to severe dengue (SD). Bulk transcriptomics data are difficult to interpret because blood consists of multiple cell types that may react differently to infection. Here we applied virus-inclusive single cell RNA-seq approach (viscRNA-Seq) to profile transcriptomes of thousands of single PBMCs derived early in the course of disease from six dengue patients and four healthy controls, and to characterize distinct DENV-associated leukocytes. Multiple genes, particularly interferon response genes, were upregulated in a cell-specific manner prior to progression to SD. Expression of MX2 in naive B cells and CD163 in CD14+ CD16+ monocytes was predictive of SD. The majority of DENV-associated cells in the blood of two patients who progressed to SD were naive IgM B cells expressing the CD69 and CXCR4 receptors and antiviral genes, followed by monocytes. Bystander uninfected B cells also demonstrated immune activation, and plasmablasts from two patients exhibited antibody lineages with convergently hypermutated heavy chain sequences. Lastly, assembly of the DENV genome revealed diversity at unexpected genomic sites. This study presents a multi-faceted molecular elucidation of natural dengue infection in humans and proposes biomarkers for prediction of SD, with implications for profiling any tissue and viral infection, and for the development of a dengue prognostic assay.SignificanceA fraction of the 400 million people infected with dengue annually progresses to severe dengue (SD). Yet, there are currently no biomarkers to effectively predict disease progression. We profiled the landscape of host transcripts and viral RNA in thousands of single blood cells from dengue patients prior to progressing to SD. We discovered cell-type specific immune activation and candidate predictive biomarkers. We also revealed preferential virus association with specific cell populations, particularly naive B cells and monocytes. We then explored immune activation of bystander cells, clonality and somatic evolution of adaptive immune repertoires, and viral genomics. This multi-faceted approach could advance understanding of pathogenesis of any viral infection, map an atlas of infected cells and promote the development of prognostics.

scholarly journals Molecular mechanisms governing circulating immune cell heterogeneity across different species revealed by single cell sequencing

2021 ◽  
Author(s):  
Zhibin Li ◽  
chengcheng Sun ◽  
Fei Wang ◽  
Xiran Wang ◽  
Jiacheng Zhu ◽  
...  
Keyword(s):  
Single Cell ◽  
Immune Cells ◽  
Evolutionary Biology ◽  
Regulatory Networks ◽  
Molecular Mechanisms ◽  
Mononuclear Cells ◽  
Immune Cell ◽  
Cell Types ◽  
Genetic Regulatory Networks ◽  
Peripheral Blood Mononuclear

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

scholarly journals CD4-Negative Cells Bind Human Immunodeficiency Virus Type 1 and Efficiently Transfer Virus to T Cells

2000 ◽  
Vol 74 (18) ◽  
pp. 8550-8557 ◽  
Author(s):  
Gene G. Olinger ◽  
Mohammed Saifuddin ◽  
Gregory T. Spear
Keyword(s):  
Human Immunodeficiency Virus ◽  
T Cells ◽  
Mononuclear Cells ◽  
Cell Types ◽  
Virus Binding ◽  
Peripheral Blood Mononuclear ◽  
Human Immunodeficiency Virus Strain ◽  
Immunodeficiency Virus

ABSTRACT The ability of human immunodeficiency virus strain MN (HIVMN), a T-cell line-adapted strain of HIV, and X4 and R5 primary isolates to bind to various cell types was investigated. In general, HIVMN bound to cells at higher levels than did the primary isolates. Virus bound to both CD4-positive (CD4+) and CD4-negative (CD4−) cells, including neutrophils, Raji cells, tonsil mononuclear cells, erythrocytes, platelets, and peripheral blood mononuclear cells (PBMC), although virus bound at significantly higher levels to PBMC. However, there was no difference in the amount of HIV that bound to CD4-enriched or CD4-depleted PBMC. Virus bound to CD4− cells was up to 17 times more infectious for T cells in cocultures than was the same amount of cell-free virus. Virus bound to nucleated cells was significantly more infectious than virus bound to erythrocytes or platelets. The enhanced infection of T cells by virus bound to CD4− cells was not due to stimulatory signals provided by CD4− cells or infection of CD4− cells. However, anti-CD18 antibody substantially reduced the enhanced virus replication in T cells, suggesting that virus that bound to the surface of CD4−cells is efficiently passed to CD4+ T cells during cell-cell adhesion. These studies show that HIV binds at relatively high levels to CD4− cells and, once bound, is highly infectious for T cells. This suggests that virus binding to the surface of CD4− cells is an important route for infection of T cells in vivo.

scholarly journals The Potential of IgG to Induce Murine and Human Thymic Maturation of IL-10+ B Cells (B10) Revealed in a Pilot Study

Cells ◽  
2020 ◽  
Vol 9 (10) ◽  
pp. 2239
Author(s):  
Amanda Harumi Sabô Inoue ◽  
Aline Aparecida de Lima Lira ◽  
Marília Garcia de-Oliveira ◽  
Thamires Rodrigues de Sousa ◽  
Fábio da Ressureição Sgnotto ◽  
...  
Keyword(s):  
B Cells ◽  
Mononuclear Cells ◽  
Inflammatory Diseases ◽  
Allergen Challenge ◽  
Serum Samples ◽  
Peripheral Blood Mononuclear ◽  
Maturation Stages ◽  
B10 Cells

Regulatory B (B10) cells can control several inflammatory diseases, including allergies; however, the origin of peripheral B10 cells is not fully understood, and the involvement of primary lymphoid organs (PLOs) as a primary site of maturation is not known. Here, using a murine model of allergy inhibition mediated by maternal immunization with ovalbumin (OVA), we aimed to evaluate whether B10 cells can mature in the thymus and whether IgG can mediate this process. Female mice were immunized with OVA, and offspring thymus, bone marrow, spleen, lung, and serum samples were evaluated at different times and after passive transfer of purified IgG or thymocytes. A translational approach was implemented using human nonatopic thymus samples, nonatopic peripheral blood mononuclear cells (PBMCs), and IgG from atopic or nonatopic individuals. Based on the expression of CD1d on B cells during maturation stages, we suggest that B10 cells can also mature in the murine thymus. Murine thymic B10 cells can be induced in vitro and in vivo by IgG and be detected in the spleen and lungs in response to an allergen challenge. Like IgG from atopic individuals, human IgG from nonatopic individuals can induce B10 cells in the infant thymus and adult PBMCs. Our observations suggest that B10 cells may mature in the thymus and that this mechanism may be mediated by IgG in both humans and mice. These observations may support the future development of IgG-based immunoregulatory therapeutic strategies.

scholarly journals Enhancement and Imputation of Peak Signal Enables Accurate Cell-Type Classification in scATAC-seq

2021 ◽  
Vol 12 ◽  
Author(s):  
Zhe Cui ◽  
Ya Cui ◽  
Yan Gao ◽  
Tao Jiang ◽  
Tianyi Zang ◽  
...  
Keyword(s):  
Single Cell ◽  
Mononuclear Cells ◽  
Cell Types ◽  
Chromatin Accessibility ◽  
Support Vector ◽  
Cell Type ◽  
Peripheral Blood Mononuclear ◽  
Copy Numbers ◽  
Genome Wide ◽  
Accessible Chromatin

Single-cell Assay Transposase Accessible Chromatin sequencing (scATAC-seq) has been widely used in profiling genome-wide chromatin accessibility in thousands of individual cells. However, compared with single-cell RNA-seq, the peaks of scATAC-seq are much sparser due to the lower copy numbers (diploid in humans) and the inherent missing signals, which makes it more challenging to classify cell type based on specific expressed gene or other canonical markers. Here, we present svmATAC, a support vector machine (SVM)-based method for accurately identifying cell types in scATAC-seq datasets by enhancing peak signal strength and imputing signals through patterns of co-accessibility. We applied svmATAC to several scATAC-seq data from human immune cells, human hematopoietic system cells, and peripheral blood mononuclear cells. The benchmark results showed that svmATAC is free of literature-based markers and robust across datasets in different libraries and platforms. The source code of svmATAC is available at https://github.com/mrcuizhe/svmATAC under the MIT license.

A single-cell map for the transcriptomic signatures of peripheral blood mononuclear cells in end-stage renal disease

2019 ◽  
Author(s):  
Ting Luo ◽  
Fengping Zheng ◽  
Kang Wang ◽  
Yong Xu ◽  
Huixuan Xu ◽  
...  
Keyword(s):  
Single Cell ◽  
End Stage Renal Disease ◽  
Mononuclear Cells ◽  
Cell Types ◽  
Cell Type ◽  
Peripheral Blood Mononuclear ◽  
Blood Mononuclear Cells ◽  
Cell Type Specific ◽  
Stage Renal Disease ◽  
End Stage

Abstract Background Immune aberrations in end-stage renal disease (ESRD) are characterized by systemic inflammation and immune deficiency. The mechanistic understanding of this phenomenon remains limited. Methods We generated 12 981 and 9578 single-cell transcriptomes of peripheral blood mononuclear cells (PBMCs) that were pooled from 10 healthy volunteers and 10 patients with ESRD by single-cell RNA sequencing. Unsupervised clustering and annotation analyses were performed to cluster and identify cell types. The analysis of hallmark pathway and regulon activity was performed in the main cell types. Results We identified 14 leukocytic clusters that corresponded to six known PBMC types. The comparison of cells from ESRD patients and healthy individuals revealed multiple changes in biological processes. We noticed an ESRD-related increase in inflammation response, complement cascade and cellular metabolism, as well as a strong decrease in activity related to cell cycle progression in relevant cell types in ESRD. Furthermore, a list of cell type-specific candidate transcription factors (TFs) driving the ESRD-associated transcriptome changes was identified. Conclusions We generated a distinctive, high-resolution map of ESRD-derived PBMCs. These results revealed cell type-specific ESRD-associated pathways and TFs. Notably, the pooled sample analysis limits the generalization of our results. The generation of larger single-cell datasets will complement the current map and drive advances in therapies that manipulate immune cell function in ESRD.

Immunosenescence in testicular cancer survivors treated with chemotherapy.

2017 ◽  
Vol 35 (15_suppl) ◽  
pp. e16037-e16037 ◽  
Author(s):  
Maria Teresa Bourlon ◽  
Hugo Eduardo Velazquez ◽  
Juan Hinojosa ◽  
Guadalupe Lima ◽  
Ricardo Rios-Corzo ◽  
...  
Keyword(s):  
B Cells ◽  
Testicular Cancer ◽  
Cancer Survivors ◽  
Mononuclear Cells ◽  
Breast Cancer Patients ◽  
Peripheral Blood Mononuclear ◽  
Cell Subpopulations ◽  
Testicular Cancer Survivors ◽  
Mean Time

e16037 Background: Cytotoxic (Ctx) chemotherapy can cure patients with advanced testicular cancer. Notwithstanding, Ctx agents could promote molecular aging and induce cellular senescence in vivo. This phenomenon has been studied in breast cancer patients exposed to adjuvant chemotherapy, however, the potential induction of premature immunosenescence in testicular cancer survivors (TCS) exposed to chemotherapy remains unknown. Methods: Case-control study. Cases were 18-55 yo TCS, treated with chemotherapy (≥3 BEP cycles), disease-free for ≥3 m. Controls were healthy subjects matched by sex and age ± 1 y. Selected subpopulations of isolated peripheral blood mononuclear cells (PBMC) depicted in Table, were analyzed flow cytometry. Statistics: Adjusted counts or relative percentage for each population were compared using student-t test or Mann-Whitney U test as appropriate. Results: We included 15 TCS and 15 controls. Mean age was 32.6 yo (24-54 y). Mean time since last chemotherapy was 53.13 months (3-192 m). All 15 patients were treated with at least 3 BEP cycles ± TIP/VIP cycles. There were no differences in total leucocyte (5128 ± 1917 vs 5850 ± 2141, p=0.36), and lymphocyte (1539 ± 592 vs 1889 ± 825, p=0.4) counts among cases and controls. Cases have a diminished percentage of CD3+ (63 ± 10 vs 71 ± 11, p=0.05) and CD4+ cells (36±8 vs 43 ± 9, p=0.03). There were no differences in pct of CD8+ or CD19+. However, there was an increase in late differentiated CD8+/CD57+ cells (31 ± 14% vs 20 ± 11%, p=0.02); and a decrease in CD4+/CD28+ cells (90 ± 9% vs 97 ± 4%, p=0.02) in cases. We observed paradoxical changes in B cell subpopulations with an increment in naïve (79 ±10 vs 67% ± 14% p=0.02) and a decrease in memory (18 ± 9 vs 31 ± 13%, p=0.01) B cells. Conclusions: TCS after chemo develop changes compatible with immunesenescence in T cell (CD3+) compartment, and an increment in naïve B cells. [Table: see text]

scholarly journals 3D Bioprinting of Model Tissues That Mimic the Tumor Microenvironment

Micromachines ◽  
2021 ◽  
Vol 12 (5) ◽  
pp. 535
Author(s):  
Florina Bojin ◽  
Andreea Robu ◽  
Maria Iulia Bejenariu ◽  
Valentin Ordodi ◽  
Emilian Olteanu ◽  
...  
Keyword(s):  
Tumor Microenvironment ◽  
Cancer Progression ◽  
Mononuclear Cells ◽  
Lattice Models ◽  
Cell Types ◽  
Cancer Drug ◽  
Peripheral Blood Mononuclear ◽  
Metropolis Monte Carlo

The tumor microenvironment (TME) influences cancer progression. Therefore, engineered TME models are being developed for fundamental research and anti-cancer drug screening. This paper reports the biofabrication of 3D-printed avascular structures that recapitulate several features of the TME. The tumor is represented by a hydrogel droplet uniformly loaded with breast cancer cells (106 cells/mL); it is embedded in the same type of hydrogel containing primary cells—tumor-associated fibroblasts isolated from the peritumoral environment and peripheral blood mononuclear cells. Hoechst staining of cryosectioned tissue constructs demonstrated that cells remodeled the hydrogel and remained viable for weeks. Histological sections revealed heterotypic aggregates of malignant and peritumoral cells; moreover, the constituent cells proliferated in vitro. To investigate the interactions responsible for the experimentally observed cellular rearrangements, we built lattice models of the bioprinted constructs and simulated their evolution using Metropolis Monte Carlo methods. Although unable to replicate the complexity of the TME, the approach presented here enables the self-assembly and co-culture of several cell types of the TME. Further studies will evaluate whether the bioprinted constructs can evolve in vivo in animal models. If they become connected to the host vasculature, they may turn into a fully organized TME.

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