Single Cell RNA Sequencing of Peripheral Blood Mononuclear Cells in Idiopathic Pulmonary Fibrosis Reveals the Cellular Origin of the Outcome Predictive 52-Gene Signature

Objectives Takayasu Arteritis (TA) is a rare non-specific vascular inflammation and has deleterious effects on patients’ health. Recent studies have advanced in TA diagnosis and treatment, but the research on the immune cell atlas of peripheral blood is still less. For this purpose, we performed single-cell RNA sequencing (scRNA-seq) to analyze the inflammatory cell types and cell markers in TA patients’ Peripheral blood mononuclear cells (PBMCs). Methods 4 TA patients and 4 health controls were enrolled in our study from 2019.10 to 2020.5. Their PBMCs samples were collected and performed scRNA-seq. We used Seurat package (v.3.2.2) in R studio (v.3.5.3) for data analysis, and 2 tests were applied for comparing the composition ratio of each cell type by SPSS 20.0. Results CD14+ monocytes, GZMB+ NKT cells, CD56dim CD16+ NK cells, and naive B cells were significantly increased in TA patients as compared to healthy controls and the expression of THBS1, CD163, AREG, IFITM1, TXNIP, and IGHGs was elevated in the peripheral blood of TA patients. Conclusion Except CD4+ T cells, monocytes, NK cells, NKT cells, B cells also play an important role in TA pathogenesis. The elevated markers have different functions in different types of PBMCs, and they can be used as potential diagnostic markers for TA diagnosis.

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Single-Cell RNA-Sequencing of Peripheral Blood Mononuclear Cells with ddSEQ

Methods in Molecular Biology - Single Cell Methods ◽

10.1007/978-1-4939-9240-9_10 ◽

2019 ◽

pp. 155-176 ◽

Cited By ~ 3

Author(s):

Shaheen Khan ◽

Kelly A. Kaihara

Keyword(s):

Single Cell ◽

Rna Sequencing ◽

Peripheral Blood Mononuclear Cells ◽

Peripheral Blood ◽

Mononuclear Cells ◽

Peripheral Blood Mononuclear ◽

Single Cell Rna Sequencing ◽

Blood Mononuclear Cells

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Transcriptomic Analysis of Mycobacterium leprae-Stimulated Response in Peripheral Blood Mononuclear Cells Reveal Potential Biomarkers for Early Diagnosis of Leprosy

Frontiers in Cellular and Infection Microbiology ◽

10.3389/fcimb.2021.714396 ◽

2021 ◽

Vol 11 ◽

Author(s):

You-Hua Yuan ◽

Jian Liu ◽

Yuan-Gang You ◽

Xiao-Hua Chen ◽

Lian-Chao Yuan ◽

...

Keyword(s):

Early Diagnosis ◽

Differentially Expressed Genes ◽

Peripheral Blood Mononuclear Cells ◽

Peripheral Blood ◽

Mononuclear Cells ◽

Mycobacterium Leprae ◽

Gene Signature ◽

Peripheral Blood Mononuclear ◽

Blood Mononuclear Cells ◽

Leprosy Patients

We aimed to identify an unique host transcriptional signature in peripheral blood mononuclear cells (PBMCs) in response to Mycobacterium leprae antigens to distinguish between patients with leprosy and non-leprosy controls for early diagnosis of the disease. Sixteen individuals were enrolled in the discovery cohort [eight patients with leprosy, comprising four multibacillary (MB) and four paucibacillary (PB); and eight non-leprosy controls, comprising four healthy house contacts (HHCs) and four endemic controls (ECs)]. The differences in the transcriptome response of PBMCs to M. leprae sonicate antigen were evaluated between leprosy patients and non-leprosy controls, and 12 differentially expressed genes (CCL2/MCP-1, IL-8, JAKM, ATP, ND1, SERP, FLJ10489, LINC00659, LOC34487, LOC101928143, MIR22, and NCF1C) were identified. The accuracy of the 12 differentially expressed genes was further validated for the diagnosis of leprosy using real-time quantitative PCR in 82 individuals (13 MB, 10 PB, 37 HHCs, and 22 ECs) in the validation cohort. We found that a 5 gene signature set IL-8, CCL2/MCP-1, SERP, LINC00659 and FLJ10489 had a suitable performance in discriminating leprosy from ECs. In addition, elevated expression of IL-8, CCL2/MCP-1, SERP and LINC00659 was associated with MB diagnosis compared with ECs, whereas increased expression of IL-8, CCL2/MCP-1, SERP and FLJ10489 was found to be useful biomarkers for PB diagnosis from ECs. Moreover, we found decreased expression of NCF1C among leprosy patients could distinguish leprosy from HHCs, whereas higher expression of CCL2 among MB than PB could distinguish different leprosy patients. In conclusion, among the 12 candidate host genes identified, a three gene signature IL-8, CCL2/MCP-1, and SERP showed the best performance in distinguishing leprosy patients from healthy controls. These findings may have implications for developing a rapid blood-based test for early diagnosis of leprosy.

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No detectable alloreactive transcriptional responses during donor-multiplexed single-cell RNA sequencing of peripheral blood mononuclear cells

10.1101/2020.02.12.946509 ◽

2020 ◽

Author(s):

Christopher S. McGinnis ◽

David A. Siegel ◽

Guorui Xie ◽

Mars Stone ◽

Zev J. Gartner ◽

...

Keyword(s):

Gene Expression ◽

Single Cell ◽

Rna Sequencing ◽

Peripheral Blood Mononuclear Cells ◽

Peripheral Blood ◽

Mononuclear Cells ◽

Transcriptional Responses ◽

Peripheral Blood Mononuclear ◽

Single Cell Rna Sequencing ◽

Blood Mononuclear Cells

ABSTRACTSingle-cell RNA sequencing (scRNA-seq) provides high-dimensional measurement of transcript counts in individual cells. However, high assay costs limit the study of large numbers of samples. Sample multiplexing technologies such as antibody hashing and MULTI-seq use sample-specific sequence tags to enable individual samples (e.g., different patients) to be sequenced in a pooled format before downstream computational demultiplexing. Critically, no study to date has evaluated whether the mixing of samples from different donors in this manner results in significant changes in gene expression resulting from alloreactivity (i.e., response to non-self immune antigens). The ability to demonstrate minimal to no alloreactivity is crucial to avoid confounded data analyses, particularly for cross-sectional studies evaluating changes in immunologic gene signatures,. Here, we compared the expression profiles of peripheral blood mononuclear cells (PBMCs) from a single donor with and without pooling with PBMCs isolated from other donors with different blood types. We find that there was no evidence of alloreactivity in the multiplexed samples following three distinct multiplexing workflows (antibody hashing, MULTI-seq, and in silico genotyping using souporcell). Moreover, we identified biases amongst antibody hashing sample classification results in this particular experimental system, as well as gene expression signatures linked to PBMC preparation method (e.g., Ficoll-Paque density gradient centrifugation with or without apheresis using Trima filtration).

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