Understanding B Lymphocyte Development: A Long Way to Go

Bhattacharya, Malavika

doi:10.5772/intechopen.79663

Cited by 5 publications

(5 citation statements)

References 132 publications

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“…Previous research has shown that B cells develop in many stages and have more of a continuous gradient in cellular developmental progress, rather than discrete stages. HLA.DR (as are other MHC class II genes) is an important marker of the progression of B cells through these different stages 28, 29 . In the SAUCIE embedding, HLA.DR-high B cells are clustered together towards the left side, whereas UMAP placed these cells at three distinct places pointing to different directions.…”

Section: Resultsmentioning

confidence: 99%

Comparative Analysis of Dimension Reduction Methods for Cytometry by Time-of-Flight Data

Wang

Yang

et al. 2022

Preprint

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Recently developed single-cell profiling technologies, such as single cell sequencing (scRNA-seq) and mass cytometry (CyTOF), provide critical biological insights from a large number of cells and a large number of features. While experimental and informatic techniques around scRNA-seq are much more advanced, research around CyTOF data analysis has severely lagged behind. However, CyTOF profiles the proteomics makeup of the single cells and are more closely related to disease phenotypes than scRNA-seq. CyTOF data are also dramatically different from scRNA-seq data in many aspects. This calls for the evaluation and development of statistical methods for CyTOF data. Dimension reduction (DR) is one of the most critical first steps of analyses of scRNA-seq and CyTOF data. Here, we benchmark 20 of these methods on 110 real and 425 synthetic CyTOF datasets, including 10 Imaging CyTOF datasets, for accuracy, scalability and usability. In particular, we checked the concordance of DR for CyTOF data against scRNA-seq data that were generated from the same samples. We found that SAUCIE and scvis surprisingly perform well across all categories, whereas UMAP particularly excels in downstream analyses and MDS preserves local and global structure well. Our results highlight the complementarity of existing tools, and that the choice of method should depend on the underlying data structure of the single cells. Based on these results, we develop a set of guidelines to help users select the best DR method for their dataset. Our freely available data and evaluation pipeline will aid in the development of improved DR algorithms specifically tailored to analyze data generated from the increasingly popular CyTOF technique.

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Section: Resultsmentioning

confidence: 99%

Comparative Analysis of Dimension Reduction Methods for Cytometry by Time-of-Flight Data

Wang

Yang

et al. 2022

Preprint

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“…Here, we used anti-CD45R/B220 antibodies to select for the B-cell populations and used anti-IgM F(ab’) 2 fragment for cross-linking BCRs. Although B220 can be used as a pan B-cell marker for mice, it is not a pan B-cell marker for human. , This is because CD45R expression on human B cells is dynamic and is downregulated during germinal center differentiation into memory/plasma B cells . Nevertheless, the anti-CD45R/B220 antibody should capture the majority of the human B cells found in PBMCs, , and the Ig class-switched memory-B cells that would not have been cross-linked by the anti-IgM F(ab’) 2 fragment.…”

Section: Discussionmentioning

confidence: 99%

Disrupting N-Glycosylation Using Type I Mannosidase Inhibitors Alters B-Cell Receptor Signaling

Huang

Kurhade

Ross

et al. 2022

ACS Pharmacol. Transl. Sci.

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Kifunensine is a known inhibitor of type I α-mannosidase enzymes and has been shown to have therapeutic potential for a variety of diseases and application in the expression of high-mannose N-glycan bearing glycoproteins; however, the compound’s hydrophilic nature limits its efficacy. We previously synthesized two hydrophobic acylated derivatives of kifunensine, namely, JDW-II-004 and JDW-II-010, and found that these compounds were over 75-fold more potent than kifunensine. Here we explored the effects of these compounds on different mice and human B cells, and we demonstrate that they affected the cells in a similar fashion to kifunensine, further demonstrating their functional equivalence to kifunensine in assays utilizing primary cells. Specifically, a dose-dependent increase in the formation of high-mannose N-glycans decorated glycoproteins were observed upon treatment with kifunensine, JDW-II-004, and JDW-II-010, but greater potency was observed with the acylated derivatives. Treatment with kifunensine or the acylated derivatives also resulted in impaired B-cell receptor (BCR) signaling of the primary mouse B cells; however, primary human B cells treated with kifunensine or JDW-II-004 did not affect BCR signaling, while a modest increase in BCR signaling was observed upon treatment with JDW-010. Nevertheless, these findings demonstrate that the hydrophobic acylated derivatives of kifunensine can help overcome the mass-transfer limitations of the parent compound, and they may have applications for the treatment of ERAD-related diseases or prove to be more cost-effective alternatives for the generation and production of high-mannose N-glycan bearing glycoproteins.

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“…Furthermore, there are some multi‐reactive natural IgM autoantibodies that can not only resist the invasion of microorganisms but also regulate excessive inflammation caused by various factors to prevent autoimmune diseases 72 . In addition to secreting antibodies, B lymphocytes can also present antigens and secrete cytokines including IL‐2, IL‐4, IL‐6, IL‐10, IL‐12, TGF‐β1, TNF, and IFN‐γ 73 . It is worth mentioning that, like the symbiotic microbiota of the gut, the normal flora in the lungs also plays a protective role for the host (Figure 1).…”

Section: Anti‐infection Mechanism Of the Lungmentioning

confidence: 99%

“… 72 In addition to secreting antibodies, B lymphocytes can also present antigens and secrete cytokines including IL‐2, IL‐4, IL‐6, IL‐10, IL‐12, TGF‐β1, TNF, and IFN‐γ. 73 It is worth mentioning that, like the symbiotic microbiota of the gut, the normal flora in the lungs also plays a protective role for the host (Figure 1 ).…”

Section: Anti‐infection Mechanism Of the Lungmentioning

confidence: 99%

Interactions between the lung microbiome and host immunity in chronic obstructive pulmonary disease

Zhu

Chang

2023

Chronic Diseases and Translational Medicine

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Chronic obstructive pulmonary disease (COPD) is a common chronic respiratory disease and the third leading cause of death worldwide. Developments in next-generation sequencing technology have improved microbiome analysis, which is increasingly recognized as an important component of disease management. Similar to the gut, the lung is a biosphere containing billions of microbial communities. The lung microbiome plays an important role in regulating and maintaining the host immune system. The microbiome composition, metabolites of microorganisms, and the interactions between the lung microbiome and the host immunity profoundly affect the occurrence, development, treatment, and prognosis of COPD. In this review, we drew comparisons between the lung microbiome of healthy individuals and that of patients with COPD. Furthermore, we summarize the intrinsic interactions between the host and the overall lung microbiome, focusing on the underlying mechanisms linking the microbiome to the host innate and adaptive immune response pathways. Finally, we discuss the possibility of using the microbiome as a biomarker to determine the stage and prognosis of COPD and the feasibility of developing a novel, safe, and effective therapeutic target. K E Y W O R D S adaptive immune response, chronic obstructive pulmonary disease, innate immune response, microbiome Highlights• The lung microbiome of healthy individuals is compared to that of patients with chronic obstructive pulmonary disease (COPD). • The role of the lung microbiome in the pathogenesis of COPD and host immune alterations is discussed. • The most representative studies are presented for accuracy and comprehensiveness. | INTRODUCTIONChronic obstructive pulmonary disease (COPD) is a common, preventable, and treatable chronic lung disease that poses a substantial burden on global health and the economy. According to the results of a 27-year global cohort study published in The Lancet, the top three causes of death worldwide in 2017 were cardiovascular disease (31.8% of all death causes), cancer (17.1% of all death causes), and chronic respiratory

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Understanding B Lymphocyte Development: A Long Way to Go

Cited by 5 publications

References 132 publications

Comparative Analysis of Dimension Reduction Methods for Cytometry by Time-of-Flight Data

Comparative Analysis of Dimension Reduction Methods for Cytometry by Time-of-Flight Data

Disrupting N-Glycosylation Using Type I Mannosidase Inhibitors Alters B-Cell Receptor Signaling

Interactions between the lung microbiome and host immunity in chronic obstructive pulmonary disease

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