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Journals
Biomolecules
Special Issues
Single Cell RNA Sequencing in Immunology
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Single Cell RNA Sequencing in Immunology

A special issue of Biomolecules (ISSN 2218-273X). This special issue belongs to the section "Molecular Genetics".

Deadline for manuscript submissions: closed (20 July 2023) | Viewed by 8372

Special Issue Editors

Dr. Peng Shao

E-Mail Website
Guest Editor
Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
Interests: T cell differentiation; infections; non-coding RNAs
Special Issues, Collections and Topics in MDPI journals
Dr. Lingling Zheng

E-Mail Website
Guest Editor
MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, Sun Yat-Sen University, Guangzhou 510275, China
Interests: multi-omics data analysis; non-coding RNAs; infectious disease; epigenomics and epitranscriptomics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Single-cell RNA sequencing (scRNA-seq) emerged after the establishment of next-generation sequencing. It offers a powerful and unbiased approach to characterize the transcriptome profiling of individual cells within complex tissues, shedding new insights into genomic heterogeneity and functional diversity at a single-cell level in health and disease. 

The focus of this Special Issue of Biomolecules will be on the application of scRNA-seq combined with advanced computational approaches to identify and functionally characterize the distinct cell subsets, new biomolecular markers and regulatory networks and reconstruct developmental trajectories in the immune system and immune-mediated diseases.

Dr. Peng Shao
Dr. Lingling Zheng
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Biomolecules is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • single cell RNA sequencing
  • scRNA-seq
  • differentiation
  • immunity
  • infection

Published Papers (3 papers)

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Research

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17 pages, 10806 KiB  
Article
Single-Cell RNA Sequencing Analysis of Gene Regulatory Network Changes in the Development of Lung Adenocarcinoma
by Dongshuo Yu, Siwen Zhang, Zhenhao Liu, Linfeng Xu, Lanming Chen and Lu Xie
Biomolecules 2023, 13(4), 671; https://doi.org/10.3390/biom13040671 - 12 Apr 2023
Cited by 1 | Viewed by 2539
Abstract
Lung cancer is a highly heterogeneous disease. Cancer cells and other cells within the tumor microenvironment interact to determine disease progression, as well as response to or escape from treatment. Understanding the regulatory relationship between cancer cells and their tumor microenvironment in lung [...] Read more.
Lung cancer is a highly heterogeneous disease. Cancer cells and other cells within the tumor microenvironment interact to determine disease progression, as well as response to or escape from treatment. Understanding the regulatory relationship between cancer cells and their tumor microenvironment in lung adenocarcinoma is of great significance for exploring the heterogeneity of the tumor microenvironment and its role in the genesis and development of lung adenocarcinoma. This work uses public single-cell transcriptome data (distant normal, nLung; early LUAD, tLung; advanced LUAD, tL/B), to draft a cell map of lung adenocarcinoma from onset to progression, and provide a cell-cell communication view of lung adenocarcinoma in the different disease stages. Based on the analysis of cell populations, it was found that the proportion of macrophages was significantly reduced in the development of lung adenocarcinoma, and patients with lower proportions of macrophages exhibited poor prognosis. We therefore constructed a process to screen an intercellular gene regulatory network that reduces any error generated by single cell communication analysis and increases the credibility of selected cell communication signals. Based on the key regulatory signals in the macrophage-tumor cell regulatory network, we performed a pseudotime analysis of the macrophages and found that signal molecules (TIMP1, VEGFA, SPP1) are highly expressed in immunosuppression-associated macrophages. These molecules were also validated using an independent dataset and were significantly associated with poor prognosis. Our study provides an effective method for screening the key regulatory signals in the tumor microenvironment and the selected signal molecules may serve as a reference to guide the development of diagnostic biomarkers for risk stratification and therapeutic targets for lung adenocarcinoma. Full article
(This article belongs to the Special Issue Single Cell RNA Sequencing in Immunology)
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25 pages, 6119 KiB  
Article
Accumulation of Fat Not Responsible for Femoral Head Necrosis, Revealed by Single-Cell RNA Sequencing: A Preliminary Study
by Yingjie Wang, Dandan Li, Haijia Chen, Zhuolin Li, Bin Feng and Xisheng Weng
Biomolecules 2023, 13(1), 171; https://doi.org/10.3390/biom13010171 - 13 Jan 2023
Cited by 2 | Viewed by 2214
Abstract
The etiology of osteonecrosis of the femoral head (ONFH) is not yet fully understood. However, ONFH is a common disease with high morbidity, and approximately one-third of cases are caused by glucocorticoids. We performed single-cell RNA sequencing of bone marrow to explore the [...] Read more.
The etiology of osteonecrosis of the femoral head (ONFH) is not yet fully understood. However, ONFH is a common disease with high morbidity, and approximately one-third of cases are caused by glucocorticoids. We performed single-cell RNA sequencing of bone marrow to explore the effect of glucocorticoid on ONFH. Bone marrow samples of the proximal femur were extracted from four participants during total hip arthroplasty, including two participants diagnosed with ONFH for systemic lupus erythematosus (SLE) treated with glucocorticoids (the case group) and two participants with femoral neck fracture (the control group). Unbiased transcriptome-wide single-cell RNA sequencing analysis and computational analyses were performed. Seventeen molecularly defined cell types were identified in the studied samples, including significantly dysregulated neutrophils and B cells in the case group. Additionally, fatty acid synthesis and aerobic oxidation were repressed, while fatty acid beta-oxidation was enhanced. Our results also preliminarily clarified the roles of the inflammatory response, substance metabolism, vascular injury, angiogenesis, cell proliferation, apoptosis, and dysregulated coagulation and fibrinolysis in glucocorticoid-induced ONFH. Notably, we list the pathways that were markedly altered in glucocorticoid-induced ONFH with SLE compared with femoral head fracture, as well as their common genes, which are potential early therapeutic targets. Our results provide new insights into the mechanism of glucocorticoid-induced ONFH and present potential clues for effective and functional manipulation of human glucocorticoid-induced ONFH, which could improve patient outcomes. Full article
(This article belongs to the Special Issue Single Cell RNA Sequencing in Immunology)
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Review

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17 pages, 855 KiB  
Review
The Application of Single-Cell RNA Sequencing in the Inflammatory Tumor Microenvironment
by Jiayi Zhao, Yiwei Shi and Guangwen Cao
Biomolecules 2023, 13(2), 344; https://doi.org/10.3390/biom13020344 - 10 Feb 2023
Cited by 6 | Viewed by 2822
Abstract
The initiation and progression of tumors are complex. The cancer evolution-development hypothesis holds that the dysregulation of immune balance is caused by the synergistic effect of immune genetic factors and environmental factors that stimulate and maintain non-resolving inflammation. Throughout the cancer development process, [...] Read more.
The initiation and progression of tumors are complex. The cancer evolution-development hypothesis holds that the dysregulation of immune balance is caused by the synergistic effect of immune genetic factors and environmental factors that stimulate and maintain non-resolving inflammation. Throughout the cancer development process, this inflammation creates a microenvironment for the evolution and development of cancer. Research on the inflammatory tumor microenvironment (TME) explains the initiation and progression of cancer and guides anti-cancer immunotherapy. Single-cell RNA sequencing (scRNA-seq) can detect the transcription levels of cells at the single-cell resolution level, reveal the heterogeneity and evolutionary trajectory of infiltrated immune cells and cancer cells, and provide insight into the composition and function of each cell group in the inflammatory TME. This paper summarizes the application of scRNA-seq in inflammatory TME. Full article
(This article belongs to the Special Issue Single Cell RNA Sequencing in Immunology)
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