International Journal of Molecular Medical Science, 2024, Vol.14, No.1, 29-41 http://medscipublisher.com/index.php/ijmms 35 Butler et al. (2018) believe that in addition to single-cell RNA sequencing technology, single-cell ATAC sequencing also plays an important role in the process of pathogen infection. This technique is able to reveal changes in the chromatin state of immune cells, thus providing important clues to understand the molecular mechanisms of immune memory. Immune memory refers to the ability of the immune system to respond quickly and effectively to another infection after it has experienced one. Through single-cell ATAC sequencing, researchers were able to gain insight into the regulatory mechanisms of gene expression in immune cells during infection, providing theoretical support for the development of novel vaccines and treatments. Kolodziejczyk et al. (2015) believe that single-cell omics technology still faces some challenges in practical application. For example, the sample acquisition and processing process may have an impact on the activity of immune cells, thus affecting the accuracy of the results. In addition, the analysis and interpretation of monocytomic data requires a high level of specialized knowledge and skills. However, with the continuous advancement of technology and optimization of methods, these problems are expected to be solved. 3.2 Immune cell heterogeneity in autoimmune diseases Autoimmune diseases are a class of complex diseases caused by the immune system mistakenly recognizing and attacking its own tissues. In recent years, with the rapid development of monocytomics technology, people have a deeper understanding of the heterogeneity of immune cells in autoimmune diseases. This heterogeneity is not only reflected in the diversity of cell types, functions and expression profiles, but also in the dynamic changes in disease development and the differences in treatment response. Wimmers et al. (2021) mentioned in their study that monocytomic technology reveals the extremely high heterogeneity of immune cells in patients with autoimmune diseases through high-resolution analysis of gene expression profiles, proteomics, metabolomics and other information of individual immune cells. This heterogeneity is manifested not only between different cell types, such as T cells, B cells, macrophages, etc., but also between different subpopulations within the same cell type. These subgroups play different roles in the onset, development and outcome of the disease, some may promote inflammatory responses, while others may suppress immune responses or participate in tissue repair. Taking systemic lupus erythematosus (SLE) and rheumatoid arthritis (RA) as examples, Gomes et al. (2019) found through single-cell RNA sequencing and TCR/BCR sequencing analysis that specific T cell and B cell subpopulations are present in these diseases, and these subpopulations show characteristic activity patterns in the pathological process of the disease. For example, certain T cell subpopulations may be overactivated and secrete large amounts of inflammatory factors, leading to tissue damage; Other T cell subpopulations may play a regulatory role in suppressing excessive immune responses. Similarly, specific subpopulations of B cells may produce antibodies against their own antigens and participate in disease progression; Other subpopulations of B cells may produce protective antibodies that help the body fight off disease. 3.3 Composition and function of immune cells in tumor microenvironment The tumor microenvironment is an extremely complex and dynamic ecosystem that includes tumor cells, immune cells, stromal cells, and a variety of growth factors and signaling molecules. In this ecosystem, immune cells play a crucial role, not only interacting with tumor cells, but also influencing tumor growth, invasion, and metastasis. With the rapid development of single-cell omics techniques, researchers are able to reveal the composition and function of immune cells in the tumor microenvironment with unprecedented resolution (Figure 2). Chen et al. (2015) mentioned in their study that with the advent of single-cell RNA sequencing technology, transcriptome analysis of a single cell can be performed to identify multiple immune cell subsets in the tumor microenvironment. These subpopulations include tumor-specific T cells, regulatory T cells, and tumor-associated macrophages, which play an important role in tumor immune response. For example, tumor-specific T cells are able to recognize and kill tumor cells, while regulatory T cells may suppress anti-tumor immune responses and promote tumor growth. In addition, tumor-associated macrophages also play an important role in the tumor microenvironment, which can influence tumor growth and invasion by secreting a variety of growth factors and signaling molecules.
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