Editorial: Spatial Transcriptome and Single-Cell Sequencing for Exploring Molecular Mechanisms of Neuroimmunity and Discovering Novel Markers of Neurological Diseases

Bowen Wang ¹ Yachen Shi ² Chao Cheng ² Jian Song ³ Yuanbo Pan ^4*

• ¹ The First Affiliated Hospital of Bengbu Medical College, Handan, Anhui Province, China
• ² Wuxi People’s Hospital Affiliated to Nanjing Medical University, Wuxi, Jiangsu Province, China
• ³ University of Münster, Münster, North Rhine-Westphalia, Germany
• ⁴ Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China

and functional characteristics of the brain but also provides a foundation for advancing precision treatment strategies [1,2]. Neuroimmunity offers a novel perspective to dissect the pathogenesis of various neurological diseases. However, central nervous system (CNS) disease diagnosis and treatment remain elusive due to intricate pathological mechanisms and limited effective therapeutic options [3]. Despite these challenges, traditional research methodologies primarily concentrate on histological, physiological, and population-level analyses. Unfortunately, these approaches are insufficient to explore the transcriptomic characteristics and the associated pathological and immune mechanisms at the single-cell level. This limitation significantly hinders our understanding of the complex regulatory networks that govern neuroimmune interactions.In recent years, breakthroughs in methodologies such as single-cell sequencing and spatial transcriptomics have revolutionized neuroimmunity research [4,5]. Single-cell sequencing facilitates the high-resolution analysis of gene expression profiles at the individual cell level, enabling the identification of distinct cell subsets and their heterogeneity [6,7]. Furthermore, spatial transcriptomics maintains the spatial integrity of samples while deepening our understanding of molecular mechanisms [8].These advanced techniques not only elucidate the complex regulatory networks within the neuroimmune system but also provide important tools for the discovery of novel molecular markers and the development of innovative therapeutic strategies [9]. With the rapid advancement of sequencing technology, apart from single-cell sequencing, there are multiple sequencing techniques (such as RNA sequencing, single-molecule real-time sequencing, nanopore sequencing, etc.). A significant number of researchers, leveraging comprehensive transcriptome analysis in conjunction with advanced sequencing technologies, are not only able to identify specific biomarkers for the accurate diagnosis and prognosis of diseases but also systematically assess treatment efficacy and predict patient clinical outcomes [10][11][12]. However, spatial transcriptomics and single-cell sequencing technologies face challenges such as huge and complex data volume, imperfect multimodal algorithms, and high cost [13]. Looking ahead, fostering innovation to address technical challenges, integrating and optimizing diverse technologies to characterize alterations in the neuroimmune microenvironment, and translating these insights into clinical strategies remain core research priorities. Such advancements could redefine disease classification and offer innovative theranostic approaches for complex neurological diseases.The studies discussed in this editorial underscore recent breakthroughs in the field of neuroimmunology and their implications for advancing our understanding of complex neurological diseases. Through the application of state-of-the-art methodologies, such as single-cell sequencing and spatial transcriptomics, researchers have not only uncovered the intricate interplay between the nervous system and the immune system but also shed novel light on the mechanisms underlying nervous system disorders.These studies elucidate critical disease-related molecules and their functional roles in pathological processes by integrating single-cell sequencing with complementary omics datasets. These studies highlight the unique advantages of single-cell technologies in analyzing disease heterogeneity and tracking dynamic changes in the immune microenvironment, thereby paving the way for precision medicine. Furthermore, this editorial emphasizes the importance of fostering interdisciplinary approaches within neuroimmunology. Collectively, these studies represent key advances in addressing major challenges in neurological research and improving clinical outcomes.