Preface for Special Issue: Single-Cell and Spatially Resolved Omics

In this special issue,we are excited to present a collection of articles focusing on the emerging and rapidly evolving field of singlecell and spatially resolved omics,including epigenomics,transcriptomics, proteomics, and metabolomics. In recent years, the development of advanced, high-throughput technologies and computational methods has enabled researchers to study individual cells at an unprecedented resolution, shedding light on their heterogeneity and the complex interplay between their various molecular components. The detailed exploration of these aspects is crucial not only for a better understanding of the fundamental biology underlying cell function and organization but also for identifying novel therapeutic targets and strategies in various disease contexts.

First, we are pleased to feature two comprehensive Review papers discussing the state-of-the-art in single-cell and spatially resolved omics. O'Connor et al. offer an in-depth perspective on the recent progress in integrative multi-omics and systems bioinformatics in translational neuroscience, summarizing data mining studies with obtaining quantitative information at the single-cell level.Zhou and colleagues provided a comprehensive introduction to and summary of the fundamental principles and research methods used for metabolomics(SRM)and spatially resolved transcriptomics (SRT) techniques, as well as a review of their applications for the in-depth study of tumors.

In addition to both Review papers, we also showcase several Original research articles showcasing the exciting developments and applications of single-cell and spatially resolved omics. Given the cover paper, Zheng and colleagues presented a spatial transcriptomics atlas to explore how ablating microglia affects astrocytic scar formation after intracerebral hemorrhage. The vital insight gleaned from their data is that sustained microglial depletion may not be a reasonable treatment strategy for early-stage intracerebral hemorrhage (ICH). Inversely, early-stage insulin like growth factor 1 (IGF1)/osteopontin (OPN) treatment combined with late-stage PLX3397 treatment is a promising therapeutic strategy.This study prompts researchers to consider the complex temporal dynamics and overall net effect of microglia and astrocytes,opening up new avenues for understanding complex temporal dynamics and overall net effect of microglia and astrocytes.

Zhang et al. conducted a study in which they constructed a single-cell transcriptome map consisting of 59,127 cells from mouse testes treated with triptolide. The results revealed an increase in macrophages and an inflammatory response in the triptolide-treated mouse testes, indicating the critical role of inflammation in triptolide-induced testis injury.They also observed elevated reactive oxygen species (ROS) signaling and downregulation of spermatid development in somatic cells,particularly Leydig and Sertoli cells, in the triptolide-treated mice. These findings suggest that dysregulation of these signaling pathways may contribute to testicular toxicity induced by triptolide. Overall, the high-resolution single-cell landscape provided by this study offers comprehensive insights into the gene expression profiles associated with triptolide in major cell types of mouse testes.This information serves as a valuable resource for understanding triptolideassociated testicular injury, discovering additional mechanisms,and identifying potential therapeutic targets for triptolideinduced male reproductive toxicity.

Through their single-cell transcriptomic analysis,Du et al.made a significant discovery regarding the presence of a distinct population of epicardial cells within the embryonic mouse heart. These epicardial cells were found to express key marker genes associated with epicardial progenitor cells.Notably,this progenitor population exhibited remarkable cellular and temporal heterogeneity throughout heart development. Gene regulatory network analysis revealed that the behavior of epicardial cells was regulated by various regulons. In summary, this research identifies Upk3b,Efemp1, Msln, and C3 as further markers of mature epicardium and underscores the critical role of extracellular matrix signaling within the mature epicardium.These findings hold promise for potential therapeutic targets in the field of heart regeneration in future clinical endeavors.

Guo et al.have made a significant breakthrough by discerning 15 distinct cell subtypes within liver tissue,employing a mouse model.Upon further analysis,it was revealed that tripterygium glycosides tablet (TGT) elicits a pronounced inflammatory response in liver endothelial cells, with variations observed across different spatial locations. Additionally, hepatocytes experience notable inflammatory responses, apoptosis, and impairments in fatty acid metabolism. The activation of hepatic stellate cells was also observed.Furthermore,TGT leads to the activation,inflammation,and phagocytosis processes in liver capsular macrophages,while also induces immune dysfunction within liver lymphocytes.Notably,TGT dysregulates intercellular communication within the liver microenvironment by modulating various signaling pathways.In summary,these findings shed light on the intricate mechanisms underlying TGTinduced acute liver injury. They hold the potential to advance safe and rational clinical applications while contributed to the identification of new biomarkers and therapeutic targets for liver protection.

In a study conducted by Yu et al.,the dynamics and functions of various subpopulations of endothelial cells, dendritic cells (DCs),and natural killer(NK)cells were characterized with the aim of understanding autoprotection against drug-induced liver injury(DILI). Acetaminophen was used as a model drug, and single-cell RNA sequencing was employed.The study revealed that DC-3 cells not only promoted angiogenesis but also facilitated liver tissue repair in the group resistant to acetaminophen-induced liver injury.This effect was achieved through crosstalk with endothelial cells via vascular endothelial growth factor-associated ligand-receptor pairs. Furthermore, subsets of natural killer cells, namely NK-3 and NK-4, as well as the Sca-1-CD62L+natural killer T cell subset, appeared to promote autoprotection through interferonγ-dependent pathways. Additionally, certain macrophage and neutrophil subpopulations with anti-inflammatory phenotypes were found to contribute to the tolerance of acetaminophen hepatotoxicity. Overall, their study provides valuable insights into the dynamics of non-parenchymal cells (NPCs) involved in the resistance to acetaminophen-induced liver injury and sheds light on the mechanism underlying autoprotection against drug-induced liver injury at a high resolution.

In an innovative study, Li and colleagues engineered a holistic and ultrasensitive proteomic technology ideally suited for singlecell or low-input mouse embryos. As this technology becomes widely adopted, researchers are now able to select between avenues of deep coverage or high throughput,as per their specific requirements. Using the pathway of deep coverage, the team delivered a pioneering and large-scale snapshot capturing the very early phases of mouse maternal-to-zygotic transition. This encompassed nearly 5,500 protein groups accrued from 20 mouse oocytes or zygotes within each sample.Crucially,the exploration of substantial protein regulatory networks centered on transcription factors and kinases, pivoting between the MII oocyte and singlecell embryo, yielded copious insights pertinent to minor zygotic gene activation.

In summary,this special issue brings together a diverse array of cutting-edge research topics in the field of single-cell and spatially resolved omics, reflecting the tremendous advances and potential of these approaches for uncovering novel biological insights and informing the development of novel therapeutics. We would like to extend our appreciation to all the authors for their valuable contributions and hope that readers find this collection of articles as stimulating and inspiring as we do.