Significance of stereologically spatiotemporal cells in molecular medicine

Abstract

Spatiotemporal distributions of intracellular elements (e.g., small molecules, proteins and organelles) dynamically altered in response to extracellular stimuli and pathogens, regulating those element movements, remodelling, and functions independently of mere changes in element abundance. To distinguish from conventional one- or two-dimensional spatialization, we define the precise three-dimensional localisation and interactions of intra- and extracellular elements at the single cell level as the "stereologically spatiotemporal cell" (SST-cell). For example, the three-dimensional construction of chromosomes ensures their proper formation and spatial positioning, facilitates the recruitment of regulatory factors, and underlies the mechanisms by which these factors maintain chromatin architecture. A large number of intracellular organelles and sub-organelles, along with their intercommunications, decide cellular biological types, subtype specification and type-specific functions. With the development of Stereo-Cell and Stereo-seq, the measurement of spatial SST-cell omics probably enables the detailed dissection of spatial heterogeneity among different cell subtypes and states, as well as their intercellular communications. Furthermore, the new approach of single SST-cell drug screening will be innovated for developing the new generation of clinical precision therapies.

Keywords: organelles; single‐cell; spatialization; stereology; temporalization.

FIGURE 1

Conceptual framework of the stereologically spatiotemporal cell (SST‐cell): decoding intracellular and extracellular spatial dynamics at single‐cell resolution. This graphical abstract illustrates the emerging concept of the stereologically spatiotemporal cell (SST‐cell), defined as a functional unit with precise three‐dimensional (3D) spatial localisation and dynamic interactions of intra‐ and extracellular components. The SST‐cell integrates subcellular organisation, molecular dynamics, and extracellular microenvironmental cues to explain cellular heterogeneity and functional diversity in complex tissues. Intracellular 3D spatial organisation: Depicted is a single cell with key organelle–organelle contact sites, including the ER–mitochondria (ER–mito), mitochondria–lysosome (mito–lyso), and ER–plasma membrane (ER–PM) interfaces. The membrane‐contact sites (MCSs) mediate spatial signalling and material exchange, governed by molecular tethers such as MFN1/2, VDAC1, IP3R, TRPML1, RAB7, STIM1, ORP5/8 and associated regulatory proteins (e.g. Grp75, TBC1D15 and FIS1). Organelle interactomes dynamically respond to physiological stimuli and pathological insults by spatial rearrangement and trans‐compartmental protein trafficking. The inset highlights 3D chromatin architecture, emphasising the importance of spatial genome organisation in regulating gene expression, epigenetic control, and cellular identity. The chromatin conformation modulates accessibility of regulatory elements, nuclear compartmentalisation, and genome stability, with implications for development and disease. Multidimensional dynamics of extracellular components: The spatial and functional diversity of cells in tissues is influenced by their 3D microenvironment, lineage history, and intercellular interactions. Technologies illustrated include: 1) 3D serial tissue sectioning combined with DNA nanoball arrays for high‐resolution spatial transcriptomics (e.g. Stereo‐seq) to resolve cellular positioning and gene expression at subcellular resolution. 2) seqFISH+ and Spateo for mapping gene expression and lineage trajectories during development and disease progression. 3) AI‐assisted spatial reconstruction to computationally integrate imaging and multi‐omics data for reconstructing cancer–immune cell interactions in the tumour microenvironment. Above tools reveal dynamic cell–cell communication, spatial heterogeneity, and the role of the microenvironment in shaping cell states and functions. Key technologies enabling SST‐cell characterisation, including single‐cell RNA sequencing (scRNA‐seq), Stereo‐seq, seqFISH+, Spateo, multi‐omics integration, and spatial imaging with artificial intelligence (AI)‐guided reconstruction. The SST‐cell framework highlights a paradigm shift in spatial cell biology, enabling detailed mechanistic insights into cell differentiation, organogenesis, cancer progression, and immune regulation. By integrating structural, functional, and molecular dimensions in space and time, SST‐cell analysis offers a transformative approach for understanding complex biological systems and advancing molecular medicine.