🧫 Cancer Research & Tumor Microenvironment
Spatiotemporal multiomics uncover tumor ecosystem dynamics during metastatic colonization.
Using integrated single-cell and spatial multiomics in liver cancer mouse models and human metastases, this study tracks disseminated tumor cells from initial seeding through overt lung metastasis. The authors uncover dynamic interactions between quiescent residual tumor cells and the evolving microenvironment that shape metastatic outgrowth.
Impact: Provides a spatiotemporal roadmap of metastatic ecosystem dynamics to inform targeted intervention of early disseminated tumor cells.
Sun Y et al., https://doi.org/10.1126/science.adz7928
Paired mutation calling and spatial transcriptomics identify cellular neighborhoods associated with the neoplastic outcome of mouse colitis.
Combining in vivo lineage tracing, mutational profiling, in silico modeling, and spatial transcriptomics in a mouse model of colitis, this work links specific epithelial- and immune-enriched cellular neighborhoods to distinct clonal fates. The study proposes that reparative tissue environments preferentially foster expansion of pro-oncogenic clones, tipping chronic inflammation toward cancer.
Impact: Reveals how spatially defined tissue niches bias clonal evolution from inflammatory lesions toward neoplasia in colitis-associated cancer.
Moutin EB et al., https://doi.org/10.1038/s41588-026-02673-0
🧠 Neurobiology & Vascular Biology
Spatial atlas of the human brain vasculature reveals specialized cell ensembles.
By profiling over 314,000 cerebrovascular transcriptomes and mapping 1.5 million cells with spatial transcriptomics, this study builds a comprehensive atlas of the human temporal cortex and hippocampal vasculature. The authors identify stereotyped “vascular cell ensembles” of endothelial, mural, fibroblast, and macrophage subsets that align along the arteriovenous axis and show distinct genetic disease susceptibilities and drug response profiles.
Impact: Delivers a high-resolution spatial blueprint of human brain vasculature that links vascular micro-communities to neurological disease risk and therapeutic targets.
Wang JC et al., https://doi.org/10.1016/j.cell.2026.07.007
🧬 Developmental Biology & Organogenesis
Single-cell spatial mapping of human kidney development implicates the microenvironment in guiding cell fate decisions.
Analyzing over 700,000 cells with single-cell RNA-seq and spatial transcriptomics, this work reconstructs the spatial organization and differentiation trajectories of the developing human kidney. The study uncovers unexpected plasticity in early patterning, shows that cell fate can be re-specified later, and links localized ligand signals and extracellular niches to fate decisions across the tissue.
Impact: Provides a spatially resolved blueprint of human kidney development that connects microenvironmental cues to dynamic cell fate choices.
Levinsohn J et al., https://doi.org/10.1038/s41588-026-02665-0
Decoding Cardiac Development and Maturation at Single-Cell and Spatial Transcriptomic Resolution.
This review synthesizes recent single-cell and spatial transcriptomic studies that dissect cardiac development from early organogenesis through postnatal maturation. It highlights how spatially resolved atlases clarify lineage trajectories, progenitor localization, and maturation programs, while outlining remaining challenges and opportunities for integrative multi-omics.
Impact: Frames how spatial and single-cell transcriptomics are reshaping our molecular understanding of cardiogenesis and guiding future regenerative strategies.
Li B et al., https://doi.org/10.1161/CIRCRESAHA.125.327473
❤️ Cardiovascular Disease & Regeneration
Macrophage adenylyl cyclase 7 protects against myocardial ischemia/reperfusion injury in male mice.
Using spatial transcriptomics, flow cytometry, and functional mouse models, this study identifies adenylyl cyclase 7 (ADCY7) as a macrophage-specific regulator that limits inflammation during myocardial ischemia/reperfusion injury. Loss of Adcy7 aggravates cardiac damage and inflammatory cell infiltration, while genetic and photoactivated enhancement of ADCY7–cAMP–PKA signaling suppresses NF-κB activity and protects heart tissue.
Impact: Positions macrophage ADCY7 as a spatially and functionally defined anti-inflammatory target for mitigating ischemia/reperfusion injury.
Xia G et al., https://doi.org/10.1038/s41467-026-74706-5
🧵 Regeneration & Liver Biology
TGF-β serves as a critical signaling determinant of liver progenitor cell activation and function.
Integrating spatial transcriptomics and single-cell sequencing in human and zebrafish models of acute liver failure, the authors map how liver progenitor cells (LPCs) receive TGF-β, HGF, and EGF cues from surrounding stellate cells and macrophages. They show that TGF-β restrains LPC proliferation yet is required, together with HGF, to drive hepatocyte gene programs, revealing a context-dependent dual role in maintaining quiescence and promoting functional maturation.
Impact: Clarifies how spatially organized TGF-β and growth factor signaling orchestrate liver progenitor cell dynamics during massive hepatic injury.
Tong C et al., https://doi.org/10.1172/JCI199913
🧪 Technology & Methods Development
NicheDeSig: Niche-aware Deconvolution and Adaptive Signature Analysis for Spatial Transcriptomics.
NicheDeSig introduces a deconvolution framework that explicitly models spatial niches when inferring cell-type compositions from spot-based spatial transcriptomics data. By allowing niche-dependent shifts in cell-type signatures, it moves beyond proportion estimates to enable functional analysis of molecular programs associated with distinct microenvironments.
Impact: Provides a niche-aware deconvolution tool that enhances the biological interpretability of spot-based spatial transcriptomics data.
Xue W et al., https://doi.org/10.1093/bioinformatics/btag578
Inference of secreted protein signaling activities in intercellular communication.
SecAct is a computational framework that infers activities of 1,170 human secreted proteins from spatial, single-cell, and bulk transcriptomics, trained on 1,258 spatial samples across 37 cancer types. Validated by perturbation datasets and in vivo experiments, it offers interactive modules to map secreted protein–mediated cell–cell communication and identifies novel regulators of tumor immunity such as LY86.
Impact: Delivers a scalable, spatially informed platform to decode secreted protein signaling and therapeutic targets from transcriptomic data.
Ru B et al., https://doi.org/10.1038/s41592-026-03172-0
🌿 Plant Spatial Omics
Decoding plants cell by cell: opportunities and challenges in single-cell and spatial biology.
This review outlines how single-cell and spatial omics are transforming plant biology by revealing cellular heterogeneity, transient states, and new developmental and stress-response programs. It also details key technical and computational bottlenecks, emphasizing integrative multi-omics, gene regulatory network inference, and thoughtful experimental design to move from descriptive maps to mechanistic insight and crop improvement.
Impact: Serves as a roadmap for harnessing spatial and single-cell omics to answer fundamental and applied questions in plant biology.
De Veylder L et al., https://doi.org/10.1093/plcell/koag223