Spatial transcriptomics is a spatial omics technology that measures transcriptomic information while preserving tissue context, making it useful for mapping cell states and microenvironments rather than only averaged bulk signals. It is integrated into multimodal training frameworks such as cross scale multimodal framework and spahe infil, where it is combined with whole-slide images or bulk/single-cell data to improve model performance and interpretability. In cancer research, it is used to study the tumor immune microenvironment, including therapy-induced remodeling and spatially organized immune niches, and it has also been reviewed for gastric cancer applications. A notable finding is that spatial transcriptomics identified a ring of lipid-associated tumor associated macrophages lining the tumour edge, highlighting its ability to resolve microanatomical immune structures. Recent studies also applied spatial profiling to a dissectible ORTHO lung cancer model to confirm immune features and local niches, and to melanoma for clinically actionable immunotherapy biomarker discovery. Overall, the literature shows spatial transcriptomics as a high-resolution, tissue-resolved modality that strengthens multimodal frameworks for cancer immunology and translational biomarker discovery.
Multimodal framework integration
- cross scale multimodal framework integrates spatial transcriptomics with bulk and single-cell transcriptomics to support cross-scale biomarker discovery in melanoma. (PMID:41840725)
- spahe infil uses spatial transcriptomics together with whole-slide images to decode tumor microenvironment infiltration from H&E-stained slides. (PMID:41971992)
- Spatial transcriptomic data were explicitly included as an omics modality for model training in SpaHE-Infil. (PMID:41971992)
- The framework described in a 2026 Human Genomics study combined bulk, single-cell, and spatial transcriptomics to identify clinically actionable immunotherapy biomarkers. (PMID:41840725)
Cancer microenvironment and immunotherapy
- Spatial transcriptomics helps study therapy-induced remodeling of the tumor immune microenvironment, providing mechanistic insight into immunotherapy response. (PMID:41813658)
- It identified a ring of lipid-associated tumor associated macrophages at the tumour edge, demonstrating spatially resolved immune architecture. (PMID:41813658)
- In a 2026 Chinese Medical Journal review, spatial transcriptomics was cited alongside single-cell sequencing as a high-resolution approach for analyzing tumor immune remodeling. (PMID:41813658)
- Spatial profiling was used to confirm immune features and local niches in a dissectible ORTHO lung cancer model. (PMID:42026061)
Disease-area reviews and translational applications
- A 2026 Cells review on advances in spatial multi-omics highlighted spatial omics technologies for gastric cancer research. (PMID:41892326)
- Spatial transcriptomics was included among the technologies reviewed for gastric cancer applications, underscoring its translational relevance. (PMID:41892326)
- Multiomics immune profiling in a patient-relevant orthotopic lung cancer model used spatial profiling to validate tissue-localized immune features. (PMID:42026061)
- The SEPARATE-Seq study in Nature Communications emphasized spatial profiling as part of multiomics immune analysis in lung cancer. (PMID:42026061)