Malignant B-cell States Orchestrate Spatially Organized Immune Ecosystems in B-cell Lymphomas

Immune-metabolic-redox ecosystems define spatially organized tumor states in head and neck squamous cell carcinoma

Background Spatial organization is increasingly recognized as a key determinant of tumor-immune interactions in head and neck squamous cell carcinoma (HNSCC). The GSE300147 Xenium spatial transcriptomic resource generated by McCord and colleagues established a framework for mapping spatially coordinated T-cell states in HNSCC. However, how tumor-enriched epithelial immune states relate to metabolic, redox, and stress-adaptive transcript programs remains incompletely defined. Methods A secondary, data-driven reanalysis of GSE300147 was performed, focusing on 17 confirmed HNSCC Xenium sections after exclusion of a non-HNSCC ameloblastoma specimen. A total of 1,148,244 cells were analyzed, including 558,867 EpCAM+ tumor-enriched epithelial cells. Tumor-enriched epithelial cells were classified into Hot, Intermediate, and Cold states using a Composite Hotness framework integrating T-cell inflammatory signature score, checkpoint-associated signaling, CD274 expression, IFN/antigen-presentation signature score (IFN/AP), and tumor-immune proximity. Six metabolic ecosystem states, neighborhood profiling, spatial permutation testing, and an integrated Immune-Metabolic-Redox Ecosystem Score (IMRES) were then applied. Results Immune activation was spatially heterogeneous across HNSCC sections. Immune-hot tumor-enriched epithelial regions showed not only inflammatory, checkpoint-associated, and antigen-presentation signature scores, but also coordinated metabolic, oxidative-redox, and stress-response transcript programs. IMRES, derived from available immune, metabolic, redox, and stress-response transcript components represented in the Xenium panel, increased progressively from Cold to Intermediate to Hot tumor-enriched epithelial states and was associated with NFE2L2, GDF15, HLA-DRA, CD274, KEAP1, and MDM2. Integrating IMRES with Composite Hotness identified a distinct Hot+IMREShigh ecosystem comprising 106,874 tumor-enriched epithelial cells. This state showed the strongest immune-active and stress-adaptive features and was positioned closer to immune populations than expected by random assignment. An alternative rank-based robustness analysis reproduced the IMRES-associated ecosystem axis and correlated with the original module-based score (Spearman r = 0.597). Conclusions This secondary reanalysis extends the original spatial T-cell framework by defining a complementary tumor-centered immune-metabolic-redox ecosystem in HNSCC. IMRES provides a transcript-derived framework for identifying Hot+IMREShigh neighborhoods where immune activation, checkpoint signaling, metabolic remodeling, and stress adaptation converge, providing a hypothesis-generating framework for studying immune resistance and therapeutic vulnerability.

The spatial architecture of tumor immunity: Emerging predictive biomarkers across cancer

Formation and remodeling of immunological niches in solid tumors: organ-specific architectures, inflammatory parallels, and therapeutic reprogramming

Tumor immunity is increasingly understood not only through the cellular composition of the tumor microenvironment, but also through spatially organized local niches that can help determine where immune recognition is initiated, constrained, suppressed, or therapeutically restored. This review develops an organ-conditioned and evidence-graded framework for tumor immunological niches as spatially localized, interaction-dependent, functionally consequential, and dynamically remodeled units. Rather than reproducing a general taxonomy of cancer immune niches, we focus on how shared niche-forming mechanisms are implemented differently by organ-specific tissue rules. We first distinguish the niche concept from broad tumor microenvironment descriptions, immune infiltration, immune compartments, and tertiary lymphoid structures. We then propose an operational evidence hierarchy that separates spatial association, recurrent interaction, functional consequence, perturbation-based validation, and therapeutic actionability. Next, we synthesize core mechanisms of niche formation, including tumor-intrinsic signaling, stromal and extracellular-matrix scaffolding, chemokine and cytokine wiring, vascular-hypoxic-metabolic boundaries, myeloid-centered suppression, and tissue-resident immune imprinting. Brain and lung tumors are treated as two organizing paradigms: immune-restricted niche architecture in the central nervous system and inflammation-primed niche architecture in the lung. Oral, liver, and pancreatic tumors are discussed comparatively to show how mucosal-microbial, tolerogenic-metabolic, and desmoplastic immune-exclusion rules reshape shared niche mechanisms. We further separate tumor-specific evidence, inflammatory analogies, and hypothesis-generating parallels to avoid overextending chronic inflammation or fibrosis models. Finally, we examine how niche architecture produces T-cell exclusion, antigen-presentation failure, suppressive myeloid-stromal feedback, and therapeutic resistance, and how release, access, and licensing strategies may guide organ-tailored combinations when supported by adequate evidence. This review argues that tumor immunological niches may serve as meso-level analytical units linking spatial organization, organ context, evidence strength, inflammatory parallels, and therapeutic vulnerability when their evidentiary status is explicitly defined.

Disease-associated microglia adopt stage-specific phenotypes that regulate T cell fate and immunity in glioma.

Malignant gliomas are lethal brain tumors characterized by profound local immunosuppression and a radically remodeled myeloid landscape. Although these tumors mobilize resident microglia and infiltrating monocyte-derived macrophages, the mechanisms governing their phenotypic convergence and diversification remain elusive. Here, we integrated single-cell profiling and spatial transcriptomics of glioma-associated microglia in the GL261 model. We identified distinct microglial states that aligned with tumor architecture, most notably Cst7-expressing disease-associated microglia (DAMs) that aggregated at the tumor invasive margin and exhibited a conserved transcriptional signature shared across various central nervous system pathologies. Interferon-γ and toll-like receptor signaling sequentially tuned stage-specific DAM features, including transient MHC-II expression and sustained PD-L1 upregulation, thereby recalibrating the local immune equilibrium by reshaping bidirectional DAM-T cell interactions during glioma progression. Our findings highlight microglial state transitions as a stage-specific layer of immune regulation in glioma that shapes T cell fate and support targeting microglial plasticity to rebalance anti-tumor immunity.

Tumor-infiltrating B cells evolve towards interferon-rich trajectories aligned with immunotherapy in melanoma

B cells are increasingly recognized regulators of antitumor immunity in melanoma, yet their differentiation states, lineage dynamics, spatial organization and integration within the immune microenvironment, and how these are influenced with immunotherapy remain incompletely defined. We conducted deep profiling of tumor-resident B cell differentiation and evolutionary features in the melanoma tumor microenvironment using bulk, single-cell and spatial transcriptomic analyses, long-read antibody sequencing and mass cytometry (Cytometry by Time-Of-Flight, CyTOF). We characterized B cell differentiation trajectories, class-switching patterns, antibody isotype usage, signaling pathways, spatial niches against clinicopathological features and immune cell communication, before and after checkpoint blockade and in clinically defined responders and non-responders. Melanoma-infiltrating B cells were enriched across primary and metastatic lesions, were preferentially associated with immune-rich tumors and correlated with T and natural killer (NK) cell densities. Long-read immunoglobulin sequencing demonstrated recurrent class switch recombination (CSR) trajectories with predominant IgG and IgA isotype usage, confirmed by bulk transcriptomic analyses. Across independent single-cell and bulk transcriptomic datasets we identified conserved class-switching, B cell receptor (BCR) activation, and pseudotime analyses showed differentiation trajectories progressing from naïve and memory states toward interferon (IFN)-driven terminal differentiation trajectories that persisted before and after immunotherapy. CyTOF analyses independently confirmed proliferative, germinal center (GC)-like, memory and class-switched B cell subsets, suggesting conserved inflammatory differentiation endpoints. Spatial transcriptomic deconvolution identified IFN-rich B cells within tertiary lymphoid structures (TLS). Following immunotherapy, B cells retained class-switched trajectories, displayed enriched GC-associated profiles, enhanced crosstalk with T cells and Dendritic Cells (DCs) and preserved or induced IFN-rich IgM + /IgD + or IgG4 + phenotypes, suggesting persistence or emergence of non-class switched and atypical class-switched isotype profiles. Transcriptomic analyses of B cells pointed to upregulated antigen-driven stimulation and BCR signaling, whereas in non-responders displayed IFN-rich B cells, IFN-associated genes, and IFN-pathway enrichment. Melanoma-infiltrating B cells follow class-switched differentiation trajectories culminating in IFN signaling, atypical antibody expressing states that persist or emerge after immunotherapy, aligning dynamic B cell evolution and atypical lineage traits with immunotherapy.

Spatial remodeling of the thymic stroma with age disrupts niches for T cell selection and tolerance

Age-associated thymic involution is a major driver of immunosenescence, yet the cellular and spatial mechanisms coordinating age-related thymic remodeling remain incompletely understood. Combining single-cell transcriptomics, chromatin accessibility profiling, and spatial transcriptomics, we generated a spatially resolved multi-omic atlas of the aging mouse thymus. We show that thymic aging is not simply a process of epithelial loss, but a spatial reorganization of the stroma into new microenvironments, including age-associated epithelial states, a fibroblast-supported epithelial progenitor niche, and tertiary lymphoid structures. This remodeling displaces niches supporting positive and negative thymocyte selection and coincides with an intrinsic decline in cortical thymic epithelial cell function. Ligand-receptor mapping identifies medullary fibroblasts as a signaling hub sustaining epithelial progenitors and promoting tertiary lymphoid structure neogenesis, linking these hallmarks of thymic aging. Together, our findings reframe thymic involution as spatial stromal reorganization that links stromal remodeling to impaired thymopoiesis, central tolerance, and immune aging.