Biology subjects

Escudero Morlanes, J.

Publications and source records attributed to Escudero Morlanes, J..

3 recordsLinked to original sources

bioRxiv2026

Highly resolved tumor architecture via matched spatial and nucleus transcriptomics from a single tissue section

Spatial transcriptomics often relies on reference-based deconvolution to infer cell types in a tissue context; however, public single-cell datasets can miss patient-specific biology. Here we introduce SIMPlex, a method that generates matched spatial and single-nucleus gene-expression profiles from the same 5 um FFPE section. We demonstrate context-matched profiles across mouse brain, breast cancer and prostate cancer tissues, resolving fine-grained cell-states with distinct spatial signatures. By extracting both spatial and nuclear layers, SIMPlex maximises the information recovered from a single tissue section, an advantage for scarce archival and clinical specimens.

molecular biology↗

bioRxiv2026

Spatial mapping of pediatric brain tumors across diagnoses and relapses

We present a spatial transcriptomic atlas of 19 pediatric brain tumor patients spanning nine major and rare diagnoses, including seven relapses, revealing their spatial cellular and molecular organization. Each tumor section resolves into 2 - 4 recurrent spatial archetypes across 11 biological themes, with some mirroring developmental lineage patterns - for example, oligodendrocyte-lineage programs in pilocytic astrocytomas. Spatially inferred copy-number analysis identifies relapse-associated putative clones. In one rare embryonal tumor, spatial niches in the primary tumor harboring putative clones colocalized with an archetype enriched for nervous system development and glioblast-lineage programs. In one ependymoma and one pilocytic astrocytoma, relapse-associated putative clones preferentially localized to the vasculature, suggesting regrowth during relapse may be seeded by clonal selection of residual tumor cells within specialized microenvironmental niches. This resource provides an open-access spatially resolved map via an interactive viewer to inform research on pediatric brain tumor ecosystems, relapse biology, and therapeutic strategies.

cancer biology↗

bioRxiv2026

Immune repertoire profiling reveals extensive clonal expansion of T and B cells in CXCL9-rich niches in sinonasal cancer

Sinonasal cancer (SNC) is a rare and aggressive head and neck cancer with limited therapeutic options and an incompletely defined immune microenvironment. Although histopathology remains central to clinical tumor evaluation, immune profiling typically requires tissue dissociation and therefore loses the spatial relationships that shape antitumor immunity. Here, we combined single-cell RNA-sequencing approaches, spatial transcriptomics and Spatial V(D)J, a technique we recently pioneered, to analyse the cellular, spatial, and clonal architecture of SNC. We found that SNC tumors were marked by a robust T cell infiltration, including substantial proportions of classical tissue resident memory (TRM) and exhausted (TExh) CD8+ T cells. This inflamed phenotype was accompanied by an immense infiltration of suppressive regulatory T (Treg) cells, which differentiated towards a Tbet+CXCR3+ phenotype. Spatially, expanded Treg, CD8 T and B cell clones concentrated within specialized peritumoral immune niches enriched for cancer-associated fibroblasts, CXCL9 tumor-associated macrophages and LAMP3IDO1 dendritic cells. T cell clones occupying these niches were clonally related to those infiltrating epithelial tumor regions, linking lymphoid hubs to the broader tumor immune response. Together, these data identify SNC as an inflamed but highly immunoregulatory tumor type and reveal a spatially organized clonal architecture in which suppressive and cytotoxic lymphocyte states coexist within CXCL9 myeloid niches.

immunology↗