Emma Muiños Lopeź, Ana López-Pérez, Laura Sudupe, Amaia Vilas‐Zornoza, Sarai Sarvide, Purificación Ripalda‐Cemboráin, Paula Aguirre‐Ruiz, Patxi San Martín‐Úriz, Marta Larráyoz, Laura Álvarez-Gigli, Marta Abengózar, Itziar Cenzano, Miguel Cócera, Javier Ruiz, Ignacio Sancho, Azari Bantan, Aleksandra Kurowska, Jin Ye, Phillip T. Newton, Bruno Paiva, Luis Esteban Tamariz-Amador, Juan R. Rodríguez-Madoz, Vincenzo Lagani, Jesper Tegnér, Borja Sáez, José A. Martinez‐Climent, Isabel A. Calvo, David Gómez-Cabrero, Felipe Prósper
The bone marrow (BM) is a complex and compartmentalized tissue where spatial context plays a critical role in regulating cell behavior, signaling, and disease progression. To capture these dynamics, we apply spatial transcriptomics using the Visium Spatial Gene Expression platform on formalin-fixed paraffin-embedded (FFPE) BM sections from both healthy and Multiple Myeloma (MM) mouse models, as well as MM patient samples. Overcoming the technical challenges of working with mineralized long bone tissue, we develop a custom analytical framework integrating spatial and single-cell transcriptomic data to map cellular composition and interactions in situ. This approach enables the spatial characterization of transcriptionally heterogeneous malignant plasma cells (MM-PC) and their surrounding microenvironments. We identify spatially distinct gene programs linked to MM pathogenesis, including signatures of NETosis and IL-17 signalling, which are reduced in MM-PC-rich regions. Additionally, a transition gradient from effector to exhausted T cell phenotype is associated with increased remoteness from MM-PC. These spatial patterns are identified in FFPE BM biopsies from MM patients with varying tumor burdens. In summary, our study demonstrates both the capabilities and limitations of Visium technology in characterizing spatially regulated mechanisms underlying MM pathogenesis.