{"entity": "researcher", "timestamp": "2026-09-24T07:37:16.491Z", "family": "Martin-Uriz", "given": "Patxi San", "initials": "PS", "orcid": "0000-0003-1483-4279", "affiliations": ["Hematology and Oncology Program, Centre for Applied Medical Research (CIMA), Instituto de Investigaciones Sanitarias de Navarra (IdiSNA), Cancer Center Clinica Universidad de Navarra (CCUN), Pamplona, Navarra, Spain."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/7165cce0460347a297f30bd381a3b817.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/7165cce0460347a297f30bd381a3b817"}}, "publications": [{"entity": "publication", "iuid": "38aa2f4e10684b4bb46ba0e87f09501f", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/38aa2f4e10684b4bb46ba0e87f09501f.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/38aa2f4e10684b4bb46ba0e87f09501f"}}, "title": "Characterization of the bone marrow architecture of multiple myeloma using spatial transcriptomics.", "authors": [{"family": "Mui\u00f1os-Lopez", "given": "Emma", "initials": "E", "orcid": "0000-0002-6618-4135", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0cac709bdc9442adb241d448a15321eb.json"}}, {"family": "Lopez-Perez", "given": "Ana Rosa", "initials": "AR"}, {"family": "Sudupe", "given": "Laura", "initials": "L"}, {"family": "Vilas-Zornoza", "given": "Amaia", "initials": "A"}, {"family": "Sarvide", "given": "Sarai", "initials": "S"}, {"family": "Ripalda-Cemborain", "given": "Purificacion", "initials": "P"}, {"family": "Aguirre-Ruiz", "given": "Paula", "initials": "P"}, {"family": "Martin-Uriz", "given": "Patxi San", "initials": "PS", "orcid": "0000-0003-1483-4279", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7165cce0460347a297f30bd381a3b817.json"}}, {"family": "Larrayoz", "given": "Marta", "initials": "M"}, {"family": "Alvarez-Gigli", "given": "Laura", "initials": "L"}, {"family": "Abengozar-Muela", "given": "Marta", "initials": "M"}, {"family": "Cenzano", "given": "Itziar", "initials": "I", "orcid": "0000-0002-9030-3069", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7868914b004b46a1bd4f78e80f387ac5.json"}}, {"family": "C\u00f3cera", "given": "Miguel", "initials": "M"}, {"family": "Ruiz", "given": "Javier", "initials": "J"}, {"family": "Sancho", "given": "Ignacio", "initials": "I"}, {"family": "Bantan", "given": "Azari", "initials": "A"}, {"family": "Kurowska", "given": "Aleksandra", "initials": "A", "orcid": "0000-0001-5950-0358", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e484660a5ece401790874403619911da.json"}}, {"family": "Ye", "given": "Jin", "initials": "J"}, {"family": "Newton", "given": "Phillip T", "initials": "PT", "orcid": "0000-0003-2142-1798", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/07e490d4b3da4741b490395399f1b8c1.json"}}, {"family": "Paiva", "given": "Bruno", "initials": "B"}, {"family": "Tamariz-Amador", "given": "Luis Esteban", "initials": "LE"}, {"family": "Rodriguez-Madoz", "given": "Juan R", "initials": "JR", "orcid": "0000-0003-4327-1866", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/032e1bae16a541928dbf35e08694d686.json"}}, {"family": "Lagani", "given": "Vincenzo", "initials": "V", "orcid": "0000-0002-6552-6076", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a8832e0f50e14a23875a47949200ca6c.json"}}, {"family": "Tegner", "given": "Jesper", "initials": "J", "orcid": "0000-0002-9568-5588", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b115e5faf68a4acbb6f947c711fd37ec.json"}}, {"family": "Saez", "given": "Borja", "initials": "B"}, {"family": "Martinez-Climent", "given": "Jose Angel", "initials": "JA", "orcid": "0000-0002-7938-3950", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d43329ea769f4fcf83f8cad698d49d05.json"}}, {"family": "Calvo", "given": "Isabel A", "initials": "IA", "orcid": "0000-0001-6619-4571", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7fa7ce0de9074d21a92dc8667b3eb6b6.json"}}, {"family": "Gomez-Cabrero", "given": "David", "initials": "D", "orcid": "0000-0003-4186-3788", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a2f7905f6b864d3286b28b99dbb59627.json"}}, {"family": "Prosper", "given": "Felipe", "initials": "F", "orcid": "0000-0001-6115-8790", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b062035045714ecd9d6cbca6fc60d433.json"}}], "type": "journal article", "published": "2025-11-20", "journal": {"title": "Commun Biol", "issn": "2399-3642", "volume": "8", "issue": "1", "pages": "1620", "issn-l": "2399-3642"}, "abstract": "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.", "doi": "10.1038/s42003-025-08975-z", "pmid": "41266582", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC12634688"}, {"db": "pii", "key": "10.1038/s42003-025-08975-z"}], "notes": [], "created": "2026-09-23T11:37:31.313Z", "modified": "2026-09-23T11:37:31.808Z"}, {"entity": "publication", "iuid": "2b361fbf6fd044c690a9776877209b17", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/2b361fbf6fd044c690a9776877209b17.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/2b361fbf6fd044c690a9776877209b17"}}, "title": "Uncovering the regulatory landscape of early human B cell lymphopoiesis and its implications in the pathogenesis of B-ALL.", "authors": [{"family": "Planell", "given": "N\u00faria", "initials": "N", "orcid": "0000-0001-7550-2433", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/335676fe9a9642dcb03f2aaf0c197993.json"}}, {"family": "Mart\u00ednez-de-Morentin", "given": "Xabier", "initials": "X", "orcid": "0000-0002-8358-9214", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/47fc54e595dd4df480155bdde603a8f1.json"}}, {"family": "Mouzo", "given": "Daniel", "initials": "D", "orcid": "0000-0002-0383-5703", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/13ea821cd2fe49128b1f8c18ed9dc256.json"}}, {"family": "Lara-Astiaso", "given": "David", "initials": "D"}, {"family": "Vilas-Zornoza", "given": "Amaia", "initials": "A"}, {"family": "Mart\u00edn-Uriz", "given": "Patxi San", "initials": "PS", "orcid": "0000-0003-1483-4279", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7165cce0460347a297f30bd381a3b817.json"}}, {"family": "Alignani", "given": "Diego", "initials": "D", "orcid": "0000-0003-0241-1375", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/96cb2a393fe94e9a826c3fc70b7c8bb7.json"}}, {"family": "Paiva", "given": "Bruno", "initials": "B", "orcid": "0000-0003-1977-3815", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/364674822f714c8293de1db32a163beb.json"}}, {"family": "Maillo", "given": "Alberto", "initials": "A", "orcid": "0000-0002-3835-9794", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4054f386499043f0b9fd8ea4ce5a605e.json"}}, {"family": "Kurowska", "given": "Aleksandra", "initials": "A"}, {"family": "Berastegui", "given": "Nerea", "initials": "N", "orcid": "0000-0002-9868-0547", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ec90f71d18ea46cd8df66804debec1e5.json"}}, {"family": "Garcia-Olloqui", "given": "Paula", "initials": "P", "orcid": "0000-0002-7983-2875", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/01b6f2e2f65842cfa64e6329ad988bca.json"}}, {"family": "Urdangarin", "given": "Arantxa", "initials": "A"}, {"family": "Noori", "given": "Peri", "initials": "P"}, {"family": "Ortega-Legarreta", "given": "Asier", "initials": "A", "orcid": "0009-0000-3563-5362", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/10a1eb932f2e41c282ae472c9ede6465.json"}}, {"family": "Hernaez", "given": "Mikel", "initials": "M", "orcid": "0000-0003-0443-2305", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/13276f226ed042afb92bf1425b67334a.json"}}, {"family": "Lagani", "given": "Vincenzo", "initials": "V", "orcid": "0000-0002-6552-6076", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a8832e0f50e14a23875a47949200ca6c.json"}}, {"family": "Kiani", "given": "Narsis", "initials": "N", "orcid": "0000-0002-0949-046X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5375b71b93f643cc8dc3a5ac8d1a67c2.json"}}, {"family": "Merkenschlager", "given": "Matthias", "initials": "M", "orcid": "0000-0003-2889-3288", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6257840a1b0c4478a38ec31b070fb13c.json"}}, {"family": "Ezponda", "given": "Teresa", "initials": "T", "orcid": "0000-0003-3682-7125", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/967a5c1eb13a428db835ef8531a69b87.json"}}, {"family": "Mart\u00edn-Subero", "given": "Jos\u00e9 I", "initials": "JI", "orcid": "0000-0001-8809-5195", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d6b1944a98214848b864342473012567.json"}}, {"family": "Ram\u00edrez", "given": "Ricardo N", "initials": "RN", "orcid": "0000-0002-1259-5406", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/606cf67d57f441008ecb07b0e3e4705d.json"}}, {"family": "Tegner", "given": "Jesper", "initials": "J", "orcid": "0000-0002-9568-5588", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b115e5faf68a4acbb6f947c711fd37ec.json"}}, {"family": "Prosper", "given": "Felipe", "initials": "F", "orcid": "0000-0001-6115-8790", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b062035045714ecd9d6cbca6fc60d433.json"}}, {"family": "Gomez-Cabrero", "given": "David", "initials": "D", "orcid": "0000-0003-4186-3788", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a2f7905f6b864d3286b28b99dbb59627.json"}}], "type": "journal article", "published": "2025-10-10", "journal": {"title": "Sci Adv", "issn": "2375-2548", "volume": "11", "issue": "41", "pages": "eadw3110", "issn-l": "2375-2548"}, "abstract": "Dysregulation of early B cell lymphopoiesis-the process guiding cellular immunity development-can lead to malignancy, making it crucial to understand its regulatory mechanisms. We generated a multiomics resource comprising paired chromatin accessibility and gene expression profiles across eight human B cell precursor populations, providing a detailed characterization of early human B cell development. Integrative analysis revealed highly cell type-specific regulatory elements and enabled the reconstruction of the gene regulatory network governing differentiation. We identified putative candidate regulons, such as ELK3, enriched in pro-B cells and potentially involved in cell cycle progression. Regulons from bulk data were projected onto single-cell data, validating their activity and refining the regulatory landscape. This resource enabled identification of active regulatory programs and transformation-associated states in B cell acute lymphoblastic leukemia. The publicly available atlas provides a valuable resource for understanding B cell development and disease, supporting future efforts to decode regulatory programs in immunity and hematologic malignancies.", "doi": "10.1126/sciadv.adw3110", "pmid": "41071881", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC12513440"}], "notes": [], "created": "2026-09-23T13:19:20.910Z", "modified": "2026-09-23T13:19:21.411Z"}]}