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In this study, single-cell RNA sequencing (scRNA-seq) was used to analyze the cellular heterogeneity of a subset of metastatic BM samples collected at initial diagnosis. Comparison of the single-cell data with bulk RNA sequencing further refined the analysis. An enrichment of regulatory T cells relative to a healthy control and activation of the CD24, CD47, and CD200 \u201cdon\u2019t eat me\u201d signals were documented. Computational analyses highlighted communication between neuroblastoma and myeloid cells via the amyloid precursor protein (APP) and midkine (MK) signaling networks. Within neuroblastoma cells, mutually exclusive adrenergic and transitory cell states were identified, and ten sub-clusters were denoted. In addition, common and unique tumor cell antigens were investigated. CNTFR and CHRNA3, as high-ranking candidates, were validated, confirming their strong selectivity for neuroblastoma cells. Taken together, these findings support the existence of a significant tumor-dependent modulation of the BM ecosystem, which should be considered when introducing immunotherapy. Furthermore, they highlight the potential to investigate new antigens at the single-cell resolution.<\/jats:p>","DOI":"10.3390\/cells15131139","type":"journal-article","created":{"date-parts":[[2026,6,23]],"date-time":"2026-06-23T17:11:49Z","timestamp":1782234709000},"page":"1139","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Comparative Study of Single-Cell and Bulk RNA Sequencing Data from Metastatic Bone Marrow Neuroblastoma Samples"],"prefix":"10.3390","volume":"15","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-3886-4360","authenticated-orcid":false,"given":"Sanja","family":"Aveic","sequence":"first","affiliation":[{"name":"Pediatric Hematology, Oncology and Hematopoietic Cell & Gene Therapy Research Area, Pediatric Research Institute, Citt\u00e0 della Speranza Foundation ETS, 35127 Padua, 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