{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,2]],"date-time":"2026-10-02T04:55:55Z","timestamp":1790916955854,"version":"4.1.0"},"reference-count":23,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2026,10,2]],"date-time":"2026-10-02T00:00:00Z","timestamp":1790899200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Genet."],"abstract":"<jats:sec>\n                    <jats:title>Background<\/jats:title>\n                    <jats:p>High-risk neuroblastoma frequently relapses after intensive therapy, but the treatment-associated malignant-neuroblast programs that inform baseline tumor risk remain incompletely defined. We used longitudinal single-cell\/single-nucleus RNA-seq data to identify post-treatment transcriptional changes in malignant neuroblasts and evaluated their prognostic relevance in diagnostic bulk RNA-seq cohorts.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>We analyzed a longitudinal single-cell\/single-nucleus RNA-seq atlas of diagnostic (DX) and post-treatment (PTX) neuroblastoma samples. Neuroblast cells were aggregated into donor- and treatment-state-level pseudo-bulk profiles, and paired differential expression analysis was performed to identify PTX-regulated malignant-neuroblast programs. PTX-down and PTX-up gene sets were functionally characterized by Hallmark over-representation analysis and Hallmark pathway activities were further estimated by GSVA in bulk cohorts. We then projected the PTX-down program onto diagnostic bulk RNA-seq cohorts by calculating a PTX-down proliferation score as the mean cohort-wise z-score of PTX-down genes. Prognostic value was evaluated in a primary diagnostic bulk RNA-seq validation cohort and three independent external diagnostic bulk RNA-seq cohorts. Clinical model increment, cross-cohort meta-analysis, clinical feature association, and Hallmark correlation analyses were performed.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>Paired pseudo-bulk analysis showed that PTX malignant-neuroblast profiles had reduced activity of a proliferative-replication program enriched for E2F targets, G2\/M checkpoint, MYC targets, DNA repair, and mitotic spindle pathways, together with relative enrichment of adaptive-state features related to hypoxia, inflammatory signaling, apoptosis, and epithelial-mesenchymal transition. In the primary validation cohort, high PTX-down proliferation score was associated with inferior OS and EFS and remained prognostic after adjustment for age, COG-defined high-risk classification, MYCN status, and INSS stage. Adding the PTX-down score improved C-index and 1-, 3-, and 5-year time-dependent AUC beyond both COG and clinical models. Across four bulk RNA-seq cohorts, higher PTX-down score was consistently associated with adverse OS (random-effects pooled HR = 1.83, 95% CI 1.20\u20132.80; P = 0.005). The score was also higher in tumors with MYCN amplification, stage 4 disease, and age \u2265 18\u00a0months. Core-gene and Hallmark correlation analyses defined the PTX-down score as an E2F\/G2M\/MYC-driven proliferative axis.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusion<\/jats:title>\n                    <jats:p>Longitudinal single-cell analysis identifies a chemotherapy-suppressed proliferative program in malignant neuroblasts. Projection of this program onto diagnostic bulk tumors captures high-risk biology, improves prognostic discrimination, and predicts adverse outcome in neuroblastoma.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.3389\/fgene.2026.1878093","type":"journal-article","created":{"date-parts":[[2026,10,2]],"date-time":"2026-10-02T04:35:38Z","timestamp":1790915738000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["Longitudinal single-cell analysis identifies a chemotherapy-suppressed proliferative program associated with adverse prognosis in neuroblastoma"],"prefix":"10.3389","volume":"17","author":[{"given":"Aiguo","family":"Zhu","sequence":"first","affiliation":[{"name":"Tianjin Cancer Hospital Airport Hospital, National Clinical Research Center for Cancer","place":["Tianjin, China"]},{"name":"Key Laboratory of Cancer Prevention and Therapy, Tianjin\u2019s Clinical Research Center for Cancer, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital","place":["Tianjin, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jian","family":"Wang","sequence":"additional","affiliation":[{"name":"Tianjin Cancer Hospital Airport Hospital, National Clinical Research Center for Cancer","place":["Tianjin, China"]},{"name":"Key Laboratory of Cancer Prevention and Therapy, Tianjin\u2019s Clinical Research Center for Cancer, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital","place":["Tianjin, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2026,10,2]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"5343","DOI":"10.1038\/s41598-025-88608-x","article-title":"Prognosis and immune infiltration prediction in neuroblastoma based on neutrophil extracellular traps-related gene signature","volume":"15","author":"Aierken","year":"2025","journal-title":"Sci. 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