p53 knockout drives stage-specific long non-coding RNA reprogramming during human neural differentiation and glioma organoid tumorigenesis

Abstract

Background Long non-coding RNAs (lncRNAs) are emerging regulators of tumor initiation and progression through their effects on stemness, lineage commitment, and transcriptional plasticity. The contribution of lncRNA reprogramming during early p53-deficient gliomagenesis remains poorly understood. Methods Human induced pluripotent stem cells (iPSCs) carrying a complete TP53 knockout were differentiated into neural progenitor cells (NPCs) and cerebral organoids. Bulk RNA sequencing was performed at multiple differentiation stages and compared with established glioblastoma cell lines (U87 and U118) to identify lncRNA expression changes associated with p53 loss and tumor-like transformation. Results p53 deficiency induced a progressive and stage-specific remodeling of the lncRNA landscape, with the most pronounced transcriptional shift observed in 40-day NPCs. This late-stage profile partially overlapped with glioblastoma-like cell lines and was characterized by the upregulation of five lncRNAs enriched in both p53-deficient neural models and glioma cells. Principal component analysis showed that these lncRNAs clustered with tumor-associated samples and were strongly co-expressed with mitotic cell-cycle genes. In particular, LINC00973 and LINC01583 were highly expressed in primary glioblastoma datasets, while RP5-875H18.9 and RP11-1094H24.4 emerged as previously unrecognized glioma-associated transcripts. Conclusion Loss of p53 drives stage-dependent lncRNA reprogramming during neural differentiation and promotes the emergence of glioma-associated transcriptional features. These findings identify candidate lncRNAs that may contribute to early gliomagenesis and represent potential biomarkers or therapeutic targets in glioblastoma. Importance of the Study TP53 alterations are among the most common events in glioma, yet the transcriptional changes that accompany the earliest stages of tumor development remain incompletely understood. Using an isogenic human model based on TP53-knockout iPSCs, neural progenitor cells, and cerebral organoids, we identified a stage-specific transcriptional shift that emerges during late neural differentiation and resembles key features of glioblastoma. This transition is accompanied by the activation of a distinct lncRNA program, including previously unreported glioma-associated transcripts. The relevance of these findings is supported by independent validation in TCGA patient cohorts. Our study provides a human developmental framework to investigate the molecular events linking p53 loss to gliomagenesis and highlights novel non-coding RNA candidates for future mechanistic and translational studies. Key Points Question How does p53 deficiency affect lncRNA expression during human neural differentiation? Findings We identified a late transcriptional program that emerges in p53-deficient neural progenitors and organoids and partially overlaps with glioblastoma cell lines. This program includes five lncRNAs co-expressed with mitotic genes, two of which have not previously been linked to glioma. Relevance These findings provide insight into the molecular changes that accompany p53 loss during early gliomagenesis and highlight novel non-coding RNA candidates for future functional studies. Highlights p53 deficiency triggers a late-onset lncRNA reprogramming specifically at the 40-day NPC stage. Five lncRNAs (LINC00973, LINC01583, RP11-1094H24.4, RP11-462L8.1, RP5-875H18.9) are co-induced with mitotic genes in p53-KO and glioma cells. RP5-875H18.9 and RP11-1094H24.4 are novel candidates not previously reported in glioma. LINC01583 high expression significantly correlates with poorer overall survival in TCGA-GBM patients. The iPSC–NPC–organoid model faithfully recapitulates the transcriptional landscape of primary GBM. Graphical Abstract Comparative bulk RNA-seq analysis of human control and TP53 knockout iPSC- derived neural progenitor cells and brain organoids identified stage-specific lncRNA reprogramming during neural differentiation. Integration with glioblastoma patient survival data revealed two prognostic lncRNAs associated with poor clinical outcome.