A patient-derived organoid platform for predominantly posterior fossa adult ependymoma: histopathologic preservation, culture-associated transcriptomic remodeling, and in vivo tumorigenicity.

Abstract

Purpose: Well-characterized patient-derived models of adult ependymoma (EPN) remain limited. We established a patient-derived organoid (PDO) platform from adult EPN and evaluated its histopathologic and immunophenotypic characteristics, transcriptomic relationship to parental tumors, and in vivo tumorigenicity.

Methods: Fresh surgical specimens from 22 adult patients with EPN were processed for PDO establishment. Tumor-PDO fidelity was assessed by histology and immunofluorescence. Three matched tumor-PDO pairs underwent RNA sequencing followed by paired differential-expression, gene-set enrichment, microenvironmental signature, and ESTIMATE analyses. Selected PDO models were further evaluated by subcutaneous and intracranial xenografting.

Results: PDOs were successfully established from 20 of 22 specimens (90.9%). Established PDOs broadly retained parental tumor morphology and expression of major ependymoma-associated and neural/progenitor markers. Selected morphologic and immunophenotypic features remained detectable during prolonged culture. Transcriptomic profiling of three matched tumor-PDO pairs demonstrated high global expression similarity (Pearson r = 0.84-0.88) together with substantial culture-associated remodeling. Endothelial signatures and ESTIMATE-derived stromal scores were reduced in all three PDOs, whereas other immune and stromal signatures showed patient-specific changes. Paired transcriptomic analysis further identified enrichment of ribosome/translation and oxidative-phosphorylation programs in PDOs, accompanied by reduced cilia- and axoneme-associated programs. Selected PDO-derived models demonstrated tumorigenic capacity in subcutaneous and intracranial settings.

Conclusion: Adult EPN can be propagated efficiently as PDOs that retain selected tumor-associated features while undergoing measurable transcriptional and microenvironment-associated adaptation to ex vivo culture. Selected models also retained tumorigenic capacity in vivo. These models provide a complementary experimental platform for studying adult EPN biology.