Plasticity, a key hallmark of cancer, enables cells to transition into different states, driving tumor heterogeneity. This cellular plasticity is associated with cancer progression, treatment resistance, and relapse. Cancer stem cells (CSCs) play a central role in this process, yet the molecular factors underlying cancer cell stemness remain poorly understood. In this study, we explored the role of XIST (X-inactive specific transcript) long noncoding RNA in ovarian cancer stemness and plasticity through in silico and in vitro analyses. We found that XIST is significantly down-regulated in ovarian tumors, with low XIST expression linked to a higher stemness index and lower overall survival. Knocking down XIST in ovarian cancer cells enhanced stemness, particularly increasing mesenchymal-like CSCs, and under hypoxic conditions, it promoted epithelial-like CSC markers. Our findings suggest that XIST loss leads to CSC enrichment and cellular plasticity in ovarian cancer, pointing to potential therapeutic targets for patients with low XIST expression.

Diffuse midline glioma (DMG) is a leading cause of brain tumor death in children. In addition to hallmark H3.3K27M mutations, significant subsets also harbor alterations of other genes, such as TP53 and PDGFRA . Despite the prevalence of H3.3K27M, the results of clinical trials in DMG have been mixed, possibly due to the lack of models recapitulating its genetic heterogeneity. To address this gap, we developed human iPSC-derived tumor models harboring TP53 ^R248Q with or without heterozygous H3.3K27M and/or PDGFRA ^D842V overexpression. The combination of H3.3K27M and PDGFRA ^D842V resulted in more proliferative tumors when gene-edited neural progenitor (NP) cells were implanted into mouse brains compared to NP with either mutation alone. Transcriptomic comparison of tumors and their NP cells of origin identified conserved JAK/STAT pathway activation across genotypes as characteristic of malignant transformation. Conversely, integrated genome-wide epigenomic and transcriptomic analyses, as well as rational pharmacologic inhibition, revealed targetable vulnerabilities unique to the TP53 ^R248Q ; H3.3K27M; PDGFRA ^D842V tumors and related to their aggressive growth phenotype. These include AREG -mediated cell cycle control, altered metabolism, and vulnerability to combination ONC201/trametinib treatment. Taken together, these data suggest that cooperation between H3.3K27M and PDGFRA influences tumor biology, underscoring the need for better molecular stratification in DMG clinical trials.

Glioblastoma (GBM) is the most common and deadly primary brain tumor in adults. While in vitro patient-derived xenografts (PDX) lines are useful for studying GBM, they often exclude astrocytes and macrophages, which contribute significantly to tumor growth, invasion, and chemoradioresistance. Integrating these cells into tumor models is difficult due to their need for serum, which triggers GBM-PDX lines to lose their stem-like properties. The aim of this study was to develop a serum-free triculture model of GBM-PDX lines, normal human astrocytes (NHAs), and macrophages. Serum-free media alternatives were formulated for NHAs and identified for THP-1 macrophages, then combined with GBM PDX media to establish “PSX,” an experimental maintenance media. Cells were transitioned to serum-free media alternatives and functionally assessed through several parameters unique to each cell type. In addition to assessing GBM “stemness,” a custom 350-gene NanoString chip was used to assess differential gene expression in monocultured PDX cells versus PDX cells exposed to NHAs and macrophages. PSX maintained canonical function in astrocytes and macrophages while preserving the stem-like properties of GBM-PDX cells. Tri-culturing all three cells increased the expression of stemness-associated transcription factors and increased the expression of genes related to stemness and hypoxia in GBM cells. GBM PDX cells exposed to NHAs and macrophages in direct triculture exhibit increases in markers of stemness and hypoxia. These findings suggest that the serum-free triculture model presented herein may better recapitulate the tumoral heterogeneity of GBM in vitro, providing a novel model to utilize in current research.