Single-cell RNA sequencing reveals the neuronal transcriptional differentiation program associated with...

Hepatoblastoma is a rare pediatric liver cancer, primarily affecting children under three years old. Stemness properties of tumor cells have been linked to tumor recurrence and therapy resistance. Ferroptosis, a form of programmed cell death, plays a role in cancer therapy resistance and is influenced by iron metabolism and lipid peroxidation.

Using the ferroviz R-package and the ferroptosis-related transcriptional program (FerrDb V2), two independent cohorts of hepatoblastoma bulk transcriptome data (GSE131329 and GSE104766) were analyzed through supervised methods. A cross-validated ferroptosis-deregulated transcriptional program was further investigated for tumor heterogeneity in single-cell RNA-sequencing data (GSE180665), which included normal liver, patient-derived xenotransplantation models, and human tumor samples. Slingshot pseudotime trajectory analysis was performed on tumor neuronal cells.

In the training cohort, 89 ferroptosis-related genes were found to be deregulated in hepatoblastoma, with a majority of upregulated molecules involved in oxidative stress response and histone modifiers (p-value = 0.0088). In the validation cohort, 96 ferroptosis genes were deregulated, including eight upregulated molecules related to oxidative stress response. Cross-validation between the two cohorts identified a common signature of 51 genes: 20 upregulated and 31 downregulated in hepatoblastoma tumors. Among the oxidative stress-related molecules, SLC7A11, GPX7, SRC, NQO1, PYCR1, and PRKAA2 were upregulated. Additionally, a network of genes involved in carboxylic acid biosynthesis was repressed in tumors. At the single-cell level, the downregulated ferroptosis program was confirmed to be repressed in tumor cells compared to normal hepatocytes. Conversely, the upregulated ferroptosis program was found to be particularly active in neuronal tumor cells, with upregulation of TGFB2, NQO1, PRKAA2, ACSL4, IGF2BP3, BEX1, SLC7A11, and SRC. In neuronal cells, ACSL4 was co-regulated with ferroptosis suppressors such as NQO1, BEX1, SRC, and IGF2BP3, while TGFB2, a ferroptosis driver with restricted expression, was co-regulated with SLC7A11 and PRKAA2. Pseudotime trajectory analysis of tumor neuronal cells associated TGFB2 expression with the regulation of the GRIN2B glutamate receptor and the LEF1 transcription factor.

This study identified a ferroptosis transcriptional program that is deregulated in two independent transcriptome cohorts. At the single-cell level, these alterations, linked to oxidative stress response, revealed insights into neuronal differentiation within human hepatoblastoma tumors.