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Updated: Aug 30, 2025
Using RNA-sequencing to Detect Novel Splice Variants Related to Drug Resistance in In Vitro Cancer Models
Published on: December 9, 2016
Single-cell transcriptomics of neuroblastoma identifies chemoresistance-associated genes and pathways
Marianna Avitabile1,2, Ferdinando Bonfiglio2,3, Vincenzo Aievola2
1Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, Napoli 80131, Italy.
Abstract:
High-Risk neuroblastoma (NB) survival rate is still <50%, despite treatments being more and more aggressive. The biggest hurdle liable to cancer therapy failure is the drug resistance by tumor cells that is likely due to the intra-tumor heterogeneity (ITH). To investigate the link between ITH and therapy resistance in NB, we performed a single cell RNA sequencing (scRNAseq) of etoposide and cisplatin resistant NB and their parental cells. Our analysis showed a clear separation of resistant and parental cells for both conditions by identifying 8 distinct tumor clusters in etoposide-resistant/parental and 7 in cisplatin-resistant/parental cells. We discovered that drug resistance can affect NB cell identities; highlighting the bi-directional ability of adrenergic-to-mesenchymal transition of NB cells. The biological processes driving the identified resistant cell subpopulations revealed genes such as (BARD1, BRCA1, PARP1, HISTH1 axis, members of RPL family), suggesting a potential drug resistance due to the acquisition of DNA repair mechanisms and to the modification of the drug targets. Deconvolution analysis of bulk RNAseq data from 498 tumors with cell subpopulation signatures showed that the transcriptional heterogeneity of our cellular models reflected the ITH of NB tumors and allowed the identification of clusters associated with worse/better survival. Our study demonstrates the distinct cell populations characterized by genes involved in different biological processes can have a role in NB drug treatment failure. These findings evidence the importance of ITH in NB drug resistance studies and the chance that scRNA-seq analysis offers in the identification of genes and pathways liable for drug resistance.
Insights
Intra-tumor heterogeneity drives neuroblastoma drug resistance by altering cell identity and activating DNA repair mechanisms. Understanding these distinct cell populations is crucial for improving neuroblastoma treatment outcomes.
Area of Science:
- Oncology
- Genomics
- Molecular Biology
Background:
- High-risk neuroblastoma (NB) has a poor survival rate (<50%) due to aggressive treatments failing to overcome drug resistance.
- Intra-tumor heterogeneity (ITH) is a major contributor to therapeutic failure in neuroblastoma.
- Understanding the molecular mechanisms underlying ITH and drug resistance is critical for developing effective treatments.
Purpose of the Study:
- To investigate the relationship between intra-tumor heterogeneity and drug resistance in neuroblastoma.
- To identify distinct cell subpopulations and their associated biological processes in drug-resistant neuroblastoma cells.
- To explore the potential of single-cell RNA sequencing (scRNAseq) in understanding neuroblastoma drug resistance.
Main Methods:
- Single-cell RNA sequencing (scRNAseq) was performed on etoposide and cisplatin-resistant neuroblastoma cells and their parental counterparts.
- Bioinformatic analysis was used to identify distinct tumor cell clusters and their transcriptional profiles.
- Deconvolution analysis of bulk RNA sequencing data from 498 neuroblastoma tumors was employed to correlate cellular heterogeneity with survival outcomes.
Main Results:
- scRNAseq revealed distinct cell clusters in resistant neuroblastoma, indicating significant intra-tumor heterogeneity.
- Drug resistance induced changes in neuroblastoma cell identity, including adrenergic-to-mesenchymal transition.
- Resistant cell subpopulations were characterized by genes involved in DNA repair mechanisms (e.g., BARD1, BRCA1, PARP1) and modification of drug targets.
- Deconvolution analysis confirmed that the identified transcriptional heterogeneity in cellular models reflects ITH in patient tumors and identified survival-associated clusters.
Conclusions:
- Distinct cell populations within neuroblastoma tumors, driven by specific biological processes, contribute to treatment failure.
- ITH plays a significant role in neuroblastoma drug resistance, highlighting the need for targeted therapeutic strategies.
- scRNAseq is a powerful tool for identifying genes and pathways responsible for drug resistance, offering new avenues for therapeutic development.
