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Updated: Jun 7, 2025
Nuclei Isolation from Fresh Frozen Brain Tumors for Single-Nucleus RNA-seq and ATAC-seq
Published on: August 25, 2020
Single Nuclei Sequencing Reveals Intratumoral Cellular Heterogeneity and Replication Stress in Adrenocortical
Abstract:
Adrenocortical carcinoma (ACC) is a rare endocrine malignancy with a poor prognosis and limited treatment options. Bulk genomic characterization of ACC has not yielded obvious therapeutic or immunotherapeutic targets, yet novel therapies are needed. We hypothesized that elucidating the intratumoral cellular heterogeneity by single nuclei RNA sequencing analyses would yield insights into potential therapeutic vulnerabilities of this disease. In addition to characterizing the immune cell and fibroblast landscape, our analyses of single nuclei gene expression profiles identified an adrenal cortex cell cluster exhibiting a program of replication stress and DNA damage response in primary and metastatic ACC. In vitro assessment of replication stress and DNA damage response using an ACC cell line and a series of newly-derived hormonally active patient-derived tumor organoids revealed ATR sensitivity. These findings provide novel mechanistic insight into ACC biology and suggest that an underlying dependency on ATR may be leveraged therapeutically in advanced ACC.
Insights
Adrenocortical carcinoma (ACC) cells exhibit replication stress and DNA damage. This suggests targeting ATR may be a new therapeutic strategy for advanced ACC.
Area of Science:
- Endocrinology
- Oncology
- Genomics
Background:
- Adrenocortical carcinoma (ACC) is a rare endocrine malignancy with limited treatment options.
- Genomic studies have not identified clear therapeutic targets for ACC.
- Novel therapeutic strategies are needed for advanced ACC.
Purpose of the Study:
- To investigate the cellular heterogeneity of ACC using single nuclei RNA sequencing.
- To identify potential therapeutic vulnerabilities in ACC.
Main Methods:
- Single nuclei RNA sequencing (snRNA-seq) was performed on primary and metastatic ACC.
- Gene expression profiles were analyzed to characterize cellular landscapes.
- In vitro studies assessed replication stress and DNA damage response in ACC cell lines and patient-derived tumor organoids.
Main Results:
- snRNA-seq identified an adrenal cortex cell cluster with a replication stress and DNA damage response program in ACC.
- In vitro models confirmed replication stress and DNA damage response.
- ACC cell lines and organoids showed sensitivity to ATR inhibition.
Conclusions:
- ACC cells exhibit an underlying dependency on ATR due to replication stress and DNA damage.
- Targeting ATR represents a potential therapeutic strategy for advanced adrenocortical carcinoma.
