Extensive patient-to-patient single nuclei transcriptome heterogeneity in pheochromocytomas and paragangliomas


Pheochromocytomas (PC) and paragangliomas (PG) are rare neuroendocrine tumors of varied genetic makeup, associated with high cardiovascular morbidity and a variable risk of malignancy. The source of the transcriptional heterogeneity of the disease and the underlying biological processes determining the outcome in PCPG remains largely unclear. We focused on PCPG tumors with germline SDHB and RET mutations, representing distinct prognostic groups with worse or better prognoses, respectively. We applied single-nuclei RNA sequencing (snRNA-seq) on tissue samples from 11 patients and found high patient-to-patient transcriptome heterogeneity of the neuroendocrine tumor cells. The tumor microenvironment also showed heterogeneous profiles mainly contributed by macrophages of the immune cell clusters and Schwann cells of the stroma. Performing non-negative matrix factorization we identified common transcriptional programs active in RET and SDHB as well as distinct modules including neuronal development, hormone synthesis and secretion, and DNA replication. Comparison of the SDHB and RET transcriptomes with that of developmental stages of adrenal gland formation suggests different developmental stages at which PC and PG tumors appear to be arrested.