Background
Pheochromocytomas and paragangliomas (PPGL) are rare neuroendocrine tumors characterized by molecular heterogeneity and limited therapeutic options. To identify actionable upstream regulators beyond gene-centric associations, we implemented an integrative strategy focused on an emerging drug target, phosphodiesterase 3A (PDE3A), combining transcriptomic modeling with functional validation in patient-derived samples.

Materials and Methods
RNA sequencing data from TCGA PCPG (n=179) were stratified by median PDE3A expression to PDE3A-high and PDE3A-low expression groups. Protein expression was validated by immunohistochemistry in an independent FFPE cohort (n=151). To investigate differentially activated pathways in PDE3A high and low expression groups, a workflow of PROGENy, DecoupleR and CARNIVAL was implemented. Computational predictions were evaluated by ex vivo drug screening of 83 compounds in an independent patient-derived ex vivo samples (n = 21).

Results
In TCGA-PCPG sample groups, CARNIVAL identified a MAPK1-RPS6KA3 and GSK3B-CCND3-CDK6 regulatory axis specific to the PDE3A high subgroup and PROGENy inferred activated hypoxia and PI3K signaling. Ex vivo screening revealed sensitivity to PDE3A modulators 5/21 (anagrelide) and 7/21 (BAY 2666605) samples. Drug sensitivity k-means clustering stratified compounds into three clusters: apoptosis causing drugs (e.g. navitoclax, cisplatin, niclosamide); a subgroup-selective cluster targeting more specific pathways such as mTOR and MEK (e.g. binimetinib, trametinib, vistusertib, AZD8055); and a low-efficacy cluster (e.g. alectinib, phenformin, olaparib) comprising agents with heterogeneous molecular targets.

Conclusions
PDE3A represents a therapeutic vulnerability in a molecularly defined subset of PPGL and integrative transcriptomic network modeling enables identification of clinically relevant drug dependencies in heterogeneous cancer types.

Co-authors: Helena Leijon, Juha Rantala, Arthur Tischler, Ron Lechan, James Powers, Tiina Vesterinen, Johanna Arola, Tom Böhling, Omar Youssef, Sami Kilpinen, Harri Sihto