Transcriptome-guided resolution of tumor microenvironment interactions in pheochromocytoma and paraganglioma subtypes

Background: Pheochromocytomas and paragangliomas (PCPG) are rare catecholamine-secreting endocrine tumors deriving from chromaffin cells of the embryonic neural crest. Although distinct molecular PCPG subtypes have been elucidated, certain characteristics of these tumors have yet to be fully examined, namely the tumor microenvironment (TME). To further understand tumor–stromal interactions in PCPG subtypes, the present study deconvoluted bulk tumor gene expression to examine ligand–receptor interactions. Methods: RNA-sequencing data primary solid PCPG tumors were derived from The Cancer Genome Atlas (TCGA). Tumor purity was estimated using two robust algorithms. The tumor purity estimates and bulk tumor expression values allowed for non-negative linear regression to predict the average expression of each gene in the stromal and tumor compartments for each PCPG molecular subtype. The predicted expression values were then used in conjunction with a previously curated ligand–receptor database and scoring system to evaluate top ligand–receptor interactions. Results: Across all PCPG subtypes compared to normal samples, tumor-to-tumor signaling between bone morphogenic proteins 7 (BMP7) and 15 (BMP15) and cognate receptors ACVR2B and BMPR1B was increased. In addition, tumor-to-stroma signaling was enriched for interactions between predicted tumor-originating delta-like ligand 3 (DLL3) and predicted stromal NOTCH receptors. Stroma-to-tumor signaling was enriched for interactions between ephrins A1 and A4 with ephrin receptors EphA5, EphA7, and EphA8. Pseudohypoxia subtype tumors displayed increased predicted stromal expression of genes related to immune-exhausted T-cell response, including those for inhibitory receptors HAVCR2 and CTLA4. Conclusion: The current exploratory study predicted stromal and tumor through compartmental deconvolution and yielded previously unrecognized interactions and putative biomarkers in PCPG.