Intertumoral lineage diversity and immunosuppressive transcriptional programs in well-differentiated gastroenteropancreatic neuroendocrine tumors
Samantha E. Hoffman, Todd W. Dowrey, Carlos Villacorta Martin, Kevin Bi, Breanna Titchen, Shreya Johri, Laura DelloStritto, Miraj Patel, Colin MacKichan, Stephanie Inga, Judy Chen, Grace Grimaldi, Sara Napolitano, Isaac Wakiro, Jingyi Wu, J. Yeung, Asaf Rotem, Ewa Sicinska, Erin Shannon, Thomas E. Clancy, Jiping Wang, Sarah Denning, Lauren K. Brais, N. Besson, Kathleen L. Pfaff, Ying Huang, Katrina Kao, Scott J. Rodig, Jason L. Hornick, Sébastien Vigneau, Jihye Park, Matthew H. Kulke, Jennifer A. Chan, Eliezer M. Van Allen, George J. Murphy
Abstract
Neuroendocrine tumors (NETs) are rare cancers that most often arise in the gastrointestinal tract and pancreas. The fundamental mechanisms driving gastroenteropancreatic (GEP)–NET growth remain incompletely elucidated; however, the heterogeneous clinical behavior of GEP-NETs suggests that both cellular lineage dynamics and tumor microenvironment influence tumor pathophysiology. Here, we investigated the single-cell transcriptomes of tumor and immune cells from patients with gastroenteropancreatic NETs. Malignant GEP-NET cells expressed genes and regulons associated with normal, gastrointestinal endocrine cell differentiation, and fate determination stages. Tumor and lymphoid compartments sparsely expressed immunosuppressive targets commonly investigated in clinical trials, such as the programmed cell death protein–1/programmed death ligand–1 axis. However, infiltrating myeloid cell types within both primary and metastatic GEP-NETs were enriched for genes encoding other immune checkpoints, including VSIR (VISTA), HAVCR2 (TIM3), LGALS9 (Gal-9), and SIGLEC10 . Our findings highlight the transcriptomic heterogeneity that distinguishes the cellular landscapes of GEP-NET anatomic subtypes and reveal potential avenues for future precision medicine therapeutics.