Immune microenvironment signatures as prognostic biomarkers in gastroenteropancreatic neuroendocrine carcinoma (GEP-NEC).

Abstract

4180 Background: GEP-NEC is an aggressive malignancy with rising incidence and limited therapeutic options. While immune checkpoint inhibitors (ICIs) have become standard of care in small cell lung cancer (SCLC), their role in GEP-NEC remains undefined. Characterizing immune cell signatures in the tumor microenvironment (TME) across different NEC histologies may help identify prognostic biomarkers and guide immunotherapy strategies. Methods: We included 4863 NEC tumors that underwent DNA (592-gene panel, whole exome) and RNA (whole transcriptome) sequencing at Caris Life Sciences. Composition of the TME was estimated from bulk RNA sequencing using QuanTIseq method. Overall survival (OS) and IO-associated OS (IO-OS) were derived from insurance claims and calculated from date of tumor biopsy (OS) or IO initiation (IO-OS) to last contact using Kaplan-Meier estimates and Cox proportional hazards models. Statistical significance was determined by Fishers Exact, Chi-square and Mann-Whitney U test with adjustments for multiple comparisons ( P < 0.05). Results: The cohort was comprised of small cell (SCNEC, n = 2320), large cell (LCNEC, 618), high-grade NEC (HGNEC, 414) and NEC not otherwise specified (NOS, 1511). Primary sites included lung (2642), pancreas (459), non-pancreatic GI (931) and other sites (831). SCNEC had lower Treg, M1 or M2 macrophage and neutrophils, and higher CD4+ T-, NK-, B- and dendritic-cell infiltration than other histologies, suggesting more lymphocyte-driven immune milieu with reduced myeloid-driven suppression. Compared with lung NEC, GEP-NEC demonstrated a more immunosuppressive TME, characterized by lower NK-, B- and dendritic-cell infiltration and higher Treg, M1/M2 macrophage and neutrophils—most pronounced in non-pancreatic GI primaries. Pancreatic NEC had reduced dendritic cells in LCNEC, HGNEC and NOS subtypes and higher neutrophils in HGNEC and NOS. Elevated B-cell infiltration was associated with improved OS in SCNEC of non-pancreatic GI (HR 0.56, 95%CI 0.37-0.85, P = 0.032) and lung (HR 0.81, 0.72-0.90, P = 0.001) origin. High M2 macrophage and NK-cell scores were associated with prolonged OS in NOS of non-pancreatic GI (M2: HR 0.35, 0.28-0.45, P < 0.001; NK: HR 0.32, 0.26-0.41, P < 0.001) and pancreas (M2: HR 0.46, 0.33-0.62, P < 0.001; NK: HR 0.64, 0.48-0.84, P = 0.010) origin. Among patients receiving ICIs (n = 1811, 910 with SCLC), only higher B-cell infiltration was associated with improved IO-OS in SCLC (HR 0.79, 0.68-0.92, P = 0.029); data was insufficient to analyze IO-OS for other histologic and anatomic subgroups. Conclusions: GEP-NEC exhibits a distinct and relatively immunosuppressive TME compared with lung NEC. B-cell, NK-cell, and macrophage signatures are prognostic across GEP-NEC subtypes. These findings support further evaluation of immune-based stratification and biomarker-driven therapeutic development in GEP-NEC.