SWI/SNF Complex-Deficient Undifferentiated Carcinoma of the Pancreas: Clinicopathologic and Genomic Analysis

: Inactivating alterations in the SWItch/Sucrose Non-Fermentable (SWI/SNF) Chromatin Remodeling Complex subunits have been described in multiple tumor types. Recent studies focused on SMARC subunits of this complex to understand their relationship with tumor characteristics and therapeutic opportunities. To date, pancreatic cancer with these alterations has not been well-studied, although isolated cases of undifferentiated carcinomas have been reported. Herein, we screened 59 pancreatic undifferentiated carcinomas for alterations in SWI/SNF complex-related [SMARCB1 (BAF47/INI1), SMARCA4 (BRG1), SMARCA2 (BRM)] proteins and/or genes using immunohistochemistry (IHC) and/or next-generation sequencing (NGS). Cases with alterations in SWI/SNF complex-related proteins/genes were compared to cases without alterations, as well as to 96 conventional pancreatic ductal adenocarcinomas (PDAC). In all tumor groups, MMR and PD-L1 protein expression were also evaluated. Thirty of 59 (51%) undifferentiated carcinomas had a loss of SWI/SNF complex-related protein expression or gene alteration. Twenty-seven of 30 (90%) SWI/SNF-deficient undifferentiated carcinomas had rhabdoid morphology [vs. 9/29 (31%) SWI/SNF-retained undifferentiated carcinomas; p < 0.001] and all expressed cytokeratin, at least focally. Immunohistochemically, SMARCB1 protein expression was absent in 16/30 (53%) cases, SMARCA2 in 4/30 (13%), and SMARCA4 in 4/30 (13%); both SMARCB1 and SMARCA2 protein expressions were absent in 1/30 (3%). Five of 8 (62.5%) SWI/SNF-deficient undifferentiated carcinomas that displayed loss of SMARCB1 protein expression by IHC were found to have corresponding SMARCB1 deletions by NGS. Analysis of canonical driver mutations for PDAC in these cases showed KRAS (2/5) and TP53 (2/5) abnormalities. Median CPS for PD-L1 (E1L3N) was significantly higher in the undifferentiated carcinomas with/without SWI/SNF deficiency compared to the conventional PDACs (p < 0.001). SWI/SNF-deficient undifferentiated carcinomas were larger (p < 0.001) and occurred in younger patients (p < 0.001). Patients with SWI/SNF-deficient undifferentiated carcinoma had worse overall survival compared to patients with SWI/SNF-retained undifferentiated carcinoma (p = 0.004) and PDAC (p < 0.001). Our findings demonstrate that SWI/SNF-deficient pancreatic undifferentiated carcinomas are frequently characterized by rhabdoid morphology, exhibit highly aggressive behavior, and have a negative prognostic impact. The ones with SMARCB1 deletions appear to be frequently KRAS wild-type. Innovative developmental therapeutic strategies targeting this genomic basis of the SWI/SNF complex and the therapeutic implications of EZH2 inhibition (NCT03213665), SMARCA2 degrader (NCT05639751), or immunotherapy are currently under investigation.