Abstract 674: Functional characterization of SMARCA4 genomic variants
Authors: Shivani Jagannathan Murali, Bharath Kumar karre, Cristina Ivan, Kelly Craven, Stephanie Williams, Shikha Mahajan, Asfetaw Abera, Chao Sima, David Spetzler, Milan Radovich, Heather O'neill, Ravi Chakra Turaga
Journal: Cancer Research (2025)

Abstract Purpose: This study aims to carry out a pan cancer analyses of SMARCA4 genomic variants, including fusions, protein truncating variants (PTVs) and non-truncating variants(non-PTVs). Histological correlation of genomic variants for SMARCA4 expression may help identify tumors deficient in SMARCA4, making them potential candidates for treatment with synthetically lethal SMARCA2 inhibitors. Methods: We analyzed 350, 413 samples from Caris Life Sciences for clinical molecular profiling at Caris Life Sciences via Caris MI Tumor Seek (Phoenix, AZ). Gene fusion detection was performed on mRNA from FFPE tumor samples using the Illumina NovaSeq platform. Fusions with ≥ 3 junction reads were reviewed for domain prediction, breakpoints, frame retention, and co-occurring alterations. WES data was also examined for pathogenic mutations to assess fusion oncogenicity. IHC for SMARCA4 (N-terminal &amp; C-terminal) and SMARCA2 was conducted on FFPE sections from 35 patients with SMARCA4 variants, with staining scored by a board-certified pathologist. Results: Pan-Cancer analysis of SMARCA4 alterations revealed that NSCLC (30.7%) cases harbored the largest percentage of mutations followed by the CRC (15%) and UTNE (10%). Further, analysis through IHC revealed that patients with PTVs such as nonsense and frameshift mutations, were typically characterized by shorter/ truncated SMARCA4 protein and exhibited complete loss of SMARCA4 expression through IHC, often accompanied by an increase in SMARCA2 expression by IHC. In contrast, patients with missense mutations (non-PTVs) retained SMARCA4 expression, with minimal changes in SMARCA2 staining. In cases with SMARCA4 fusions detected, IHC analysis revealed an ambiguous result with some fusions retaining expression of SMARCA4 protein and others that did not. Patient cases harboring SMARCA4 fusions that displayed loss of SMARCA4 and concordant increase in SMARCA2 staining, would make good candidates for SMARCA2 inhibitor treatment. WTS analyses also revealed a decrease in SMARAC4 expression in PTVs, but not in non-PTVs. Further, we noted that other prevalent co-occurring mutations included TP53(55.7%), KRAS(19.7%) and ARID1A(16.7%) to be the most prominent alterations in patients with SMARCA4 alterations. Patients with SMARCA4 PTVs had poor prognosis compared to those without SMARCA4 variants in the NSCLC and UTNE indication. Conclusion: SMARCA4 mutations, including frameshift and nonsense mutations, are common in NSCLC, UTNE, and OSEC. These alterations, particularly PTVs, make SMARCA4-deficient tumors potential targets for SMARCA2 inhibitor therapy. Some cases with SMARCA4 fusions or missense mutations may also be eligible for treatment, but these should be assessed individually, considering co-occurring mutations, copy number amplifications and fusion partners. This will aid in refining patient selection and improving treatment outcomes using companion diagnostics. Citation Format: Shivani Jagannathan Murali, Bharath Kumar karre, Cristina Ivan, Kelly Craven, Stephanie Williams, Shikha Mahajan, Asfetaw Abera, Chao Sima, David Spetzler, Milan Radovich, Heather O'neill, Ravi Chakra Turaga. Functional characterization of SMARCA4 genomic variants [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 674.