Abstract 1240: Genomic characterization of changes in the molecular profile of locally advanced rectal cancer treated with neoadjuvant therapy

Background: Locally advanced rectal cancer (LARC) patients exhibit a widely heterogeneous degree of response to neoadjuvant therapy (NAT) and many experience disease relapse. By examining tumors at multiple timepoints before and after NAT, we investigated 1) pre-treatment genomic predictors of metastasis to specific anatomic sites that could potentially inform future therapeutic strategies and 2) genomic mechanisms driving tumor evolution under NAT stress. Methods: We analyzed 687 specimens from LARC patients treated at Memorial Sloan Kettering Cancer Center (MSKCC). This included 473 endoscopic biopsies collected before NAT and 214 samples after NAT. Post-NAT specimens included 99 surgical resections (SR), 19 local recurrences (LR) and 96 distant recurrences (DR). The DR set included 33 liver, 33 lung, and 30 metastases located in other organs. All samples underwent targeted DNA sequencing with MSK-IMPACT, an assay that identifies genomic alterations in 341-505 genes. We assessed somatic DNA alterations at the gene and the pathway levels, tumor mutational burden (TMB), fraction genome altered by copy number changes (FGA), tumor purity and whole-genome doubling (WGD) status. Results: Pre-NAT biopsies from patients who never developed any metastasis had higher Wnt pathway alterations than those whole developed metastases (85.9% vs 73.2%, p=0.0055), driven by APC alterations (84.6 vs 71.1%, p=0.0046), and higher rates of FBXW7 (17.8 vs 9.3%, p=0.044) and BCL2L1 alterations (6.7 vs 1%, p=0.01). In contrast, patients who develop metastases tend to have more alterations in KRAS (51.6 vs 39.6%, p=0.038) and PTEN (6.2 vs 1.1%, p = 0.0065). Liver metastases tend to occur earlier than lung metastases (median 12.9 vs 16.1 months from end of NAT, p=0.034). Pre-NAT specimens had higher rates of APC alterations than post-NAT specimens (81.8% vs 74.3%, p=0.025), while TGFβ pathway alteration rate was higher post-NAT (15.4% vs 24.3%, p=0.0074), driven by SMAD4 inactivation (10.8 vs 17.8%, p=0.014). LR specimens exhibited higher FGA (median 0.8 vs 0.55, p<0.001), higher rates of WGD (68.8% vs 37.5%, p=0.017), and lower rates of APC (52.6% vs 80.2%, p=0.007) than non-LR specimens. Among DR samples, KRAS alterations were more frequent in lung than liver metastases (60.6% vs 39.4%, p=0.14), while the opposite trend was observed for SMAD4 alterations (9.1% vs 30.3%, p=0.06). Conclusion: We observed significant differences in alteration rates in several driver genes in LARC specimens sequenced before and after NAT, which might be explained by NAT stress driving tumor evolution. The distinct genomic profile of LRs may be indicative of differences in their biological mechanisms of emergence. Differences in the somatic landscape of liver and lung metastases may have translational implications for the treatment of patients with advanced disease. Citation Format: Sharafudeen D. Abubakar, Christina I. Lee, Farheen Shah, Chin-Tung Chen, Paolo Manca, Henry Walch, Walid K. Chatila, Rona Yaeger, Julio Garcia-Aguilar, Francisco Sanchez-Vega. Genomic characterization of changes in the molecular profile of locally advanced rectal cancer treated with neoadjuvant therapy [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 1240.