Comprehensive genomic profiling of patients with cancer of unknown primary (CUP).

Abstract

e15188 Background: Carcinoma of unknown primary (CUP) remains a clinical entity with limited standardized treatment options. However, recent studies have demonstrated that broad next-generation sequencing (NGS) panels provide clinically meaningful insights, enabling identification of actionable genomic alterations, refinement of tissue-of-origin hypotheses, and improved therapeutic stratification. A substantial proportion of CUP tumors harbor potentially targetable alterations, and a subset exhibits high tumor mutational burden (TMB-H) and/or high microsatellite instability (MSI-H) status. In this study, we assessed the clinical utility of comprehensive genomic profiling panels in CUP cases. Methods: Overall, 103 patients were analysed, including 74 tissue-based and 29 liquid biopsy cases. Matched leukocyte DNA was used to exclude clonal hematopoiesis–related variants. Targeted-capture NGS analysis was performed using two CE-IVD GenePlus assays covering 1021 cancer-related genes and 38 fusion genes, with integrated assessment of TMB and MSI. Sequencing was carried out on an MGI sequencing platform (DNBSEQ-T7). Results: NGS analysis revealed that 29% (30/103) of patients derived clinical benefit from pan-cancer biomarkers. Specifically, BRAF V600 mutations were detected in 5 cases, indicating sensitivity to BRAF/MEK inhibitors. TMB ≥10 muts/Mb was observed in 19 tissue samples, while TMB ≥16 muts/Mb was identified in 4 liquid biopsy samples, both suggesting eligibility for immunotherapy. Additionally, 2 cases were also MSI-H, supporting potential response to immune checkpoint inhibitors. Genomic alterations with potential relevance for off-label targeted therapy were identified in 30% of patients. The most frequently mutated gene was KRAS (18 pts), indicating potential sensitivity to KRAS/MEK inhibitors. Additional alterations were observed in PIK3CA/PTEN, ERBB2, IDH, FGFR2 (fusion), and homologous recombination deficiency–related genes (BRCA2, ATM, BAP1), suggesting possible responsiveness to PI3K/AKT/mTOR inhibitors, ERBB2-directed therapies, IDH, FGFR and PARP inhibitors, respectively. Finally, 29% of the patients were considered eligible for clinical trial enrolment, based on their molecular profiles. Conclusions: Therapeutically relevant molecular profiling results were identified in 59% of CUP patients. These findings support the integration of molecular profiling into routine CUP evaluation, facilitating biomarker-driven precision oncology strategies aimed at improving patient outcomes.