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Desmoid tumors, also known as aggressive fibromatosis, are rare, benign soft tissue neoplasms characterized by local invasiveness and a high recurrence rate. They can mimic malignant tumors, particularly in patients with a history of gastrointestinal stromal tumors (GISTs). We report a case of a 60-year-old male who developed intra-abdominal desmoid tumors five years after undergoing laparoscopy and endoscopy cooperative surgery (LECS) for gastric GIST, followed by adjuvant imatinib therapy. Imaging studies, including contrast-enhanced computed tomography (CT) and positron emission tomography-computed tomography (PET-CT), revealed two mesenteric masses. The larger lesion demonstrated elevated fluorodeoxyglucose (FDG) uptake (SUVmax = 6.7), raising suspicion for recurrent GIST. Surgical resection was performed, and histopathological examination confirmed the diagnosis of desmoid tumors. Immunohistochemical analysis showed positive β-catenin staining, with negative markers for CD34, desmin, and c-kit, distinguishing it from recurrent GIST. This case highlights the diagnostic challenge of differentiating desmoid tumors from GIST recurrence based on imaging alone. Histopathological confirmation remains crucial for accurate diagnosis. Surgical resection is the primary treatment for symptomatic desmoid tumors, but given their high recurrence rate, long-term follow-up and a multidisciplinary approach are essential for optimal management.