Next-generation sequencing study of inflammatory spindle cell lesions focused on receptor tyrosine kinase gene rearrangements most frequently occurring in inflammatory myofibroblastic tumor.

Background: A group of inflammatory spindle cell lesions (ISCLs) includes many nosological entities with a common histological image consisting of spindle-shaped cells and inflammatory infiltrate. Diverse diseases indicate different prognoses that can be difficult to predict. The most well-known neoplasm from the group is an inflammatory myofibroblastic tumor (IMT) that harbors tyrosine kinase gene rearrangement frequently affecting ALK, ROS1, RET, PDGFRB, NTRK, and IGF1R genes. In contrast, a reactive mass-forming lesion is regarded as an inflammatory pseudotumor (IPT).

Objectives: This study aimed to: 1) investigate the accuracy of the primary diagnosis of IMT and IPT with the diagnostics using extended analysis of clinical data, re-evaluation of histopathological slides and next-generation sequencing (NGS); and 2) to establish prognostic and diagnostic factors.

Material and methods: Finally, 46 cases of ISCLs were retrieved. The authors revised diagnoses and performed NGS based on ribonucleic acids isolated from selected paraffin blocks. Clinical and paraclinical data were also collected. The final diagnoses were made as a result of available information integration.

Results: The sequencing confirmed 4 IMTs and detected 4 fusion gene types - EML4-ALK, RANBP2-ALK, and ETV6-NTRK3. Additionally, 1 afunctional EGFR-PPARGC1A rearrangement was found in gastric inflammatory fibroid polyp. A subset of reactive lesions also contained some mutations, which is consistent with actual knowledge. Neoplasms with ganglion-like cells, nuclear atypia and increased mitotic activity gave local recurrences. A higher percentage of necrosis indicated IMTs and patients who died in the analyzed period. No relation between genetic alterations and relapse was found.

Conclusions: A final diagnosis can be made based on all clinical and paraclinical data. The prognosis after the treatment is dependent on the pathological diagnosis, disease location and resection completeness, presence of ganglion-like cells, nuclear atypia, mitotic index, and necrosis. Not only neoplastic but also reactive lesions can recur. The presence of gene rearrangements and necrosis can have diagnostic value.