Molecular or morphology? Challenges in pathologic diagnoses

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Shi Wei, MD, PhD
Gene P. Siegal, MD, PhD

October 2021—Recent molecular genetic advances have dramatically expanded diagnostic options, thus revolutionizing the diagnosis of many tumor types, especially those of soft tissue and bone. Advances in the discovery of molecular alterations underlying neoplastic pathogenesis have also provided insights into novel therapeutic targets and prognostic biomarkers. These improvements have led to the reclassification of a growing list of previously established tumor types, resulting in significant challenges for practicing pathologists, as exemplified herein.

First, many different tumor types demonstrate no identifiable differentiation on histomorphology and, frequently, immunophenotyping, but they harbor unique molecular genetic alterations yielding a specific diagnosis.¹ Undifferentiated small round cell sarcomas of bone and soft tissue are among the best examples in this regard, as outlined in the recent (fifth edition) WHO Classification of Tumours: Soft Tissue and Bone Tumours. The Ewing sarcoma/PNET family of tumors was historically thought to be different entities, but these tumors are now generally accepted as one and the same fundamental neoplastic process as they share common genetic abnormalities. This emerging change has resulted in improvement in the correct classification of this group of lesions. While diagnosing a small blue round cell as Ewing sarcoma is no longer as great a challenge given its recurrent EWSR1 gene rearrangement in more than 90 percent of all cases (available in virtually all FISH and molecular laboratories), a small subset of Ewing sarcomas we’ve come to now understand harbor a fusion between a member of the FET family of genes other than EWSR1 (i.e. FUS) and a member of the ETS family of transcription factors other than FLI1, including ERG, ETV1, ETV4, and FEV, thus necessitating molecular testing to reach an accurate diagnosis.

A greater challenge and diagnostic pitfall resides in a small group of entities previously regarded as Ewing-like sarcomas. These lesions share various degrees of similarity with Ewing sarcoma clinically, histologically, and immunophenotypically. However, they are characterized by EWSR1-non-ETS fusions and thus are lacking the pathognomonic molecular hallmark of Ewing sarcoma. The reported fusion partners thus far include NFATc2, PATZ1, SMARCA5, and SP3. It remains unclear whether these tumors represent one or more standalone pathologic entities or are better classified as variants of Ewing sarcoma. Their rarity thus requires additional examples to ensure accurate classification. Furthermore, a number of emerging Ewing-like undifferentiated round cell sarcomas have been identified with overlapping immunophenotypes (i.e. CD99), including CIC-rearranged sarcomas and sarcomas with BCOR-genetic alterations (most commonly BCOR-CCNB3). While most are treated similarly to Ewing sarcoma, CIC-rearranged sarcomas generally show unfavorable outcomes. The prognosis of BCOR-CCNB3 sarcomas appears similar to that of Ewing sarcoma, whereas other tumors in the BCOR family are not well characterized.

Second, with increasingly identified molecular alterations, it is not uncommon to encounter different entities with seemingly similar histomorphology, overlapping immunophenotypes, and cytogenetic characteristics. Aneurysmal bone cyst, a giant cell-rich neoplasm of the bone characteristically harboring the USP6 gene rearrangement, may rarely originate within soft tissue, and thus can be confused with other soft tissue lesions radiologically and histologically.² USP6 rearrangements have also been found in cases with classic radiological and histologic features of myositis ossificans; however, an extended clinical course suggested that they might be better classified as evolving aneurysmal bone cyst (i.e. local recurrence after complete resection).³ Settling this issue requires the relationship between these neoplasms to be better characterized. Even more confusing to the classical morphologist, nodular fasciitis shares the same USP6 rearrangement but looks nothing like these other lesions radiologically or under light microscopy.