Molecular testing of soft tissue tumors

Abstract

Background: The diagnosis of soft tissue tumors is challenging, especially when the evaluable material procured is limited. As a result, diagnostic ancillary testing is frequently needed. Moreover, there is a trend in soft tissue pathology toward increasing use of molecular results for tumor classification and prognostication. Hence, diagnosing newer tumor entities such as CIC-rearranged sarcoma explicitly requires molecular testing. Molecular testing can be accomplished by in situ hybridization, polymerase chain reaction, as well as next generation sequencing, and more recently such testing can even be accomplished leveraging an immunohistochemical proxy.

Conclusion: This review evaluates the role of different molecular tests in characterizing soft tissue tumors belonging to various cytomorphologic categories that have been sampled by small biopsy and cytologic techniques.

Keywords: cytopathology; fluorescent in situ hybridization; molecular; next-generation sequencing; polymerase chain reaction; sarcoma; soft tissue.

FIGURE 1

Immunohistochemical stains may act as a proxy for molecular alterations. The alteration may lead to overexpression of a protein, as with STAT6 in solitary fibrous tumor (A, STAT6 immunostain, 20×), or there may be loss of expression as is seen in malignant peripheral nerve sheath tumor, which loses the ability to methylate certain amino acids in histone proteins such as histone 3 lysine 27 (B, H3K27me3 immunostain, 20×). Note that the non‐neoplastic endothelial cells retain H3K27me3 expression. In rare cases, the chimeric fusion protein can be detected, as in synovial sarcoma (C, SS18‐SSX immunostain, 20×).

FIGURE 2

In dermatofibrosarcoma protuberans, RNA in situ hybridization for PDGFB allows for detection of a COL1A1‐PDGFB fusion without the need for FISH or PCR by demonstrating upregulation of PDGFB RNA expression. A tumor is considered positive if there are either five puncta or one aggregate in greater than 25% of tumor cells.

FIGURE 3

An inflammatory myofibroblastic tumor (IMT) seen on fine needle aspiration. The Diff‐Quik stain (A, 40×) and cell block (B, H&E, 20×) show clusters of mildly pleomorphic spindle cells within a background of chronic inflammation. An ALK immunostain (C, 10×) is positive in the tumor cells, suggesting the presence of an ALK rearrangement and confirming the diagnosis of IMT.

FIGURE 4

Representative photomicrographs of fluorescent in situ hybridization (FISH) of NR4A3 (A) and EWSR1 (B) dual‐color break‐apart probes showing separate red and green signals, indicating rearrangements of the NR4A3 and EWSR1 genes, respectively.