NTRK Gene Fusion Detection in Atypical Spitz Tumors

Abstract

Atypical Spitz tumors (AST) deviate from stereotypical Spitz nevi for one or more atypical features and are now regarded as an intermediate category of melanocytic tumors with uncertain malignant potential. Activating NTRK1/NTRK3 fusions elicit oncogenic events in Spitz lesions and are targetable with kinase inhibitors. However, their prevalence among ASTs and the optimal approach for their detection is yet to be determined. A series of 180 ASTs were screened with pan-TRK immunohistochemistry and the presence of NTRK fusions was confirmed using FISH, two different RNA-based NGS panels for solid tumors, and a specific real time RT-PCR panel. Overall, 26 ASTs showed pan-TRK immunostaining. NTRK1 fusions were detected in 15 of these cases showing cytoplasmic immunoreaction, whereas NTRK3 was detected in one case showing nuclear immunoreaction. Molecular tests resulted all positive in only two ASTs (included the NTRK3 translocated), RNA-based NGS and real time RT-PCR were both positive in three cases, and FISH and real time RT-PCR in another two cases. In seven ASTs NTRK1 fusions were detected only by FISH and in two cases only by real time RT-PCR. The frequency of NTRK fusions in ASTs is 9%, with a clear prevalence of NTRK1 compared to NTRK3 alterations. Pan-TRK immunohistochemistry is an excellent screening test. Confirmation of NTRK fusions may require the use of different molecular techniques.

Cutaneous Melanomas: A Single Center Experience on the Usage of Immunohistochemistry Applied for the Diagnosis

“…), but this is beyond the scope of this article [ 6 ]. Since these genetic alterations lead to an over- and/or aberrant expression of specific molecules, and the latter are associated with well-defined histological features of the melanocytic lesion, an expert dermatopathologist could suspect a specific genetic alteration from just the H&E exam and prove it with the immunohistochemistry [ 6 , 108 , 109 , 110 , 111 , 112 , 113 , 114 , 115 , 116 , 117 , 118 , 119 , 120 , 121 ]. In our routine practice, we do not use standard panels; the choice of immunohistochemical panels is performed case-by-case, based on the H&E exam.…”

“…Specifically, the antibodies we use in our laboratory and specific histological entities, related to their over- and/or aberrant expression, are the following: -BRAF V600E: melanocytic lesions in intermittently sun-exposed skin (superficial spreading cM, simple lentigo, conventional and/or lentiginous cN, and dysplastic cN), deep-penetrating cN, BAP1 -inactivated melanocytic lesions, pigmented epithelioid melanocytoma (PEM), acral melanocytic lesions (especially cM), nodular cM (less frequent), and nevoid cM (less frequent); -c-Kit/CD117: acral melanocytic lesions (especially cM), and lentigo maligna; -ALK, ROS1, pan-TRK (NTRK1, NTRK2, and NTRK3), RET, and MET: Spitz lesions (also Reed cN) and acral melanocytic lesions (especially cM); -β-catenin: deep-penetrating cN, rare cases of cM with a “deep-penetrating like silhouette”; -PRKAR1A: PEM; -BAP-1: BAP1 -inactivated melanocytic lesions, cM arising in blue cN and atypical cellular blue tumor (rare cases); -NF1: lentigo maligna, desmoplastic cM, and acral melanocytic lesions (especially cM); -IDH1: recently introduced category of melanocytoma. In this diagnostic setting, although the immunohistochemistry has shown excellent concordance rates with molecular biology techniques (PCR, FISH, and NGS) and, therefore, represents a reliable, feasible, time- and money-saving tool for investigating these lesions, it is usually adopted as a “screening tool”, and the molecular biology techniques are adopted to confirm and expand the genetic background of the analyzed lesions [ 108 , 109 , 110 , 111 , 112 , 113 , 114 , 115 , 116 , 117 , 118 , 119 , 120 , 121 ]. These techniques, differently from the immunohistochemistry, are able to identify the specific mutations and/or fusion partners; these data could provide relevant pathogenetic, prognostic, and therapeutic indications (specific mutations are associated with pharmacological resistances; additionally, specific fusions are associated with marked pharmacological sensitivity to kinase inhibitors) [ 108 , 109 , 110 , 111 , 112 , 113 , 114 , 115 , 116 , 117 , 118 , 119 , 120 , 121 ].…”

Conceptual Evolution and Current Approach to Spitz Tumors

“…In more recent years, genomic studies have shown that most Spitz neoplasms harbor serine–threonine kinase mutations (HRAS, or more rarely MAP2K1) or receptor tyrosine and serine–threonine kinase fusions (ALK, ROS1, NTRK1, NTRK3, MAP3K8, more rarely BRAF, RET, MET, NTRK2, ERB4, FGFR1, MAP3K3, PRKDC) [ 32 , 33 , 34 , 35 , 36 , 37 , 38 ]. Of note, BRAF or MAP3K8-fused cases may pursue a more aggressive course compared with tyrosine kinase–fused cases, especially in the presence of TERT promoter mutations.…”

“…The diagnosis of Spitz tumors may be difficult on clinical, dermoscopic, and histologic grounds [ 31 , 32 , 33 , 34 , 35 , 36 , 37 , 38 , 39 , 40 , 41 , 42 , 43 , 44 , 45 ]. Clinically, they may present either as pigmented, hypopigmented, or non-pigmented lesions.…”

“…Histologic diagnosis is currently based on microscopic characteristics (large spindle and/or epithelioid cells), possibly confirmed by an immunohistochemical or molecular evaluation of the genetic profile, including the presence of HRAS/MAP2K1 mutations and receptor tyrosine/serine–threonine kinase fusions. Importantly, Spitz tumors do not harbor GNAQ/GNA11 mutations, occurring in blue tumors, CTNNB1 mutation or APC loss, observed in deep penetrating tumors, PRKAR1A or PRKCA mutations, common in pigmented epithelioid melanocytomas, and BAP1 inactivation, characteristic of BAP1-inactivated melanocytic tumors [ 36 , 38 ] ( Table 1 ). By definition, Spitz melanoma has a kinase-fusion or HRAS aberration, while it does not carry the driver mutation of a conventional melanoma, such as BRAF/NRAS or NF1 mutation.…”