Is pigmented spindle cell nevus of Reed the result of genomic fusions?
Acta Eruditorum
Dr. Schwarzenberger is the former physician editor of DermWorld. She interviews the author of a recent study each month.
By Kathryn Schwarzenberger, MD, February 1, 2019
In this month’s Acta Eruditorum column, Physician Editor Kathryn Schwarzenberger, MD, talks with Pedram Gerami, MD, about his recent American Journal of Surgical Pathology article, “Genomic fusions in pigmented spindle cell nevus of Reed.”
Dr. Schwarzenberger: You and your colleagues recently published your findings on the genomic fusions in pigmented spindle cell nevus (PSCN) of Reed. Can you briefly summarize your findings for those who may have not yet read your article?
Dr. Gerami: Pigmented spindle cell nevus of Reed is considered a morphologic variant of Spitz nevus — characterized by heavily pigmented spindle-shaped melanocytes. It can often be confused with, or misdiagnosed as, melanoma from both a clinical and histologic perspective. Recently it has been recognized that a significant proportion of Spitz nevi are the result of genomic fusions resulting in activation of certain oncogenes. These genes may be rearranged to a number of partners, but these fusions in melanocytic neoplasms result in constitutive activation of the kinase and increase cellular proliferation, leading to development of a Spitzoid neoplasm. Because of their similarities to Spitz, we hypothesized that PSCN of Reed might also be initiated by similar kinase fusions.
When we performed mRNA sequencing on 23 PSCN of Reed, we found more than half of our cases had a specific fusion involving the gene NTRK3. When we included other fusions previously described in Spitz, 78% of these PSCN of Reed had a fusion as an initiating genomic event. Each case only had one initiating event, and none had an initiating somatic mutation typically associated with melanocytic lesions like BRAF or NRAS. In terms of histology, the cases with NTRK3 fusions had classic features of Reed nevi but tended to have adnexal involvement and to occur in younger patients. We also sequenced a number of other atypical melanocytic neoplasms, including acral and mucosal melanomas, pigmented epithelioid melanocytomas, Spitz nevi, atypical Spitz tumors, and Spitzoid melanomas. Of these atypical lesions, we only found NTRK3 fusions in 3% of Spitz nevi and none in the other types. Interestingly, these NTRK3 Spitz had exclusively spindle-shaped melanocytes and adnexal involvement — similar to our PSCN of Reed — but were different in that they had very little pigment.
Altogether, these findings suggested to us that NTRK3 fusions are the most common and characteristic initiating genomic event for PSCN of Reed. In contrast, NTRK3 fusions have rarely been found or reported in melanoma.
Dr. Schwarzenberger: Can you help us understand the techniques that allowed you to make these findings?
Dr. Gerami: Our work has been enabled by next generation sequencing, which is the most comprehensive genomic assay and is becoming more popular. NGS can help us look at the whole genome, exome, transcriptome, or epigenome, or take a more targeted approach to understand the genomic changes in a tumor.
Compared to traditional Sanger sequencing, NGS can generate more genomic data with a smaller initial amount of DNA or RNA with a relatively short turnaround time. In simple terms, like in Sanger sequencing, a sequencer detects the addition of fluorescently-labeled nucleotides to template DNA strands. The advantage is that NGS analyzes millions of DNA fragments at the same time.
We used mRNA sequencing in this study to look for structural rearrangements, such as gene fusions. We looked at the whole transcriptome to find areas of mRNA transcripts that would code for a functional protein, but contain two genes that would not normally be located next to each other. Then, using fluorescence in situ hybridization, we used fluorescent probes to confirm that the genes we identified moved to a new location in the DNA of the tumor.
Fortunately, NGS is becoming cheaper and more precise, but much more work must be done to understand what changes in the genome are important in determining the classification and behavior of melanocytic tumors.
Dr. Schwarzenberger: Do these and other molecular abnormalities detected in spitzoid nevi have clinical significance, or are they used more as a way to classify these pigmented lesions?
Dr. Gerami: Because of recent advances in sequencing technology and our understanding of genomics, we are now able to incorporate this molecular data into the classification of melanocytic lesions in addition to clinical and histopathologic features. While most Spitz and Reed nevi can be diagnosed by microscopic methods alone, there are some cases with overlapping features with melanoma. Since NTRK3 fusions are rare in melanoma and contrastingly the most common melanoma mutations such as BRAF or NRAS mutations are rare in Spitz and Reed nevi, these differences can be leveraged to help diagnose difficult cases. While no single finding is definitive, the genomic initiating event can be included in the assessment when diagnosing morphologically challenging cases.
Dr. Schwarzenberger: Will these and other molecular studies help us distinguish between a PSCN of Reed and a melanoma?
Dr. Gerami: While no single data point can tell with 100% certainty if a melanocytic lesion is a PSCN of Reed or a melanoma, the identification of the initiating genomic event can be part of this assessment. The identification of an NTRK3 fusion highly favors a diagnosis of Reed nevus over melanoma. Although uncommon, it is possible for a NTRK3 fusion neoplasm to progress to melanoma. Alternatively, canonical BRAF and NRAS mutations — which are so typical of melanoma — are relatively rare in PSCN. Hence, this information can be included in the pathologist’s assessment.
Dr. Schwarzenberger: Next gen sequencing or fluorescent in situ hybridization (FISH): Should we order one or both, and, if so, when? Does the clinician need to request these studies, or will the pathologist know when to order them?
Dr. Gerami: Next generation sequencing is currently used for theragnostic purposes. By using identification-specific drivers, this can inform oncologists of potential therapeutic options in known cases of melanoma. Currently, next generation sequencing has a limited role in diagnosis and more studies are needed to show that the specific data points and mutations identified can play a role in diagnosing tumors. I believe this will happen over time. Currently, fluorescence in situ hybridization is a simpler targeted method with proven value as a diagnostic tool.
Dr. Gerami is the director of the Skin Cancer Institute of Northwestern Medical Group (SCIN-Med), and the director of the Melanoma Program at SCIN-Med. He also serves as professor of dermatology and pathology at Northwestern Medicine. His article appeared in The American Journal of Surgical Pathology. doi: 10.1097/PAS.0000000000001074.
