NGS-Based Analysis of Atypical Deep Penetrating Nevi

Abstract

Deep penetrating nevi (DPNs) are rare melanocytic neoplasms consisting of pigmented spindled or epithelioid melanocytes with a distinctive wedge-shaped configuration showing activation of the WNT pathway, with unusual cyto-architectural features. It is unclear whether they show a distinct genomic profile associated with a diverse metastatic potential. We describe herein a cohort of 21 atypical DPNs analyzed by next-generation sequencing using the Ion AmpliSeq™ Comprehensive Cancer Panel. We found that β-catenin exon 3 was mutated in 95% and MAP kinase pathway genes in 71% of the cases. Less frequent mutations were observed in HRAS (19%) and MAP2K1 (24%). Isocitrate dehydrogenases 1 (IDH1) mutations, including R132C, V178I, and S278L, were identified in 38% of cases and co-existed with BRAF/HRAS mutations. The only case with progressive nodal disease carried alterations in the β-catenin pathway and mutations in IDH1 and NRAS (codon 61). By a comprehensive mutation analysis, we found low genetic heterogeneity and a lack of significant associations between specific gene mutations and histopathological features, despite atypical features. Whether the acquisition of an NRAS or IDH1 mutation in an atypical DPN may represent a molecular evolution implying a pathway to melanoma progression should be confirmed in a larger series.

Keywords: atypical deep penetrating nevus; borderline/atypical deep penetrating nevus; deep penetrating nevus (DPN); next-generation sequencing (NGS); β-catenin.

Figure 1

Case 2—male, 12 years old, shoulder. (A) Melanocytic tumor with an inverted triangle-like downward architecture in the dermis and subcutis. (40×, scale bar 500 µm); (B) short fascicles of spindled, ovoid, and occasionally epithelioid melanocytes (100×, scale bar 100 µm); (C) melanocytes intermingled with scattered melanophages (200×, scale bar 50 µm); (D) some melanocytes showing enlarged and hyperchromatic nuclei (400×, scale bar 25 µm). Inset: β-catenin staining shows nuclear positivity (400×, scale bar 25 µm). (E) Mutational profile: driver gene mutations and additional pathogenic alterations.

Figure 2

Case 3—female, 19 years old, back. (A) Clinical image showing a dome-shaped pigmented nodule on the back; (B) highly cellular dermal-based proliferation with a deep wedge-shaped configuration (40×, scale bar 500 µm); (C) scattered melanophages admixed with melanocytes (200×, scale bar 50 µm); (D) enlarged, hyperchromatic nuclei (400×, scale bar 25 µm). Inset: β-catenin immunohistochemical expression at nuclear level (400×, scale bar 25 µm). (E) Mutational profile: driver gene mutations and additional pathogenic alterations.

Figure 3

Case 9—male, 16 years old, back. (A) Wedge-shaped silhouette of a pigmented combined melanocytic tumor involving the dermis (40×, scale bar 500 µm); (B) fascicles and large aggregates of plump oval and epithelioid melanocytes combined with ovoid conventional melanocytes (100×, scale bar 100 µm); (C) oval melanocytes show a pale or dusty cytoplasm and contain fine melanin granules (200×, scale bar 50 µm); (D) oval melanocytes with hyperchromatic nuclei and pseudo-nuclear inclusions are seen intermingled with cytologically bland conventional melanocytes (400×, scale bar 25 µm). Inset: β-catenin staining shows nuclear positivity (400×, scale bar 25 µm). (E) Mutational profile: driver gene mutations and additional pathogenic alterations.

Figure 4

Case 16—male, 46 years old, right ear. (A) Asymmetric pigmented melanocytic tumor involving the dermis and subcutis and showing an expansile bulbous pattern at the base (40×, scale bar 500 µm); (B) the tumor is highly cellular and is composed of pigmented cells in plexiform pattern (100×, scale bar 100 µm); (C) several melanophages are seen within the melanocytic proliferation (200×, scale bar 50 µm); (D) melanocytes show a dusty-appearing pigmented cytoplasm and show enlarged nuclei (400×, scale bar 25 µm). Inset: Tumor cells show β-catenin expression at nuclear level (400×, scale bar 25 µm). (E) Mutational profile: driver gene mutations and additional pathogenic alterations.

Figure 5

Case 17—female, 43 years old, second interdigital space, right hand. (A) Asymmetric melanocytic tumor involving the dermis and subcutis (40×, scale bar 500 µm); (B) the tumor is composed of pigmented spindle and ovoid cells in a plexiform growth pattern (200×, scale bar 100 µm); (C) melanocytes contain fine melanin granules, and melanophages are admixed (400×, scale bar 50 µm). Inset: Immunostaining for β-catenin shows that melanocytes retain nuclear expression for this marker (400×, scale bar 25 µm). (D) Representative image of hematoxylin and eosin (H&E) staining of the positive right axillary sentinel lymph node; subsequent lymphadenectomy showed an additional positive axillary lymph node (200×, scale bar 50 µm). (E) Mutational profile: driver gene mutations and additional pathogenic alterations.