Perilesional Epigenomes Distinguish Melanocytic Nevus Subtypes.

Clinical Implications•Methylation patterns of normal skin may impact nevus evolution and presentation.•The epigenome of normal skin adjacent to primary melanocytic neoplasms may give insight into melanoma development.•Epigenetic profiling of healthy skin may reveal fertile soil more likely to give rise to melanocytic neoplasms. •Methylation patterns of normal skin may impact nevus evolution and presentation.•The epigenome of normal skin adjacent to primary melanocytic neoplasms may give insight into melanoma development.•Epigenetic profiling of healthy skin may reveal fertile soil more likely to give rise to melanocytic neoplasms. Melanocytic nevi are pigmented lesions commonplace in human skin and are often acquired during adolescence. Although most acquired melanocytic nevi (AMN) are clinically banal, their increased prevalence can indicate a higher risk for melanoma. Although there are several types of dermatoscopic nevus patterns (globular, reticular/nonspecific, and homogenous), the etiologies underlying each unique pattern are poorly understood. In their letter entitled “Distinct HOX gene family DNA methylation profiles in histologically normal skin dependent on dermoscopic pattern of adjacent nevi,” Muse et al., 2023Muse M.E. Schaider H. Oey H. Soyer H.P. Christensen B.C. Stark M.S. Distinct HOX gene family DNA methylation profiles in histologically normal skin dependent on dermoscopic pattern of adjacent nevi [e-pub ahead of print].J Invest Dermatol. 2023; (accessed XXX)https://doi.org/10.1016/j.jid.2023.03.1653Google Scholar report that the DNA methylation patterns within the normal skin adjacent to nevi are distinct between the globular and reticular nevi subtypes. Specifically, a series of HOX genes are hypermethylated and transcriptionally suppressed in the keratinocytes adjacent to globular nevi. These observations support two intriguing hypotheses: (i) that the epigenetic state of the keratinocyte, in conjunction with the mutational landscape of the melanocyte, dictates the growth pattern of AMN subtypes or (ii) that specific AMN subtypes epigenetically reprogram the surrounding keratinocytes. Globular nevi are often raised and are dermatoscopically characterized by brown globules throughout the lesion (Figure 1). Histologically, globular nevi are characterized by having junctional nests that correspond to brown globules and a prominent dermal component that gives the nevus its characteristic globular pattern (Figure 1). Reticular nevi are often flat and are dermatoscopically characterized by a pigmented and interconnected network that manifests histologically as a junctional nevus with thin and lengthened rete ridges (Figure 1). Cross-sectional studies have noted trends in the age and anatomic location distribution of dermoscopic nevus subtypes (Zalaudek et al., 2011Zalaudek I. Schmid K. Marghoob A.A. Scope A. Manzo M. Moscarella E. et al.Frequency of dermoscopic nevus subtypes by age and body site: a cross-sectional study.Arch Dermatol. 2011; 147: 663-670Google Scholar). Globular nevi have been reported to be more common during childhood and more prevalent on the upper trunk, whereas reticular/nonspecific nevi are more common during adulthood and more prevalent on the middle and lower back (Scope et al., 2016Scope A. Marchetti M.A. Marghoob A.A. Dusza S.W. Geller A.C. Satagopan J.M. et al.The study of nevi in children: principles learned and implications for melanoma diagnosis.J Am Acad Dermatol. 2016; 75: 813-823Google Scholar). However, these trends are not obligatory. The distinction between globular and reticular pigment networks in nevi appears to have a multifactorial influence, and the underlying cause of each respective subtype is unknown. To investigate the molecular differences between AMN subtypes, a team led by Mitchell Stark and Rick Sturm previously assembled a cohort of subtyped AMN specimens with matched uninvolved perilesional skin. In previous reports, the team documented the molecular characteristics of globular and reticular/nonspecific nevi using various DNA-profiling techniques (Muse et al., 2022Muse M.E. Bergman D.T. Salas L.A. Tom L.N. Tan J.M. Laino A. et al.Genome-scale DNA methylation analysis identifies repeat element alterations that modulate the genomic stability of melanocytic nevi.J Investig Dermatol. 2022; 142: 1893-1902.e7Google Scholar; Stark et al., 2018Stark M.S. Tan J.M. Tom L. Jagirdar K. Lambie D. Schaider H. et al.Whole-exome sequencing of acquired nevi identifies mechanisms for development and maintenance of benign neoplasms.J Invest Dermatol. 2018; 138 ([published correction appears in J Invest Dermatol 2018;138:2085]): 1636-1644Google Scholar; Tan et al., 2018Tan J.M. Tom L.N. Jagirdar K. Lambie D. Schaider H. Sturm R.A. et al.The BRAF and NRAS mutation prevalence in dermoscopic subtypes of acquired naevi reveals constitutive mitogen-activated protein kinase pathway activation.Br J Dermatol. 2018; 178: 191-197Google Scholar). In 2018, Stark et al., 2018Stark M.S. Tan J.M. Tom L. Jagirdar K. Lambie D. Schaider H. et al.Whole-exome sequencing of acquired nevi identifies mechanisms for development and maintenance of benign neoplasms.J Invest Dermatol. 2018; 138 ([published correction appears in J Invest Dermatol 2018;138:2085]): 1636-1644Google Scholar described an increase in insertions and deletions as well as copy number alterations (CNAs) in reticular/nonspecific nevi compared with those in globular nevi. In 2022, Muse et al., 2022Muse M.E. Bergman D.T. Salas L.A. Tom L.N. Tan J.M. Laino A. et al.Genome-scale DNA methylation analysis identifies repeat element alterations that modulate the genomic stability of melanocytic nevi.J Investig Dermatol. 2022; 142: 1893-1902.e7Google Scholar observed that reticular/nonspecific nevi had ∼60,000 differentially methylated (DM) CpG loci compared with adjacent normal skin, with the promoter of PTEN having the greatest proportion of hypermethylation. Globular nevi had no significant DM loci compared with normal skin. Both of these studies present evidence that different subtypes of benign AMN may have distinct developmental paths to nevus maturation driven by molecular disparities intrinsic to the melanocyte. In their latest effort to catalog the molecular characteristics of different AMN subtypes, Muse et al., 2023Muse M.E. Schaider H. Oey H. Soyer H.P. Christensen B.C. Stark M.S. Distinct HOX gene family DNA methylation profiles in histologically normal skin dependent on dermoscopic pattern of adjacent nevi [e-pub ahead of print].J Invest Dermatol. 2023; (accessed XXX)https://doi.org/10.1016/j.jid.2023.03.1653Google Scholar took a new approach: instead of comparing the nevi, they conducted a multiomic comparison of the uninvolved skin adjacent to each subtype. Although the cellular composition of the perilesional skin did not differ, Muse et al., 2023Muse M.E. Schaider H. Oey H. Soyer H.P. Christensen B.C. Stark M.S. Distinct HOX gene family DNA methylation profiles in histologically normal skin dependent on dermoscopic pattern of adjacent nevi [e-pub ahead of print].J Invest Dermatol. 2023; (accessed XXX)https://doi.org/10.1016/j.jid.2023.03.1653Google Scholar reported 696 hypermethylated loci in the skin adjacent to globular nevi compared with those in the skin adjacent to reticular/nonspecific nevi. The DM loci were enriched for HOX genes (including HOXA9, HOXA10-AS, and HOXD4), which were not only hypermethylated within globular perilesional skin but also correspondingly transcriptionally suppressed (Figure 1). One interpretation of these observations is that the differential expression of HOX genes in keratinocytes dictates the positioning and subtype of an incipient nevus. Indeed, previous studies have shown that distal dermal fibroblast cell states are epigenetically maintained through the expression of HOXA13 (Rinn et al., 2008Rinn J.L. Wang J.K. Allen N. Brugmann S.A. Mikels A.J. Liu H. et al.A dermal HOX transcriptional program regulates site-specific epidermal fate.Genes Dev. 2008; 22: 303-307Google Scholar). Furthermore, the microenvironment in which a melanocyte grows can influence its phenotype (Weiss et al., 2022Weiss J.M. Hunter M.V. Cruz N.M. Baggiolini A. Tagore M. Ma Y. et al.Anatomic position determines oncogenic specificity in melanoma.Nature. 2022; 604: 354-361Google Scholar; Yamaguchi et al., 2004Yamaguchi Y. Itami S. Watabe H. Yasumoto K.I. Abdel-Malek Z.A. Kubo T. et al.Mesenchymal-epithelial interactions in the skin: increased expression of dickkopf1 by palmoplantar fibroblasts inhibits melanocyte growth and differentiation.J Cell Biol. 2004; 165: 275-285Google Scholar). It is therefore plausible that the DM observed in this study drives site-specific HOX gene expression in human skin and the subsequent site-specific preference for globular nevi formation. This intriguing hypothesis could be confirmed in future studies using cohorts assembled to directly query the relationship between anatomic site and specific HOX gene DM. The presented study is among a growing body of evidence that the growth and presentation of primary melanocytic neoplasms adhere to a seed and soil model comparable with that so often invoked to describe metastatic organotropism. Recent studies have shown that the microenvironments in which genetically transformed melanocytes grow dictate the subtype of melanoma that arises. Transformation in primary human melanocytes in vitro by BRAFV600E is dependent on the environmental conditions in which the cells are grown (McNeal et al., 2021McNeal A.S. Belote R.L. Zeng H. Urquijo M. Barker K. Torres R. et al.BRAFV600E induces reversible mitotic arrest in human melanocytes via microRNA-mediated suppression of AURKB.Elife. 2021; 10e70385Google Scholar). Recent work in zebrafish supports a model in which only the correct combination of a specific anatomic location of a melanocyte to a specific oncogenic alteration triggers transformation. Specifically, anatomic-specific HOX13 genes in the fins of fish determine the transformation capacity of melanocytes driven by CRKL amplification (Weiss et al., 2022Weiss J.M. Hunter M.V. Cruz N.M. Baggiolini A. Tagore M. Ma Y. et al.Anatomic position determines oncogenic specificity in melanoma.Nature. 2022; 604: 354-361Google Scholar). Cell states of normal melanocytes are also influenced by neighboring stromal cells. Anatomic-specific signaling from fibroblasts in volar skin decreases melanin production in melanocytes (Yamaguchi et al., 2004Yamaguchi Y. Itami S. Watabe H. Yasumoto K.I. Abdel-Malek Z.A. Kubo T. et al.Mesenchymal-epithelial interactions in the skin: increased expression of dickkopf1 by palmoplantar fibroblasts inhibits melanocyte growth and differentiation.J Cell Biol. 2004; 165: 275-285Google Scholar). These studies broadly support the hypothesis that skin in different anatomic sites comprises unique microenvironments (soils) that are selectively permissive to distinct melanocyte phenotypes in normal and pathologic situations, including the oncogenic growth of specific combinations of melanocyte transcriptomes and mutational landscapes (seeds). The Letter by Muse et al., 2023Muse M.E. Schaider H. Oey H. Soyer H.P. Christensen B.C. Stark M.S. Distinct HOX gene family DNA methylation profiles in histologically normal skin dependent on dermoscopic pattern of adjacent nevi [e-pub ahead of print].J Invest Dermatol. 2023; (accessed XXX)https://doi.org/10.1016/j.jid.2023.03.1653Google Scholar presents evidence for the seed and soil hypothesis for AMN subtype growth using clinical specimens. By this model, a subset of skin that expresses HOXA9, HOXA10-AS, and HOXD4 is permissive to the growth of melanocytes transformed by high CNA, resulting in a subsequent AMN of the reticular/nonspecific nevi subtype. However, the study does not profile skin specimens from comparable anatomic locations that are distant from nevi. Moreover, this interpretation does not account for reports that nevi patterns can undergo transitions from globular to reticular over time (Fortina et al., 2012Fortina A.B. Zattra E. Bernardini B. Alaibac M. Peserico A. Dermoscopic changes in melanocytic naevi in children during digital follow-up.Acta Derm Venereol. 2012; 92: 427-429Google Scholar). Thus, an equally intriguing and plausible interpretation is a terraforming model, whereby high CNA melanocytes of the reticular/nonspecific nevi subtype epigenetically reprogram adjacent skin. Globular AMN that acquire additional genetic alterations might then influence DNA methylation in perilesional skin and undergo a subtype transition. This interpretation is consistent with the findings of longitudinal studies that observe a higher incidence of globular nevi in young children than a higher incidence of reticular nevi in adulthood. These two models are not mutually exclusive: molecular changes intrinsic to tumor cells could trigger epigenetic alterations within perilesional skin, which in turn could influence the growth pattern of the nevus. In summary, Muse et al., 2023Muse M.E. Schaider H. Oey H. Soyer H.P. Christensen B.C. Stark M.S. Distinct HOX gene family DNA methylation profiles in histologically normal skin dependent on dermoscopic pattern of adjacent nevi [e-pub ahead of print].J Invest Dermatol. 2023; (accessed XXX)https://doi.org/10.1016/j.jid.2023.03.1653Google Scholar have provided compelling evidence from clinical specimens that the epigenetic state of perilesional skin is distinct between AMN subtypes. Their identification of differential HOX gene expression, in particular, suggests that differential keratinocyte DNA methylation influences the positioning of nevocytes. Their data are consistent with two fascinating models: a seed and soil model whereby the epigenetic state of the surrounding skin environment dictates the type of acquired melanocytic neoplasm growth and presentation and a tumor terraforming model whereby distinct subtypes of nevi differentially reprogram the epigenomes of the adjacent skin cells. Future studies should be initiated to distinguish between these models as well as to investigate the extent to which these mechanisms influence the growth and presentation of malignant melanocytic neoplasms. The authors state no conflict of interest. Distinct HOX gene family DNA methylation profiles in histologically normal skin dependent on dermoscopic pattern of adjacent neviJournal of Investigative DermatologyPreviewAcquired melanocytic nevi can be classified using dermoscopy and have previously been demonstrated to have to distinct molecular profiles (Muse et al., 2022, Stark et al., 2018, Tan et al., 2018). Perilesional skin occurring adjacent to nevi is variable due to differences in skin color, body site, and sun damage which may include solar elastosis, freckling, and increase in pigmented solar lentigines (Rosendahl and Marozava, 2019). Sun-exposed skin has been found to be awash with somatic mutations (Martincorena et al., 2015, Stark et al., 2018), which vary according to body site (Fowler et al., 2021), and are also commonly found in cutaneous malignancies including melanoma. Full-Text PDF