Genetic Analysis of Epidermal Inclusion Cysts Reveals NEK9 Variants as a Common Driver of Comedogenesis and Cyst Formation.

Genetic Analysis of Epidermal Inclusion Cysts Reveals NEK9 as a Common Driver of Comedogenesis and Cyst Formation - PMC Skip to main content An official website of the United States government Here's how you know Here's how you know Search Log in Primary site navigation Search Log in Search PMC Full-Text Archive Search in PMC Journal List User Guide As a library, NLM provides access to scientific literature. Inclusion in an NLM database does not imply endorsement of, or agreement with, the contents by NLM or the National Institutes of Health. Learn more: PMC Disclaimer | PMC Copyright Notice J Invest Dermatol . Author manuscript; available in PMC: 2026 Jun 1. Published in final edited form as: J Invest Dermatol. 2024 Dec 18;145(6):1516–1519.e1. doi: 10.1016/j.jid.2024.07.039 Genetic Analysis of Epidermal Inclusion Cysts Reveals NEK9 as a Common Driver of Comedogenesis and Cyst Formation Katharine T Ellis 1, 2 , Peggy Myung 2, 3, 4, 5, 6 , Jeffrey Cohen 2, 7 , Keith A Choate 1, 2, 3 Author information Article notes Copyright and License information 1 Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA 2 Department of Dermatology, Yale University School of Medicine, New Haven, CT 06520, USA 3 Department of Pathology, Yale University School of Medicine, New Haven, CT 06520, USA 4 Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520, USA 5 Yale Cancer Center, New Haven, CT 06520, USA 6 Yale Stem Cell Center, New Haven, CT 06520, USA. 7 Department of Biomedical Informatics and Data Science, Yale University School of Medicine, CT 06520, USA Author Contributions Statement Conceptualization: KTE, KAC; Formal Analysis: KTE; Resources: JC; Writing- Original Draft: KTE; Writing - Review and Editing: KTE, PM, JC, KAC ✉ Corresponding Author: Keith A. Choate, Department of Dermatology, Yale University School of Medicine, 333 Cedar Street, New Haven, Connecticut 06510, USA. keith.choate@yale.edu Issue date 2025 Jun. Keywords: comedone, somatic mosaicism, blackhead, epidermoid cyst, keratinocyte differentiation PMC Copyright notice PMCID: PMC12103287  NIHMSID: NIHMS2043200  PMID: 39706256 The publisher's version of this article is available at J Invest Dermatol To the Editor, Follicular occlusion is a process central to many inflammatory and cystic disorders of the skin. ( Cunliffe et al., 2004 , Pink et al., 2018 ). In comedogenesis, follicular occlusion occurs as keratinaceous debris produced by infundibular cells within hair follicles forms a plug, referred to as a comedone ( Cunliffe et al., 2004 ). Comedones vary in size and severity, with some progressing to cyst formation. These lesions can become inflamed, with persistent inflammation leading to destruction of follicular architecture. Comedones can be precipitated by hormonal fluctuations, pathogens such as C. acnes , inflammation, and chemical exposures ( Toyoda and Morohashi, 2001 ). While most frequently associated with acne vulgaris (AV) in the setting of puberty, comedones also present across the lifespan as components of genetic disorders. Both monogenic inherited and somatic mosaic genodermatoses featuring comedones have been identified, including nevus comedonicus (NC), and disorders related to FGFR2 variants. Apert syndrome, associated with germline variants in FGFR2, presents with early onset, severe AV in many cases ( Solomon et al., 1970 ). Somatic FGFR2 variants have been reported in segmental acneiform nevus, a localized form of Apert syndrome with streaks of comedones ( Xie et al., 2023 ). Similarly, NC presents at birth with smooth, linear patches of comedones with inflammatory cysts developing over time. NC is associated with somatic, damaging NEK9 variants acquired in utero ( Levinsohn et al., 2016 ). Because genetic variants have been associated with comedogenesis in these disorders, we posited that acquired somatic variants could contribute to the pathogenesis of comedogenesis in other comedonal disorders. Epidermal inclusion cysts (EICs) are a common acquired comedonal disorder consisting of an isolated lesion comprised of a single comedone with an underlying cyst. Like comedonal lesions in NC, EICs are filled with keratinaceous debris and can become inflamed ( Figure 1b ). There is a correlation between EIC incidence and age that parallels the increase in somatic variant burden with age, thus EICs represent a comedonal disorder in which somatic variants may contribute to pathogenesis ( Zito, 2023 ). To investigate contributions of somatic variants to comedogenesis, we recruited 7 male and 6 female subjects (mean age 56) undergoing routine excision of EICs ( Supplementary Data Table S1. ). Subjects provided written, informed consented to a protocol approved by the Yale University Human Investigation Committee (#0809004252). Fresh tissue and saliva were obtained. DNA extraction, sequencing, and analyses were performed according to published methods ( Levinsohn et al., 2016 ). Briefly, exome capture was performed by the Yale Center for Genomic Analysis (xGen V2 capture kit, IDT), sequencing performed via Illumina NovaSeq 6000 sequencer (150bp paired-end reads) to 200X (tissue) and 80X (saliva). Read processing and variant identification was performed using GATK best practices. Variants with allele frequencies >0.01 in the gnomAD database, variants shared by saliva and EIC tissue (presumed germline), synonymous, intronic, and benign (ClinVar) variants were excluded. Figure 1. Epidermal Inclusion Cysts Share Genetic Similarities with Nevus Comedonicus. Open in a new tab a) Gross morphology of EIC with comedone shown at asterisk (left). b) H&E staining of NC and EIC lesions. Normal hair follicle (left), NC (center) and EIC (right) sections of subcutaneous cystic structure lined by an acanthotic epithelium with granular differentiation marked with arrowhead (white in NC, black in EIC) and accumulated keratin within the lumen with asterisk (white in NC, black in EIC). Scale bars = 500μm. c) Distribution of NEK9 variants identified in NC alone (orange), NC and EICs (purple), or EICs alone (blue) across NEK9 functional domains. We found heterozygous damaging, somatic, recurrent NEK9 variants present in tissue and absent from saliva in 12/14 cases. 9/12 variants were previously identified in NC. The 3 previously unidentified variants affect residues adjacent to reported variants within the RCC1 domain, within in a 19-amino acid stretch ( Fig. 1c ). The concentration of variants at a single locus within the kinase domain and a 19-residue stretch of the RCC1 domain indicates these two regions of the NEK9 protein may be essential to follicular function. The median age of subjects was 56, accounting for a moderate protein-damaging somatic variant burden (range: 0.4–4 variants/megabase) consistent with previously published values ( Martincorena et al., 2015 ). NEK9 was the only gene with recurrent, somatic, rare, damaging variants identified in >2 samples. NEK9 variants were absent from excised normal skin adjacent to EIC-10. EIC-11 and EIC-12 samples were excised from the same individual, 20cm apart. Each contained a different NEK9 variant, indicating independent mutational events. The presence of these variants in 12/14 EICs, their absence in saliva and unaffected adjacent tissue, and their independent identification from two lesions from one patient together highlight a robust association (probability of identifying NEK9 variant vs. any other locus in genome 12 times = 7.85 E−73 ) between acquired somatic NEK9 variants and EIC pathogenesis. There was no statistically significant correlation between gender and body site, nor age and variant domain (data not shown). NEK9 is a mitotic spindle kinase with roles in multiple cellular processes; the heterozygous nature of these mutations suggest they are gain of function. Our lab has previously shown the p.I167T variant results in increased phosphorylation of the activating reside of NEK9 in vitro , consistent with a gain-of-function variant ( Levinsohn et al., 2016 ). Surprisingly, no UV signature (C>T, G>A) was observed, suggesting other mechanisms may drive mutagenesis. Prior studies suggest that specific cell populations, such as infundibular keratinocytes, drive comedogenesis via an unknown mechanism ( Clayton et al., 2019 ). We show ectopic expression of the epidermal differentiation marker keratin 10 (K10), normally restricted to terminally differentiated epidermal keratinocytes, within the cyst wall of EICs, consistent with defective keratinocyte differentiation ( Figure 2a ). We therefore propose EICs and similar comedogenic disorders may arise from genotoxic insults which induce NEK9 variants in epidermal and follicular keratinocytes, alter their functions, and result in dysregulated differentiation and proliferation within hair follicles ( Figure 2b ). Because of its involvement in multiple comedogenic and cystic genodermatoses, we propose NEK9 and its associated cellular functions to be central to the molecular underpinnings driving these processes. Figure 2. Keratinocyte differentiation is dysregulated in EICs. Open in a new tab a) Immunolocalization of Keratin 10 (K10) in green on FFPE section from healthy control (left) and EIC (right). Sebaceous gland marked with white dashed line. Brightness and contrast increased identically across channels and images for visual clarity. Scale bars = 200μm. b) Schematic showing the suggested mechanism of acquired somatic NEK9 variants leading to ectopic expression of epidermal (K10, green) markers in EIC cyst wall. Sebaceous gland shown in beige. Here we show somatic mosaic damaging heterozygous variants in NEK9 drive comedogenesis in EICs. We sequenced fresh tissue from 14 EICs, finding somatic NEK9 variants in 12/14. 9/12 were identical to variants we previously reported in NC, a rare mosaic genodermatoses that presents at birth. We show ectopic K10 expression within EIC cyst wall, indicating that comedogenesis involves aberrant keratinocyte differentiation within the follicular unit. Together with our previous reports, these genetic analyses of NC and EICs support NEK9 variants as a driver of comedogenesis during both follicular cytodifferentiation in embryogenesis and hair cycling. The heterozygous nature of these somatic NEK9 variants implies the NEK9 protein may play central role in follicular homeostasis. Mechanistically, we propose NEK9 variants likely accrue in follicular keratinocytes, resulting in dysfunctional NEK9 activity which may drive fate specification defects, specifically a transition from follicular to epidermal fates within the follicle, as a key component of comedogenesis. Ultimately, the presence of NEK9 variants in both NC and EICs represents a shared biologic origin for comedones that can be used as a paradigm to study the process of comedogenesis in vivo. Beyond the scope of comedonal disorders, our work emphasizes the critical role genetic variation, particularly somatic mosaicism, can play in explaining common dermatologic diseases of previously unknown origins. Supplementary Material 1 NIHMS2043200-supplement-1.pdf (43.2KB, pdf) Acknowledgements. We would like to thank the photographed patient for granting permission to publish their image. We would also like to extend our thanks and gratitude to Jing Zhou, Ronghua Hu, and the Yale Center for Genomic Analysis (YCGA) for technical assistance. We would like to thank Jim Knight for computational assistance. Research was supported by NIAMS R01AR071491 (KAC) and NIAMS F31AR082696 (KTE), the NIH Medical Scientist Training Program Training Grant T32GM136651 (KTE), NIAMS R01AR076420 (PM), and 1S10OD030363–01A1 (YCGA). Abbreviations: AV acne vulgaris NC nevus comedonicus EIC epidermal inclusion cysts K10 keratin 10 Footnotes Conflict of Interest Statement. KAC is an investigator in clinical trials sponsored by Abbvie, Boehringer Ingelheim, Janssen, and Regeneron. He is a consultant for Mitsubishi Tanabe. JMC serves on a data and safety monitoring board for Advarra and has been a consultant for Novartis and Takeda. Ethics Statement. This study was performed in accordance with the Declaration of Helsinki. Collection of human tissue samples for this study was approved as part of the study protocol. This human study was approved by Yale University Human Investigation Committee-approval: 0809004252. All adult participants provided written informed consent to participate in this study. Publisher's Disclaimer: This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. Data Availability Statement: Datasets related to this article can be found at https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs003776.v1.p1 , hosted at dbGaP. References Clayton RW, Göbel K, Niessen CM, Paus R, van Steensel MAM, Lim X. Homeostasis of the sebaceous gland and mechanisms of acne pathogenesis. Br J Dermatol 2019;181(4):677–90. [ DOI ] [ PubMed ] [ Google Scholar ] Cunliffe WJ, Holland D, Jeremy A. Comedone formation: etiology, clinical presentation, and treatment. Clinics in dermatology 2004;22(5):367–74. [ DOI ] [ PubMed ] [ Google Scholar ] Levinsohn JL, Sugarman JL, McNiff JM, Antaya RJ, Choate KA. Somatic mutations in NEK9 cause nevus comedonicus. The American Journal of Human Genetics 2016;98(5):1030–7. [ DOI ] [ PMC free article ] [ PubMed ] [ Google Scholar ] Martincorena I, Roshan A, Gerstung M, Ellis P, Van Loo P, McLaren S, et al. High burden and pervasive positive selection of somatic mutations in normal human skin. Science 2015;348(6237):880–6. [ DOI ] [ PMC free article ] [ PubMed ] [ Google Scholar ] Pink A, Anzengruber F, Navarini AA. Acne and hidradenitis suppurativa. Br J Dermatol 2018;178(3):619–31. [ DOI ] [ PubMed ] [ Google Scholar ] Solomon LM, Fretzin D, Pruzansky S. Pilosebaceous abnormalities in Apert’s syndrome. Archives of Dermatology 1970;102(4):381–5. [ PubMed ] [ Google Scholar ] Toyoda M, Morohashi M. Pathogenesis of acne. Medical Electron Microscopy 2001;34:29–40. [ DOI ] [ PubMed ] [ Google Scholar ] Xie Y, Liu B, Wu Z. Segmental hypopigmented acneiform nevus with FGFR2 gene mutation. An Bras Dermatol 2023;98(5):710–2. [ DOI ] [ PMC free article ] [ PubMed ] [ Google Scholar ] Zito PS R Epidermoid Cysts. StatPearls; 2023. [ Google Scholar ] Associated Data This section collects any data citations, data availability statements, or supplementary materials included in this article. Supplementary Materials 1 NIHMS2043200-supplement-1.pdf (43.2KB, pdf) Data Availability Statement Datasets related to this article can be found at https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs003776.v1.p1 , hosted at dbGaP. ACTIONS View on publisher site PDF (1004.5 KB) Cite Collections Permalink RESOURCES Similar articles Cited by other articles Links to NCBI Databases Follow NCBI NCBI on X (formerly known as Twitter) NCBI on Facebook NCBI on LinkedIn NCBI on GitHub NCBI RSS feed Connect with NLM NLM on X (formerly known as Twitter) NLM on Facebook NLM on YouTube National Library of Medicine 8600 Rockville Pike Bethesda, MD 20894 Web Policies FOIA HHS Vulnerability Disclosure Help Accessibility Careers NLM NIH HHS USA.gov Back to Top

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