Although squamous cell carcinomas (SCC) are the most frequent human solid tumor at many anatomic sites, the driving molecular alterations underlying their progression from precursor lesions are poorly understood, especially in the context of photodamage. Therefore, we used high-depth, targeted next-generation sequencing (NGS) of RNA and DNA from routine tissue samples to characterize the progression of both well- (cutaneous) and poorly (ocular) studied SCCs. We assessed 56 formalin-fixed paraffin-embedded (FFPE) cutaneous lesions (n = 8 actinic keratosis, n = 30 carcinoma in situ [CIS], n = 18 invasive) and 43 FFPE ocular surface lesions (n = 2 conjunctival/corneal intraepithelial neoplasia, n = 20 CIS, n = 21 invasive), from institutions in the US and Brazil. An additional seven cases of advanced cutaneous SCC were profiled by hybrid capture-based NGS of >1500 genes. The cutaneous and ocular squamous neoplasms displayed a predominance of UV-signature mutations. Precursor lesions had highly similar somatic genomic landscapes to SCCs, including chromosomal gains of 3q involving SOX2, and highly recurrent mutations and/or loss of heterozygosity events affecting tumor suppressors TP53 and CDKN2A. Additionally, we identify a novel molecular subclass of CIS with RB1 mutations. Among TP53 wild-type tumors, human papillomavirus transcript was detected in one matched pair of cutaneous CIS and SCC. Amplicon-based whole-transcriptome sequencing of select 20 cutaneous lesions demonstrated significant upregulation of pro-invasion genes in cutaneous SCCs relative to precursors, including MMP1, MMP3, MMP9, LAMC2, LGALS1, and TNFRSF12A. Together, ocular and cutaneous squamous neoplasms demonstrate similar alterations, supporting a common model for neoplasia in UV-exposed epithelia. Treatment modalities useful for cutaneous SCC may also be effective in ocular SCC given the genetic similarity between these tumor types. Importantly, in both systems, precursor lesions possess the full complement of major genetic changes seen in SCC, supporting non-genetic drivers of invasiveness.
Subscribe to Journal
Get full journal access for 1 year
only $33.25 per issue
All prices are NET prices.
VAT will be added later in the checkout.
Tax calculation will be finalised during checkout.
Rent or Buy article
Get time limited or full article access on ReadCube.
All prices are NET prices.
Dotto GP, Rustgi AK. Squamous cell cancers: a unified perspective on biology and genetics. Cancer Cell. 2016;29:622–37.
Campbell JD, Yau C, Bowlby R, Liu Y, Brennan K, Fan H, et al. Genomic, pathway network, and immunologic features distinguishing squamous carcinomas. Cell Rep. 2018;23:194–212.
Pickering CR, Zhou JH, Lee JJ, Drummond JA, Peng SA, Saade RE, et al. Mutational landscape of aggressive cutaneous squamous cell carcinoma. Clin Cancer Res. 2014;20:6582–92.
Li YY, Hanna GJ, Laga AC, Haddad RI, Lorch JH, Hammerman PS. Genomic analysis of metastatic cutaneous squamous cell carcinoma. Clin Cancer Res. 2015;21:1447–56.
Inman GJ, Wang J, Nagano A, Alexandrov LB, Purdie KJ, Taylor RG, et al. The genomic landscape of cutaneous SCC reveals drivers and a novel azathioprine associated mutational signature. Nat Commun. 2018;9:3667.
Chitsazzadeh V, Coarfa C, Drummond JA, Nguyen T, Joseph A, Chilukuri S, et al. Cross-species identification of genomic drivers of squamous cell carcinoma development across preneoplastic intermediates. Nat Commun. 2016;7:12601.
Mueller SA, Gauthier MA, Ashford B, Gupta R, Gayevskiy V, Ch’ng S, et al. Mutational patterns in metastatic cutaneous squamous cell carcinoma. J Invest Dermatol. 2019;139:1449.
Zilberg C, Lee MW, Yu B, Ashford B, Kraitsek S, Ranson M, et al. Analysis of clinically relevant somatic mutations in high-risk head and neck cutaneous squamous cell carcinoma. Mod Pathol. 2018;31:275–87.
Galor A, Karp CL, Sant D, Joag M, Shalabi N, Gustafson CB, et al. Whole exome profiling of ocular surface squamous neoplasia. Ophthalmology. 2016;123:216–7.
Tabbara KF, Kersten R, Daouk N, Blodi FC. Metastatic squamous cell carcinoma of the conjunctiva. Ophthalmology. 1988;95:318–21.
Sayed-Ahmed IO, Palioura S, Galor A, Karp CL. Diagnosis and medical management of ocular surface squamous neoplasia. Expert Rev Ophthalmol. 2017;12:11–19.
Rosen T, Lebwohl MG. Prevalence and awareness of actinic keratosis: barriers and opportunities. J Am Acad Dermatol. 2013;68:S2–9.
Rowert-Huber J, Patel MJ, Forschner T, Ulrich C, Eberle J, Kerl H, et al. Actinic keratosis is an early in situ squamous cell carcinoma: a proposal for reclassification. Br J Dermatol. 2007;156(Suppl 3):8–12.
Boukamp P. Non-melanoma skin cancer: what drives tumor development and progression? Carcinogenesis. 2005;26:1657–67.
Campbell JD, Mazzilli SA, Reid ME, Dhillon SS, Platero S, Beane J, et al. The case for a Pre-Cancer Genome Atlas (PCGA). Cancer Prev Res. 2016;9:119–24.
Teixeira VH, Pipinikas CP, Pennycuick A, Lee-Six H, Chandrasekharan D, Beane J, et al. Deciphering the genomic, epigenomic, and transcriptomic landscapes of pre-invasive lung cancer lesions. Nat Med. 2019;25:517–25.
Bosic M, Kirchner M, Brasanac D, Leichsenring J, Lier A, Volckmar AL, et al. Targeted molecular profiling reveals genetic heterogeneity of poromas and porocarcinomas. Pathology. 2018;50:327–32.
Harms PW, Hovelson DH, Cani AK, Omata K, Haller MJ, Wang ML, et al. Porocarcinomas harbor recurrent HRAS-activating mutations and tumor suppressor inactivating mutations. Hum Pathol. 2016;51:25–31.
Shain AH, Yeh I, Kovalyshyn I, Sriharan A, Talevich E, Gagnon A, et al. The genetic evolution of melanoma from precursor lesions. N Engl J Med. 2015;373:1926–36.
Rodriguez-Paredes M, Bormann F, Raddatz G, Gutekunst J, Lucena-Porcel C, Kohler F, et al. Methylation profiling identifies two subclasses of squamous cell carcinoma related to distinct cells of origin. Nat Commun. 2018;9:577.
Kanellou P, Zaravinos A, Zioga M, Stratigos A, Baritaki S, Soufla G, et al. Genomic instability, mutations and expression analysis of the tumour suppressor genes p14(ARF), p15(INK4b), p16(INK4a) and p53 in actinic keratosis. Cancer Lett. 2008;264:145–61.
Nelson MA, Einspahr JG, Alberts DS, Balfour CA, Wymer JA, Welch KL, et al. Analysis of the p53 gene in human precancerous actinic keratosis lesions and squamous cell cancers. Cancer Lett. 1994;85:23–9.
Rehman I, Takata M, Wu YY, Rees JL. Genetic change in actinic keratoses. Oncogene. 1996;12:2483–90.
Jin Y, Jin C, Salemark L, Wennerberg J, Persson B, Jonsson N. Clonal chromosome abnormalities in premalignant lesions of the skin. Cancer Genet Cytogenet. 2002;136:48–52.
Garcia-Diez I, Hernandez-Munoz I, Hernandez-Ruiz E, Nonell L, Puigdecanet E, Bodalo-Torruella M, et al. Transcriptome and cytogenetic profiling analysis of matched in situ/invasive cutaneous squamous cell carcinomas from immunocompetent patients. Genes Chromosomes Cancer. 2019;58:164–74.
Mortier L, Marchetti P, Delaporte E, Martin de Lassalle E, Thomas P, Piette F, et al. Progression of actinic keratosis to squamous cell carcinoma of the skin correlates with deletion of the 9p21 region encoding the p16(INK4a) tumor suppressor. Cancer Lett. 2002;176:205–14.
Robinson DR, Wu YM, Vats P, Su F, Lonigro RJ, Cao X, et al. Activating ESR1 mutations in hormone-resistant metastatic breast cancer. Nat Genet. 2013;45:1446–51.
Gao J, Aksoy BA, Dogrusoz U, Dresdner G, Gross B, Sumer SO, et al. Integrative analysis of complex cancer genomics and clinical profiles using the cBioPortal. Sci Signal. 2013;6:pl1.
Cerami E, Gao J, Dogrusoz U, Gross BE, Sumer SO, Aksoy BA, et al. The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data. Cancer Disco. 2012;2:401–4.
Lazo de la Vega L, Samaha MC, Hu K, Bick NR, Siddiqui J, Hovelson DH, et al. Multiclonality and marked branched evolution of low-grade endometrioid endometrial carcinoma. Mol Cancer Res. 2019;17:731–40.
Mootha VK, Lindgren CM, Eriksson KF, Subramanian A, Sihag S, Lehar J, et al. PGC-1alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes. Nat Genet. 2003;34:267–73.
Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci USA. 2005;102:15545–50.
Alexandrov LB, Ju YS, Haase K, Van Loo P, Martincorena I, Nik-Zainal S, et al. Mutational signatures associated with tobacco smoking in human cancer. Science. 2016;354:618–22.
Martincorena I, Roshan A, Gerstung M, Ellis P, Van Loo P, McLaren S. et al. Tumor evolution. High burden and pervasive positive selection of somatic mutations in normal human skin. Science. 2015;348:880–6.
Durinck S, Ho C, Wang NJ, Liao W, Jakkula LR, Collisson EA, et al. Temporal dissection of tumorigenesis in primary cancers. Cancer Discov. 2011;1:137–43.
Kim N, Song M, Kim S, Seo Y, Kim Y, Yoon S. Differential regulation and synthetic lethality of exclusive RB1 and CDKN2A mutations in lung cancer. Int J Oncol. 2016;48:367–75.
Knudsen ES, Knudsen KE. Tailoring to RB: tumour suppressor status and therapeutic response. Nat Rev Cancer. 2008;8:714–24.
Pinto AP, Miron A, Yassin Y, Monte N, Woo TY, Mehra KK, et al. Differentiated vulvar intraepithelial neoplasia contains Tp53 mutations and is genetically linked to vulvar squamous cell carcinoma. Mod Pathol. 2010;23:404–12.
Yizhak K, Aguet F, Kim J, Hess JM, Kubler K, Grimsby J, et al. RNA sequence analysis reveals macroscopic somatic clonal expansion across normal tissues. Science. 2019;364:eaaw0726.
Reeves MQ, Kandyba E, Harris S, Del Rosario R, Balmain A. Multicolour lineage tracing reveals clonal dynamics of squamous carcinoma evolution from initiation to metastasis. Nat Cell Biol. 2018;20:699–709.
Cimino PJ, Robirds DH, Tripp SR, Pfeifer JD, Abel HJ, Duncavage EJ. Retinoblastoma gene mutations detected by whole exome sequencing of Merkel cell carcinoma. Mod Pathol. 2014;27:1073–87.
Harms PW, Harms KL, Moore PS, DeCaprio JA, Nghiem P, Wong MKK, et al. The biology and treatment of Merkel cell carcinoma: current understanding and research priorities. Nat Rev Clin Oncol. 2018;15:763–76.
Toll A, Salgado R, Yebenes M, Martin-Ezquerra G, Gilaberte M, Baro T, et al. MYC gene numerical aberrations in actinic keratosis and cutaneous squamous cell carcinoma. Br J Dermatol. 2009;161:1112–8.
Toll A, Salgado R, Yebenes M, Martin-Ezquerra G, Gilaberte M, Baro T, et al. Epidermal growth factor receptor gene numerical aberrations are frequent events in actinic keratoses and invasive cutaneous squamous cell carcinomas. Exp Dermatol. 2010;19:151–3.
South AP, Purdie KJ, Watt SA, Haldenby S, den Breems N, Dimon M, et al. NOTCH1 mutations occur early during cutaneous squamous cell carcinogenesis. J Invest Dermatol. 2014;134:2630–8.
Hosoda W, Chianchiano P, Griffin JF, Pittman ME, Brosens LA, Noe M, et al. Genetic analyses of isolated high-grade pancreatic intraepithelial neoplasia (HG-PanIN) reveal paucity of alterations in TP53 and SMAD4. J Pathol. 2017;242:16–23.
Baker SJ, Fearon ER, Nigro JM, Hamilton SR, Preisinger AC, Jessup JM, et al. Chromosome 17 deletions and p53 gene mutations in colorectal carcinomas. Science. 1989;244:217–21.
Lambert SR, Mladkova N, Gulati A, Hamoudi R, Purdie K, Cerio R, et al. Key differences identified between actinic keratosis and cutaneous squamous cell carcinoma by transcriptome profiling. Br J Cancer. 2014;110:520–9.
Ateenyi-Agaba C, Dai M, Le Calvez F, Katongole-Mbidde E, Smet A, Tommasino M, et al. TP53 mutations in squamous-cell carcinomas of the conjunctiva: evidence for UV-induced mutagenesis. Mutagenesis. 2004;19:399–401.
Seshacharyulu P, Ponnusamy MP, Haridas D, Jain M, Ganti AK, Batra SK. Targeting the EGFR signaling pathway in cancer therapy. Expert Opin Ther Targets. 2012;16:15–31.
Chae YK, Ranganath K, Hammerman PS, Vaklavas C, Mohindra N, Kalyan A, et al. Inhibition of the fibroblast growth factor receptor (FGFR) pathway: the current landscape and barriers to clinical application. Oncotarget. 2017;8:16052–74.
Mizrachi A, Shamay Y, Shah J, Brook S, Soong J, Rajasekhar VK, et al. Tumour-specific PI3K inhibition via nanoparticle-targeted delivery in head and neck squamous cell carcinoma. Nat Commun. 2017;8:14292.
Fitzgerald K, Tsai KK. Systemic therapy for advanced cutaneous squamous cell carcinoma. Semin Cutan Med Surg. 2019;38:E67–74.
Migden MR, Rischin D, Schmults CD, Guminski A, Hauschild A, Lewis KD, et al. PD-1 blockade with cemiplimab in advanced cutaneous squamous-cell carcinoma. N Engl J Med. 2018;379:341–51.
Guthoff R, Marx A, Stroebel P. No evidence for a pathogenic role of human papillomavirus infection in ocular surface squamous neoplasia in Germany. Curr Eye Res. 2009;34:666–71.
Manderwad GP, Kannabiran C, Honavar SG, Vemuganti GK. Lack of association of high-risk human papillomavirus in ocular surface squamous neoplasia in India. Arch Pathol Lab Med. 2009;133:1246–50.
Carreira H, Coutinho F, Carrilho C, Lunet N. HIV and HPV infections and ocular surface squamous neoplasia: systematic review and meta-analysis. Br J Cancer. 2013;109:1981–8.
Shrestha T, Choi W, Kim GE, Yang JM, Yoon KC. Human papilloma virus identification in ocular surface squamous neoplasia by p16 immunohistochemistry and DNA chip test: a strobe-compliant article. Medicine. 2019;98:e13944.
Griffin H, Mudhar HS, Rundle P, Shiraz A, Mahmood R, Egawa N, et al. Human papillomavirus type 16 causes a defined subset of conjunctival in situ squamous cell carcinomas. Mod Pathol. 2020;33:74–90.
This research was supported in part by NIH K08EY026654 (to RCR), P30CA046592 (to the University of Michigan Comprehensive Cancer Center); the Research to Prevent Blindness (to the University of Michigan Kellogg Eye Center and RCR), A. Alfred Taubman Medical Research Institute Leslie and Abigail Wexner Emerging Scholar Program (to RCR), A. Alfred Taubman Medical Research Institute A. Alfred Taubman Emerging Scholar Program (to SAT), Grossman Research Fund (to RCR), Leonard G. Miller Professorship and Ophthalmic Research Fund at the Kellogg Eye Center (to RCR), Barbara Dunn Research Fund (to RCR), Roz Greenspon Research Fund (to RCR), Beatrice & Reymont Paul Foundation (to RCR), and March Hoops to Beat Blindness (to RCR). NIH/NEI 5K08EY027464-02 (to ABD), Research to Prevent Blindness Career Development Award (to ABD), AMC is an NCI Outstanding Investigator (R35CA231996), Howard Hughes Medical Institute Investigator, A. Alfred Taubman Scholar, and American Cancer Society Professor.
Conflict of interest
SAT has had a prior sponsored research agreement with ThermoFisher Scientific that provided access to the OCP. SAT is a co-founder of, prior consultant to, equity holder in, and current employee of Strata Oncology. AMC is a consultant and SAB member of Tempus.
Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
About this article
Cite this article
Lazo de la Vega, L., Bick, N., Hu, K. et al. Invasive squamous cell carcinomas and precursor lesions on UV-exposed epithelia demonstrate concordant genomic complexity in driver genes. Mod Pathol 33, 2280–2294 (2020). https://doi.org/10.1038/s41379-020-0571-7