Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

Invasive squamous cell carcinomas and precursor lesions on UV-exposed epithelia demonstrate concordant genomic complexity in driver genes

Abstract

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.

Access options

Rent or Buy article

Get time limited or full article access on ReadCube.

from$8.99

All prices are NET prices.

Fig. 1: Cutaneous squamous carcinoma and precursor lesions by light microscopy (left) and molecular features (right).
Fig. 2: Somatic copy number profiles.
Fig. 3: Integrated heatmap of prioritized mutations and copy number aberrations identified by next-generation sequencing.
Fig. 4: Two-level concentric pie charts and CDKN2A variant mapping.
Fig. 5: Whole-transcriptome amplicon-based RNA-seq expression data for high-quality cutaneous tissue specimens.

References

  1. 1.

    Dotto GP, Rustgi AK. Squamous cell cancers: a unified perspective on biology and genetics. Cancer Cell. 2016;29:622–37.

    CAS  PubMed  PubMed Central  Google Scholar 

  2. 2.

    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.

    CAS  PubMed  PubMed Central  Google Scholar 

  3. 3.

    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.

    CAS  PubMed  PubMed Central  Google Scholar 

  4. 4.

    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.

    CAS  PubMed  PubMed Central  Google Scholar 

  5. 5.

    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.

    PubMed  PubMed Central  Google Scholar 

  6. 6.

    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.

    CAS  PubMed  PubMed Central  Google Scholar 

  7. 7.

    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.

    CAS  PubMed  Google Scholar 

  8. 8.

    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.

    CAS  PubMed  Google Scholar 

  9. 9.

    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.

    PubMed  Google Scholar 

  10. 10.

    Tabbara KF, Kersten R, Daouk N, Blodi FC. Metastatic squamous cell carcinoma of the conjunctiva. Ophthalmology. 1988;95:318–21.

    CAS  PubMed  Google Scholar 

  11. 11.

    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.

    CAS  PubMed  Google Scholar 

  12. 12.

    Rosen T, Lebwohl MG. Prevalence and awareness of actinic keratosis: barriers and opportunities. J Am Acad Dermatol. 2013;68:S2–9.

    PubMed  Google Scholar 

  13. 13.

    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.

    PubMed  Google Scholar 

  14. 14.

    Boukamp P. Non-melanoma skin cancer: what drives tumor development and progression? Carcinogenesis. 2005;26:1657–67.

    CAS  PubMed  Google Scholar 

  15. 15.

    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.

    CAS  Google Scholar 

  16. 16.

    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.

    CAS  PubMed  Google Scholar 

  17. 17.

    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.

    CAS  PubMed  Google Scholar 

  18. 18.

    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.

    CAS  PubMed  Google Scholar 

  19. 19.

    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.

    PubMed  Google Scholar 

  20. 20.

    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.

    PubMed  PubMed Central  Google Scholar 

  21. 21.

    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.

    CAS  PubMed  Google Scholar 

  22. 22.

    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.

    CAS  PubMed  Google Scholar 

  23. 23.

    Rehman I, Takata M, Wu YY, Rees JL. Genetic change in actinic keratoses. Oncogene. 1996;12:2483–90.

    CAS  PubMed  Google Scholar 

  24. 24.

    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.

    CAS  PubMed  Google Scholar 

  25. 25.

    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.

    CAS  PubMed  Google Scholar 

  26. 26.

    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.

    CAS  PubMed  Google Scholar 

  27. 27.

    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.

    CAS  PubMed  PubMed Central  Google Scholar 

  28. 28.

    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.

    PubMed  PubMed Central  Google Scholar 

  29. 29.

    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.

    Google Scholar 

  30. 30.

    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.

    CAS  PubMed  Google Scholar 

  31. 31.

    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.

    CAS  Google Scholar 

  32. 32.

    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.

    CAS  Google Scholar 

  33. 33.

    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.

    CAS  PubMed  PubMed Central  Google Scholar 

  34. 34.

    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.

    CAS  PubMed  PubMed Central  Google Scholar 

  35. 35.

    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.

    CAS  PubMed  PubMed Central  Google Scholar 

  36. 36.

    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.

    CAS  PubMed  Google Scholar 

  37. 37.

    Knudsen ES, Knudsen KE. Tailoring to RB: tumour suppressor status and therapeutic response. Nat Rev Cancer. 2008;8:714–24.

    CAS  PubMed  PubMed Central  Google Scholar 

  38. 38.

    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.

    CAS  PubMed  Google Scholar 

  39. 39.

    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.

  40. 40.

    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.

    CAS  PubMed  PubMed Central  Google Scholar 

  41. 41.

    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.

    CAS  PubMed  Google Scholar 

  42. 42.

    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.

    PubMed  PubMed Central  Google Scholar 

  43. 43.

    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.

    CAS  PubMed  Google Scholar 

  44. 44.

    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.

    PubMed  Google Scholar 

  45. 45.

    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.

    CAS  PubMed  PubMed Central  Google Scholar 

  46. 46.

    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.

    CAS  PubMed  PubMed Central  Google Scholar 

  47. 47.

    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.

    CAS  PubMed  Google Scholar 

  48. 48.

    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.

    CAS  PubMed  Google Scholar 

  49. 49.

    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.

    CAS  PubMed  Google Scholar 

  50. 50.

    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.

    CAS  PubMed  PubMed Central  Google Scholar 

  51. 51.

    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.

    PubMed  Google Scholar 

  52. 52.

    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.

    CAS  PubMed  PubMed Central  Google Scholar 

  53. 53.

    Fitzgerald K, Tsai KK. Systemic therapy for advanced cutaneous squamous cell carcinoma. Semin Cutan Med Surg. 2019;38:E67–74.

    PubMed  Google Scholar 

  54. 54.

    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.

    CAS  PubMed  Google Scholar 

  55. 55.

    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.

    PubMed  Google Scholar 

  56. 56.

    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.

    CAS  PubMed  Google Scholar 

  57. 57.

    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.

    CAS  PubMed  PubMed Central  Google Scholar 

  58. 58.

    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.

    CAS  PubMed  PubMed Central  Google Scholar 

  59. 59.

    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.

    CAS  PubMed  Google Scholar 

Download references

Acknowledgements

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.

Author information

Affiliations

Authors

Contributions

LLV, NB, SAT, RCR, and PWH substantially contributed to conception or design of the work. LLV, NB, KH, SER, CDS, SM, PP, XW, AS, HKS, SIM, DRR, AMC, HD, ABD, FW, CGE, SAT, RCR, and PWH contributed to acquisition, analysis, or interpretation of data. LLV, NB, SAT, RCR, and PWH drafted the work and significantly revised it. All authors have approved the submitted version, and have agreed both to be personally accountable for the authors’ own contributions and to ensure that questions related to the accuracy or integrity of any part of the work, even ones in which the author was not personally involved, are appropriately investigated, resolved, and the resolution documented in the literature.

Corresponding authors

Correspondence to Rajesh C. Rao or Paul W. Harms.

Ethics declarations

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.

Additional information

Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Supplementary information

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

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

Download citation

Further reading

Search

Quick links