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


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.

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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.


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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.

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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.

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

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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.

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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).

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