Bencomo Tomas, Lee Carolyn S
Stanford Program in Epithelial Biology, Stanford University, Stanford, CA, USA.
Medical Scientist Training Program, University of Washington, Seattle, WA, USA.
Br J Dermatol. 2024 Oct 17;191(5):760-774. doi: 10.1093/bjd/ljae249.
Cutaneous squamous cell carcinomas (cSCCs) are the second most common human cancer and have been characterized by RNA sequencing (RNA-Seq); however, the transferability of findings from individual studies may be limited by small sample sizes and diverse analysis protocols.
To define the transcriptome landscape at different stages in the progression of normal skin to cSCC via a meta-analysis of publicly available RNA-Seq samples.
Whole-transcriptome data from 73 clinically normal skin samples, 46 actinic keratoses (AK) samples, 16 in situ SCC samples, 13 keratoacanthoma (KA) samples and 147 cSCC samples [including 30 samples from immunocompromised patients and 8 from individuals with recessive dystrophic epidermolysis bullosa (RDEB)] were uniformly processed to harmonize gene expression. Differential expression, fusion detection and cell-type deconvolution analyses were performed.
Individual RNA-Seq studies of cSCC demonstrated study-specific clustering and varied widely in their differential gene expression detection. Following batch correction, we defined a consensus set of differentially expressed genes (DEGs), including those altered in the preinvasive stages of cSCC development, and used single-cell RNA-Seq data to demonstrate that DEGs are often - but not always - expressed by tumour-specific keratinocytes (TSKs). Analysis of the cellular composition of cSCC, KA and RDEB-cSCC identified an increase in differentiated keratinocytes in KA, while RDEB-cSCC contained the most TSKs. Compared with cSCC arising in immunocompetent individuals, cSCC samples from immunosuppressed patients demonstrated fewer memory B cells and CD8+ T cells. A comprehensive and unbiased search for fusion transcripts in cSCC and intermediate disease stages identified few candidates that recurred in >1% of all specimens, suggesting that most cSCC are not driven by oncogenic gene fusions. Finally, using Genotype-Tissue Expression (GTEx) data, we distilled a novel 300-gene signature of chronic sun exposure that affirms greater cumulative ultraviolet (UV) exposure in later stages of cSCC development.
Our results define the gene expression landscape of cSCC progression, characterize cell subpopulation heterogeneity in cSCC subtypes that contribute to their distinct clinical phenotypes, demonstrate that gene fusions are not a common cause of cSCC and identify UV-responsive genes associated with cSCC development.
皮肤鳞状细胞癌（cSCC）是人类第二常见的癌症，已通过RNA测序（RNA-Seq）进行了特征描述；然而，个体研究结果的可转移性可能受到样本量小和分析方案多样的限制。
通过对公开可用的RNA-Seq样本进行荟萃分析，确定正常皮肤向cSCC进展不同阶段的转录组图谱。
对73份临床正常皮肤样本、46份光化性角化病（AK）样本、16份原位鳞状细胞癌样本、13份角化棘皮瘤（KA）样本和147份cSCC样本[包括30份免疫功能低下患者的样本和8份隐性营养不良性大疱性表皮松解症（RDEB）患者的样本]的全转录组数据进行统一处理，以协调基因表达。进行差异表达、融合检测和细胞类型反卷积分析。
cSCC的个体RNA-Seq研究显示出特定研究的聚类，其差异基因表达检测差异很大。经过批次校正后，我们定义了一组一致的差异表达基因（DEG），包括在cSCC发展的侵袭前阶段发生改变的基因，并使用单细胞RNA-Seq数据证明DEG通常（但不总是）由肿瘤特异性角质形成细胞（TSK）表达。对cSCC、KA和RDEB-cSCC的细胞组成分析发现，KA中分化的角质形成细胞增加，而RDEB-cSCC中TSK最多。与免疫功能正常个体发生的cSCC相比，免疫抑制患者的cSCC样本中记忆B细胞和CD8 + T细胞较少。对cSCC和中间疾病阶段的融合转录本进行全面且无偏倚的搜索，发现很少有候选物在所有标本的>1%中出现，这表明大多数cSCC不是由致癌基因融合驱动的。最后，使用基因型-组织表达（GTEx）数据蒸馏出一种新的300基因慢性阳光暴露特征，证实了在cSCC发展后期累积紫外线（UV）暴露更多。
我们的结果定义了cSCC进展的基因表达图谱，表征了cSCC亚型中导致其不同临床表型的细胞亚群异质性，证明基因融合不是cSCC的常见原因，并确定了与cSCC发展相关的紫外线反应基因。
