Epigenomic and transcriptomic characterization of cutaneous squamous cell carcinoma (cSCC) in xeroderma pigmentosum (XP)

着色性干皮病 (XP) 皮肤鳞状细胞癌 (cSCC) 的表观基因组和转录组特征

• 批准号: 499597103
• 负责人: Dr. Manuel Rodríguez Paredes
• 金额: --
• 依托单位: Abteilung Epigenetik
• 依托单位国家: 德国
• 项目类别: Research Grants
• 资助国家: 德国
• 项目状态: 未结题
• 来源: https://gepris.dfg.de/gepris/projekt/499597103?language=en
• 关键词: Epigenomic; transcriptomic; characterization; cutaneous; squamous

Xeroderma pigmentosum (XP) is a rare genetic disease typically caused by an autosomal recessive mutation in any of the genes of the nucleotide excision repair (NER) system. Furthermore, a small group of patients (those from complementation group V, XP-V) present mutations in the POLH gene, which encodes the DNA polymerase η responsible for error-free translesional synthesis past DNA photoproducts. Since these factors are responsible for repairing DNA damage caused by UV radiation, the effects of this disease are especially manifested in skin areas exposed to sunlight, where XP patients often show very early in life a strong sensitivity to light, hyperpigmentation, signs of premature aging and different kinds of skin tumors. DNA methylation is an epigenetic modification that occurs mainly in CpG dinucleotides and that, through the control of chromatin accessibility and gene expression, determines both cellular states and identity. Previous work showed that DNA methylation profiles in normal (non-XP) epidermal keratinocytes undergo photoaging-related changes in skin areas exposed to sunlight. Furthermore, it is known that these changes are maintained during the development of non-melanoma skin cancer (NMSC), which is also mainly produced by sun exposure. However, the effects of UV radiation on the methylome of XP-derived NMSC tumors, which constitute the main cause of death in patients with this disease, remain unknown. In this project we will use Infinium MethylationEPIC BeadChip microarrays, the gold standard for DNA methylation studies, as well as RNA sequencing (RNA-seq) to analyze and integrate for the first time the methylomes and transcriptomes of sun-exposed and NMSC epidermal samples from XP-V patients. Different comparisons between these datasets and others generated from non-XP individuals will allow us to investigate the epigenomic deregulation associated with the disease, deepen our understanding of the effects of the extrinsic aging caused by UV radiation and evaluate its influence on the development of NMSC. Importantly, our analyses will also allow us to identify and characterize the transcriptomic differences between non-XP NMSC tumors and those particularly aggressive from XP patients. Differentially expressed markers that ultimately confer increased proliferation or invasion capabilities to XP tumors will finally be determined by CRISPR inactivation (CRISPRi)- and CRISPR activation (CRISPRa)-based candidate gene testing approaches on a cSCC model cell line.

着色性干皮病(XP)是一种罕见的遗传性疾病，通常由核苷酸切除修复系统(NER)中任何基因的常染色体隐性突变引起。此外，一小部分患者(来自互补V组的患者，XP-V)存在POLH基因的突变，该基因编码dna聚合酶η，负责通过dna光产物进行无错误的转位合成。由于这些因素负责修复紫外线辐射造成的DNA损伤，这种疾病的影响在暴露在阳光下的皮肤区域尤为明显，那里的XP患者通常在生命的早期对光线、色素沉着、过早衰老的迹象和不同类型的皮肤肿瘤表现出强烈的敏感性。DNA甲基化是一种表观遗传修饰，主要发生在CpG二核苷酸中，通过控制染色质的可及性和基因表达，决定细胞状态和身份。以前的工作表明，正常(非XP)表皮角质形成细胞的DNA甲基化特征在暴露在阳光下的皮肤区域经历了与光老化相关的变化。此外，众所周知，这些变化在非黑色素瘤皮肤癌(NMSC)的发展过程中保持不变，NMSC也主要是由阳光照射引起的。然而，紫外线辐射对XP衍生的NMSC肿瘤甲基组的影响仍不清楚，这构成了这种疾病患者死亡的主要原因。在这个项目中，我们将使用DNA甲基化研究的黄金标准Infinium MethylationEPIC珠芯片微阵列，以及RNA测序(RNA-seq)，首次分析和整合来自XP-V患者的阳光照射和NMSC表皮样本的甲基组和转录本。将这些数据集与来自非XP个体的其他数据集进行不同的比较，将使我们能够调查与疾病相关的表观基因组去调控，加深我们对紫外线辐射引起的外在衰老影响的理解，并评估其对NMSC发展的影响。重要的是，我们的分析还将使我们能够识别和表征非XP NMSC肿瘤和那些来自XP患者的特别侵袭性肿瘤之间的转录差异。最终增强XP肿瘤增殖或侵袭能力的差异表达标记最终将通过基于CRISPR失活(CRISPRi)和CRISPR激活(CRISPRa)的候选基因测试方法在CSCC模型细胞系上确定。