Identification and characterization of a potential Biomarker and Modulator for HCC development derived from cancer type-specific long noncoding (Lnc) RNAs.

源自癌症类型特异性长非编码 (Lnc) RNA 的 HCC 发展潜在生物标志物和调节剂的鉴定和表征。

• 批准号: 422417499
• 负责人: Privatdozent Dr. Doan Duy Tran, Ph.D., since 7/2021
• 金额: --
• 依托单位: Klinik für Gastroenterologie, Hepatologie und Endokrinologie
• 依托单位国家: 德国
• 项目类别: Research Grants
• 财政年份: 2019
• 资助国家: 德国
• 起止时间: 2018-12-31 至 2022-12-31
• 项目状态: 已结题
• 来源: https://gepris.dfg.de/gepris/projekt/422417499?language=en
• 关键词: Identification; characterization; potential; Biomarker; Modulator

Cancer research has entered a new phase in which information from genomics, bioinformatics and modern genetics are beginning to provide new indications of potential cancer type-specific biomarkers. Recent Ribo-seq data revealed that 40% of all long noncoding (lnc) RNAs expressed in human cells are translated as “hidden peptides.”. Since lncRNAs express human cell- specific, cell type-specific and cancer- specific properties, these hidden peptides may be cancer type-specific antigens and may also be associated with biological functions. Unraveling the patterns of genomic alterations in heterogeneous tumors such as Hepatocellular carcinoma (HCC) is pivotal for identifying biomarkers in risk groups, and for targeted therapies that could improve patient care. Indeed, we recently found that Linc00176 is spliced within Exon 2 in an HCC specific manner and is translated into a polypeptide 189 amino acids long. In addition, we detected 30 HepG2 specific potential “hidden peptides” by analyzing Ribo-seq data. This application is to undertake the following: Firstly, novel lncRNAs and splice variants of lncRNAs will be identified using nanopore technology that has recently been established in our laboratory. Secondly, to examine whether these peptides are endogenously synthesized and are stable in cells, we will generate synthetic peptide specific antibodies against potential “hidden peptides.”. Thirdly, we will isolate and sequence small peptides from HepG2 cells. Furthermore, to examine their biological functions, the first methionine residue will be replaced by a stop codon using CRISPER and the phenotype will be examined. Finally, using antibodies against these peptides we will examine whether they are expressed in primary HCC, hepatocellular adenoma, liver cirrhosis, and normal liver to determine whether these are useful as biomarkers for pre-HCCs and HCCs. In the future, antigen presentation of these peptides will be examined.

癌症研究已经进入了一个新的阶段，来自基因组学、生物信息学和现代遗传学的信息开始为潜在的癌症类型特异性生物标志物提供新的指示。最近的Ribo-seq数据显示，在人类细胞中表达的所有长非编码（lnc）RNA中有40%被翻译为“隐藏肽”。由于lncRNA表达人细胞特异性、细胞类型特异性和癌症特异性性质，这些隐藏的肽可以是癌症类型特异性抗原，并且也可以与生物学功能相关。揭示异质性肿瘤（如肝细胞癌（HCC））中的基因组改变模式对于识别风险组中的生物标志物以及可以改善患者护理的靶向治疗至关重要。事实上，我们最近发现Linc 00176以HCC特异性方式在外显子2内剪接，并翻译成189个氨基酸长的多肽。此外，通过分析Ribo-seq数据，我们检测到30个HepG 2特异性潜在的“隐藏肽”。本申请将进行以下工作：首先，将使用我们实验室最近建立的纳米孔技术鉴定新型lncRNA和lncRNA的剪接变体。其次，为了检查这些肽是否是内源性合成的，并且在细胞中是否稳定，我们将产生针对潜在的“隐藏肽"的合成肽特异性抗体。第三，我们将从HepG 2细胞中分离和测序小肽。此外，为了检查它们的生物学功能，使用CRISPER将第一个甲硫氨酸残基替换为终止密码子，并检查表型。最后，使用针对这些肽的抗体，我们将检查它们是否在原发性HCC、肝细胞腺瘤、肝硬化和正常肝脏中表达，以确定这些是否可用作前HCC和HCC的生物标志物。在未来，这些肽的抗原呈递将被检查。