Department of Animal Biotechnology, College of Veterinary Science & Animal Husbandry, Anand Agricultural University, Anand, Gujarat, 388001, India.
Funct Integr Genomics. 2020 Jan;20(1):75-87. doi: 10.1007/s10142-019-00700-4. Epub 2019 Jul 31.
Long non-coding RNA (lncRNA) was previously considered as a non-functional transcript, which now established as part of regulatory elements of biological events such as chromosome structure, remodeling, and regulation of gene expression. The study presented here showed the role of lncRNA through differential expression analysis on cancer-related coding genes in horn squamous cell carcinoma of Indian zebu cattle. A total of 10,360 candidate lncRNAs were identified and further analyzed for its coding potential ability using three tools (CPC, CPAT, and PLEK) that provide 8862 common lncRNAs. Pfam analysis of these common lncRNAs gave 8612 potential candidates for lncRNA differential expression analysis. Differential expression analysis showed a total of 59 significantly differentially expressed genes and 19 lncRNAs. Pearson's correlation analysis was used to identify co-expressed mRNA-lncRNAs to established relation of the regulatory role of lncRNAs in horn cancer. We established a positive relation of seven upregulated (XLOC_000016, XLOC_002198, XLOC_002851, XLOC_ 007383, XLOC_010701, XLOC_010272, and XLOC_011517) and one downregulated (XLOC_011302) lncRNAs with eleven genes that are related to keratin family protein, keratin-associated protein family, cornifelin, corneodesmosin, serpin family protein, and metallothionein that have well-established role in squamous cell carcinoma through cellular communication, cell growth, cell invasion, and cell migration. These biological events were found to be related to the MAPK pathway of cell cycle regulation indicating the role of lncRNAs in manipulating cell cycle regulation during horn squamous cell carcinomas that will be useful in identifying molecular portraits related to the development of horn cancer.
长链非编码 RNA（lncRNA）以前被认为是一种无功能的转录物，现在被确定为生物事件的调节元件的一部分，如染色体结构、重塑和基因表达的调节。本研究通过对印度瘤牛角鳞状细胞癌中与癌症相关的编码基因进行差异表达分析，展示了 lncRNA 的作用。总共鉴定出 10360 个候选 lncRNA，并使用三个工具（CPC、CPAT 和 PLEK）进一步分析其编码潜能能力，这三个工具提供了 8862 个常见的 lncRNA。对这些常见 lncRNA 的 Pfam 分析为 lncRNA 差异表达分析提供了 8612 个潜在的候选者。差异表达分析显示，共有 59 个显著差异表达基因和 19 个 lncRNA。Pearson 相关性分析用于识别共表达的 mRNA-lncRNA，以建立 lncRNA 在角癌中的调节作用的关系。我们建立了七个上调的（XLOC_000016、XLOC_002198、XLOC_002851、XLOC_007383、XLOC_010701、XLOC_010272 和 XLOC_011517）和一个下调的（XLOC_011302）lncRNA 与十一个与角蛋白家族蛋白、角蛋白相关蛋白家族、角蛋白、角蛋白结合蛋白、丝氨酸蛋白酶家族蛋白和金属硫蛋白相关的基因之间的正相关关系，这些基因在鳞状细胞癌中通过细胞通讯、细胞生长、细胞侵袭和细胞迁移等方面具有良好的作用。这些生物学事件与细胞周期调节的 MAPK 途径有关，表明 lncRNA 在角鳞状细胞癌中调节细胞周期调节的作用，这将有助于识别与角癌发生相关的分子特征。
