Choudhary Ratan K, Choudhary Shanti, Mukhopadhyay C S, Pathak Devendra, Verma Ramneek
School of Animal Biotechnology, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana, Punjab, 141004, India.
Department of Animal and Veterinary Sciences, University of Vermont, Burlington, VT, 05405, USA.
Funct Integr Genomics. 2019 Mar;19(2):349-362. doi: 10.1007/s10142-018-0645-5. Epub 2018 Nov 23.
Although water buffaloes are the main milk-producing animals in Indian subcontinent, only limited attempts have been made to identify canonical pathways and gene regulatory networks operating within the mammary glands of these animals. Such information is important for identifying unique transcriptome signatures in the mammary glands of diseased animals. In this report, we analyzed the transcription profile of 3 prepubertal buffalo mammary glands and identified common genes (mean FPKM > 0.2 in all samples) operating in the glands. Among 19,994 protein coding genes, 14,678 genes expressed and 5316 unique genes did not express in prepubertal buffalo mammary glands. Of these 14,678 expressed genes, 79% comprised a ubiquitous transcriptome that was dominated by very lowly expressed genes (51%). The percentage of rarely, moderately, and abundantly expressed genes was 25%, 2%, and 1%, respectively. Gene Ontology (GO) terms reflected in the expression of common genes (mean FPKM > 5.0) for molecular function were related to binding and catalytic activity. Products of these genes were involved in metabolic and cellular processes and belong to nucleic acid binding proteins. The canonical pathways for growth of mammary glands included integrin signaling, inflammation, GnRH and Wnt pathways. KEGG enriched pathways revealed many pathways of cancer including ribosome, splisosome, endocytosis, and ubiquitin-mediated proteolysis, pathways for viral infection, and bacterial invasion of epithelial. Highly expressed genes (mean FPKM > 500 included beta-actin (ACTB), beta-2 microglobulin (B2M), caseins (CSN2, CNS3), collagens (COL1A1, COL3A1), translation elongation factors (EEF1A1, EEF1G, EEF2), keratins (KRT15, KRT19), major histocompatibility complex genes (CD74, JSP.1), vimentin (VIM), and osteopontin (SPP1). Interestingly, expression of milk protein genes in prepubertal glands opens possible roles of these genes in development of mammary glands. We report the whole transcriptomic signature of prepubertal buffalo mammary gland and indicated its molecular signature is similar to cancer type.
尽管水牛是印度次大陆主要的产奶动物，但在识别这些动物乳腺内的经典通路和基因调控网络方面所做的尝试有限。此类信息对于识别患病动物乳腺中的独特转录组特征非常重要。在本报告中，我们分析了3个青春期前水牛乳腺的转录谱，并确定了在这些腺体中起作用的共同基因（所有样本中平均FPKM>0.2）。在19994个蛋白质编码基因中，14678个基因表达，5316个独特基因在青春期前水牛乳腺中不表达。在这14678个表达基因中，79%构成了一个普遍存在的转录组，其中极低表达基因占主导（51%）。低表达、中度表达和高表达基因的比例分别为25%、2%和1%。分子功能方面，共同基因（平均FPKM>5.0）表达中反映的基因本体（GO）术语与结合和催化活性有关。这些基因的产物参与代谢和细胞过程，属于核酸结合蛋白。乳腺生长的经典通路包括整合素信号传导、炎症、促性腺激素释放激素（GnRH）和Wnt通路。京都基因与基因组百科全书（KEGG）富集通路揭示了许多癌症相关通路，包括核糖体、剪接体、内吞作用和泛素介导的蛋白水解、病毒感染通路以及细菌对上皮细胞的侵袭。高表达基因（平均FPKM>500）包括β-肌动蛋白（ACTB）、β-2微球蛋白（B2M）、酪蛋白（CSN2、CNS3）、胶原蛋白（COL1A1、COL3A1）、翻译延伸因子（EEF1A1、EEF1G、EEF2）、角蛋白（KRT15、KRT19）、主要组织相容性复合体基因（CD74、JSP.1）、波形蛋白（VIM）和骨桥蛋白（SPP1）。有趣的是，青春期前腺体中乳蛋白基因的表达揭示了这些基因在乳腺发育中的可能作用。我们报告了青春期前水牛乳腺的全转录组特征，并表明其分子特征与癌症类型相似。
