Jangravi Zohreh, Tabar Mehdi Sharif, Mirzaei Mehdi, Parsamatin Pouria, Vakilian Haghighat, Alikhani Mehdi, Shabani Mohammad, Haynes Paul A, Goodchild Ann K, Gourabi Hamid, Baharvand Hossein, Salekdeh Ghasem Hosseini
Molecular Systems Biology Department at Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR , Tehran, Iran.
Biochemistry Department, Iran University of Medical Sciences , Tehran, Iran.
J Proteome Res. 2015 Sep 4;14(9):3492-502. doi: 10.1021/acs.jproteome.5b00333. Epub 2015 Aug 10.
One of the major objectives of the Human Y Chromosome Proteome Project is to characterize sets of proteins encoded from the human Y chromosome. Lysine (K)-specific demethylase 5D (KDM5D) is located on the AZFb region of the Y chromosome and encodes a JmjC-domain-containing protein. KDM5D, the least well-documented member of the KDM5 family, is capable of demethylating di- and trimethyl H3K4. In this study, we detected two novel splice variants of KDM5D with lengths of 2650bp and 2400bp that correspond to the 100 and 80 kDa proteins in the human prostate cancer cell line, DU-145. The knockdown of two variants using the short interfering RNA (siRNA) approach increased the growth rate of prostate cancer cells and reduced cell apoptosis. To explore the proteome pattern of the cells after KDM5D downregulation, we applied a shotgun label-free quantitative proteomics approach. Of 820 proteins present in all four replicates of two treatments, the abundance of 209 proteins changed significantly in response to KDM5D suppression. Of these, there were 102 proteins observed to be less abundant and 107 more abundant in KDM5D knockdown cells compared with control cells. The results revealed that KDM5D knockdown altered the abundance of proteins involved in RNA processing, protein synthesis, apoptosis, the cell cycle, and growth and proliferation. In conjunction, these results provided new insights into the function of KDM5D and its splice variants. The proteomics data are available at PRIDE with ProteomeXchange identifier PXD000416.
人类Y染色体蛋白质组计划的主要目标之一是对人类Y染色体编码的蛋白质组进行表征。赖氨酸（K）特异性去甲基化酶5D（KDM5D）位于Y染色体的AZFb区域，编码一种含JmjC结构域的蛋白质。KDM5D是KDM5家族中研究最少的成员，能够使二甲基和三甲基H3K4去甲基化。在本研究中，我们在人前列腺癌细胞系DU-145中检测到两种新的KDM5D剪接变体，长度分别为2650bp和2400bp，分别对应100kDa和80kDa的蛋白质。使用短干扰RNA（siRNA）方法敲低这两种变体可提高前列腺癌细胞的生长速率并减少细胞凋亡。为了探索KDM5D下调后细胞的蛋白质组模式，我们应用了一种鸟枪法无标记定量蛋白质组学方法。在两种处理的所有四个重复样本中存在的820种蛋白质中，有209种蛋白质的丰度因KDM5D抑制而发生了显著变化。其中，与对照细胞相比，在KDM5D敲低的细胞中观察到102种蛋白质丰度降低，107种蛋白质丰度增加。结果表明，KDM5D敲低改变了参与RNA加工、蛋白质合成、细胞凋亡、细胞周期以及生长和增殖的蛋白质丰度。综合来看，这些结果为KDM5D及其剪接变体的功能提供了新的见解。蛋白质组学数据可在PRIDE上获取，其ProteomeXchange标识符为PXD000416。
