Multi-omics study to dissect the transcriptional control of PRDM1 in human NK-cells

PRDM1 has been shown to be expressed throughout NK-cell development, and its expression has been demonstrated to be important for NK cell maturation in mouse. It is also a tumor suppressor that is frequently inactivated/lost in NK-cell malignancies. Here we conducted an extensive study on PRDM1 regulation in human NK cells cultured at different conditions that showed quite different growth. NK-cells were able to rapidly proliferate with low apoptosis for more than a month with feeder cells, while IL-2 alone could only maintain human NK cell survival in vitro with limited proliferation for about a week. By comparing binding of PRDM1, difference in chromatin accessibility and gene expression between the two conditions through ChIP-seq, ATAC-seq, and RNA-seq, we investigated the regulatory role of PRDM1 in human NK cells. In addition, we also did knockout and overexpression of PRDM1 in human NK cells and KHYG1 cell line to investigate gene expression regulation by the PRDM1.

已有研究证实，PR结构域锌指蛋白1（PRDM1）在自然杀伤细胞（Natural Killer cell，简称NK细胞）的整个发育过程中均有表达，且其表达对小鼠体内NK细胞的成熟至关重要。同时，PRDM1亦是一种肿瘤抑制因子，在NK细胞恶性肿瘤中常发生失活或缺失。本研究针对不同培养条件下的人源NK细胞中PRDM1的调控机制展开了系统性探究，不同培养条件下NK细胞的生长状态差异显著。在饲养层细胞（feeder cells）共培养体系中，NK细胞可快速增殖且凋亡率极低，存活时长超过1个月；而仅依靠白细胞介素2（Interleukin-2，IL-2）的培养体系仅能在体外维持人NK细胞存活，增殖能力有限，存活时长仅约1周。本研究通过染色质免疫共沉淀测序（Chromatin Immunoprecipitation sequencing，ChIP-seq）、转座酶可及性测序（Assay for Transposase-Accessible Chromatin using sequencing，ATAC-seq）及RNA测序（RNA sequencing，RNA-seq），对比两种培养条件下PRDM1的结合位点、染色质可及性差异以及基因表达差异，以此探究PRDM1在人NK细胞中的调控功能。此外，本研究还在人NK细胞及KHYG1细胞系中分别进行了PRDM1基因敲除与过表达实验，以进一步解析PRDM1对基因表达的调控作用。