Gene expression profile of colorectal carcinoma HT29 PARP13 KO cells cultivated in 2D or 3D cell culture models

Among the key players in the DDR networks are members of the 17 PARP (poly-ADP-ribose polymerase) protein family. Beyond their involvement in various biological processes - such as transcription control, cell death, and inflammation – some PARPs specifically contribute to attracting repair proteins to sites of DNA damage. PARP1 and PARP2, the most well-studied members, act as DNA damage sensors and signal transducers synthesizing poly-ADP-ribose chains that recruits DNA repair factors and can remodel chromatin structure around damaged DNA. In addition to the well-characterized PARPs, other members of this family hold promise for cancer therapeutic applications as they are also involved in the DNA damage response. In the present study, we investigated PARP13-dependent changes in gene expression in colorectal carcinoma HT29 cell lines. Agilent microarray technology was used to analyze gene expression levels in cells cultured under 2D and 3D culture conditions. The results of our study demonstrate the pivotal role of PARP13 in the immune response and the potential for using this target for therapeutic purposes. The profile of differentially expressed genes identified in the present study could be used for further development of diagnostic and therapeutic applications in CRC. The transcriptome of HT29 PARP13 KO cells was evaluated in comparison to the transcriptome of wt cells. RNA was harvested from HT29 colorectal cancer cells cultured under 2D and 3D cell culture conditions for 48 hours.

PARP（多聚ADP核糖聚合酶，poly-ADP-ribose polymerase）蛋白家族的17个成员，是DNA损伤应答（DNA Damage Response, DDR）网络中的核心参与者。除参与转录调控、细胞死亡与炎症反应等多种生物学过程外，部分PARP还可特异性将修复蛋白招募至DNA损伤位点。其中研究最为深入的PARP1与PARP2，可作为DNA损伤传感器与信号转导因子，合成多聚ADP核糖链以招募DNA修复因子，并重塑损伤DNA周边的染色质结构。除功能已得到充分解析的PARP家族成员外，该家族其余成员也因参与DNA损伤应答而具备癌症治疗的应用潜力。本研究针对结直肠癌HT29细胞系中依赖于PARP13的基因表达变化展开探究，采用安捷伦微阵列技术分析了2D与3D培养条件下细胞的基因表达水平。本研究结果证实了PARP13在免疫应答中的核心作用，以及将该靶点用于治疗的潜在价值。本研究中鉴定出的差异表达基因谱，可用于结直肠癌（colorectal carcinoma, CRC）诊断与治疗相关应用的后续开发。本研究以野生型（wild type, wt）细胞的转录组为对照，评估了HT29 PARP13敲除（knockout, KO）细胞的转录组特征。本研究从经2D与3D培养48小时的HT29结直肠癌细胞中提取RNA。