DNA damage responses in murine Pre-B cells with genetic deficiencies in damage response genes

DNA damage can be generated in multiple ways from genotoxic and physiologic sources. Genotoxic damage is known to disrupt cellular functions and is lethal if not repaired properly. We compare the transcriptional programs activated in response to genotoxic DNA damage induced by ionizing radiation (IR) in abl pre-B cells from mice deficient in DNA damage response (DDR) genes Atm, Mre11, Mdc1, H2ax, 53bp1, and DNA-PKcs. We identified a core IR-specific transcriptional response that occurs in abl pre-B cells from WT mice and compared the response of the other genotypes to the WT response. We also identified genotype specific responses and compared those to each other. The WT response includes many processes involved in lymphocyte development and immune response, as well as responses associated with the molecular mechanisms of cancer, such as TP53 signaling. As expected, there is a range of similarity in transcriptional profiles in comparison to WT cells, with Atm-/- cells being the most different from the core WT DDR and Mre11 hypomorph (Mre11A/A) cells also very dissimilar to WT and other genotypes. For example, NF-kB-related signaling and CD40 signaling are deficient in both Atm-/- and Mre11A/A cells, but present in all other genotypes. In contrast, IR-induced TP53 signaling is seen in the Mre11A/A cells, while these responses are not seen in the Atm-/- cells. By examining the similarities and differences in the signaling pathways in response to IR when specific genes are absent, our results further illustrate the contribution of each gene to the DDR. The microarray gene expression data discussed in this paper have been deposited in NCBI’s Gene Expression Omnibus (GEO) (http://www.ncbi.nlm.nih.gov/geo/) and are accessible under accession number GSE116388.

DNA损伤可通过遗传毒性（genotoxic）与生理（physiologic）来源的多种途径产生。遗传毒性损伤已知会破坏细胞功能，若未能得到正确修复则可导致细胞死亡。本研究比较了经电离辐射（ionizing radiation, IR）诱导遗传毒性DNA损伤后，DNA损伤应答（DNA damage response, DDR）基因Atm、Mre11、Mdc1、H2ax、53bp1及DNA-PKcs缺陷小鼠的abl前B细胞中激活的转录程序。我们鉴定出野生型（wild type, WT）小鼠abl前B细胞中特有的IR核心转录应答，并将其余各基因型的应答与野生型应答进行对比。此外，我们还鉴定了基因型特异性应答，并对这些应答彼此间进行了比较。野生型应答涵盖淋巴细胞发育与免疫应答相关的诸多生物学过程，同时包含与癌症分子机制相关的应答，例如TP53信号通路。正如预期，与野生型细胞相比，各转录谱存在不同程度的相似性：其中Atm敲除（Atm-/-）细胞与野生型核心DDR应答差异最为显著，Mre11低突变体（Mre11A/A）细胞同样与野生型及其他基因型细胞差异极大。例如，NF-κB相关信号通路与CD40信号通路在Atm-/-与Mre11A/A细胞中均存在缺陷，但在其余所有基因型细胞中均正常激活。与之相反，电离辐射诱导的TP53信号通路可在Mre11A/A细胞中被观测到，而此类应答在Atm-/-细胞中并未出现。通过分析缺失特定基因时电离辐射应答信号通路的异同，本研究结果进一步阐明了每个基因在DDR通路中的具体贡献。本文所讨论的微阵列基因表达数据已提交至美国国家生物技术信息中心（National Center for Biotechnology Information, NCBI）的基因表达综合数据库（Gene Expression Omnibus, GEO）（http://www.ncbi.nlm.nih.gov/geo/），登录号为GSE116388。