Genomic predictors of interindividual differences in response to DNA damaging agents

Abstract

Human lymphoblastoid cells derived from different healthy individuals display considerable variation in their transcription profiles.Here we show that such variation in gene expression underlies interindividual susceptibility to DNA damaging agents. The results demonstrate the massive differences in sensitivity across a diverse cell line panel exposed to an alkylating agent. Computational models identified 48 genes with basal expression that predicts susceptibility with 94% accuracy. Modulating transcript levels for two member genes, MYH and C21ORF56, confirmed that their expression does indeed influence alkylation sensitivity. Many proteins encoded by these genes are interconnected in cellular networks related to human cancer and tumorigenesis. The interindividual differences in disease susceptibility, responsiveness to chemotherapeutics, and susceptibility to environmental exposures across human populations are influenced by a combination of gene-environment interactions. Over the past few years, studies aimed at dissecting the genetic basis underlying human phenotypic variation have built off of the dense genotyping established by the HapMap Consortium. A wealth of genome-wide association studies (GWAS) have described how human genetic variation, at the level of single nucleotide differences, is linked to such complex diseases as diabetes and breast cancer (Hunter et al. 2007;Zeggini and McCarthy 2007). In addition, GWAS have also linked DNA polymorphic variants to gene expression variation across populations (Cheung et al. 2005;Stranger et al. 2005Stranger et al. , 2007Dixon et al. 2007).However, while it is known that human lymphoblastoid cells derived from different healthy individuals display considerable variation in their transcription profiles (Cheung et al. 2003(Cheung et al. , 2005Stranger et al. 2005Stranger et al. , 2007Dixon et al. 2007), the influence this variation has on the response to environmental and chemotherapeutic agents is unknown. In this study, a panel of 24 cell lines previously derived from unrelated, healthy individuals with diverse ancestry (Collins et al. 1998) was tested for variation in sensitivity to the DNA damaging agent, N-methyl-NЈ-nitro-N-nitrosoguanidine (MNNG). MNNG induces a variety of alkylated DNA bases, among which O 6 -methylguanine (O 6 MeG) is known to be particularly toxic as well as mutagenic because it pairs with thymine during replication. O 6 MeG can be repaired by the MGMT DNA repair methyltransferase (Pegg 1990(Pegg , 2000, but left unrepaired, the ensuing O 6 MeG:T base pair can be processed by the DNA mismatch repair (MMR) pathway, and such processing actually triggers apoptotic cell death and cytotoxicity (Kaina et al. 1997; Samson 1999, 2004). Therefore, cells deficient in MGMT but proficient for MMR are extremely sensitive to MNNG-induced killing, whereas cells deficient in both MGMT and MMR are extremely resistant or tolerant to MNNG, but at the cost of increased mutation (Karran 2001). While MGMT and MMR status are thus known to be associated w...

Single cell trapping and DNA damage analysis using microwell arrays

“…Additionally, it appears that no significant difference exists between the repair capacities of these cell lines for IR-induced damage. In contrast, these same cells were previously shown to have significantly different sensitivities to the methylating agent N-methyl-N′-nitro-N-nitrosoguanidine (MNNG) (33). Whereas the majority of IR-induced DNA damage is repaired by the BER pathway (4) (Fig.…”

Pharmacogenomic Discovery Using Cell-Based Models

“…Likewise, gene expression signatures in response to ionizing radiation were distinct in LCLs from patients with breast cancer who had pathogenic BRCA1 or BRCA2 mutations and those without (Waddell et al, 2008). In some cases, such as the alkylating agent N-methyl-NЈ-nitro-N-nitrosoguanidine, almost all (94%) of the variation in sensitivity to drug in LCLs can be explained by basal expression levels of a relatively small number of genes (Fry et al, 2008).…”

DNA methylation contributes to natural human variation

“…These CpG sites of local adaptation include immune (CERK, CDK11B, HTATIP2) and xenobiotic (GSTT1, SPATC1L) response factors, suggesting that they might be driven by differences in local pathogen and environmental pressure. In particular, SPATC1L (spermatogenesis and centriole associated 1-like) is an interesting case, because it was previously related to the response to alkylating agents, suggesting that epivariation contributes to the variable response to chemotherapeutic treatment (Fry et al 2008). It is also tempting to speculate that the selective pressure that gives rise to the polymorphisms originates from carcinogens such as nitrosamides, which introduce alkyl groups on guanine bases, the mechanism used by alkylating drugs.…”