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Table S1. Relative sensitivity of lymphoblastoid cell lines to alkylating agents; Table S2. DNA repair capacity data for 24 cell lines. Table S3. Correlation coefficients for pairwise linear relationships between DNA repair capacity in multiple pathways in 24 lymphoblastoid cell lines. Table S4. Statistical significance of linear relationships between DNA repair capacity in multiple pathways in 24 lymphoblastoid cell lines. Table S5. Correlation coefficients for pairwise linear relationships between DNA repair capacity and sensitivity to killing with DNA damaging agents in 24 lymphoblastoid cell lines. Table S6. Statistical significance of linear relationships between DNA repair capacity and sensitivity to killing with DNA damaging agents in 24 lymphoblastoid cell lines. Table S7. DNA Repair capacity for indicated repair pathways in PDX models of GBM. Figure S1. Computational Workflow. Figure S2. Diagram of a linear model relating MGMT activity to sensitivity to MNNG. Figure S3. Correlation between MGMT activity (as measured by FM-HCR) and sensitivity to a DNA damaging agent. Figure S4. Scatter plots of observed sensitivity (% Control Growth) versus predicted sensitivity calculated from leave-one-out analysis of the models listed in Table 1. Figure S5. Predicted and observed sensitivity of paired GBM xenograft lines with differential TMZ sensitivities. Figure S6. Correlation between MGMT activity and promoter methylation status.

Cancer cells can resist the effects of DNA-damaging therapeutic agents via utilization of DNA repair pathways, suggesting that DNA repair capacity (DRC) measurements in cancer cells could be used to identify patients most likely to respond to treatment. However, the limitations of available technologies have so far precluded adoption of this approach in the clinic. We recently developed fluorescence-based multiplexed host cell reactivation (FM-HCR) assays to measure DRC in multiple pathways. Here we apply a mathematical model that uses DRC in multiple pathways to predict cellular resistance to killing by DNA-damaging agents. This model, developed using FM-HCR and drug sensitivity measurements in 24 human lymphoblastoid cell lines, was applied to a panel of 12 patient-derived xenograft (PDX) models of glioblastoma to predict glioblastoma response to treatment with the chemotherapeutic DNA-damaging agent temozolomide. This work showed that, in addition to changes in O6-methylguanine DNA methyltransferase (MGMT) activity, small changes in mismatch repair (MMR), nucleotide excision repair (NER), and homologous recombination (HR) capacity contributed to acquired temozolomide resistance in PDX models and led to reduced relative survival prolongation following temozolomide treatment of orthotopic mouse models in vivo. Our data indicate that measuring the combined status of MMR, HR, NER, and MGMT provided a more robust prediction of temozolomide resistance than assessments of MGMT activity alone. Cancer Res; 77(1); 198–206. ©2016 AACR.

Supplementary Figures S1-S14. p53 levels in p53 knockdown GBM cells (S1); TMZR3 cells obtained from a p53 deficient background display increased ploidy (S2); H2AX activation in temozolomide treated parental and TMZR3 GBM cells (S3); In-cell Host cell reactivation (HCR) assays used to assess the MGMT and MMR repair capacity of GBM cells (S4); MSH6 and MSH2 levels in MSH6 and MSH2 knockdown GBM cells (S5); Cell cycle profiles and quantitation of cell cycle changes in TMZ-treated MSH6 knockdown cells two cell cycle times post-TMZ treatment (S6); Cell cycle profiles and quantitation of cell cycle changes in TMZ-treated MSH2 knockdown cells two cell cycle times post-TMZ treatment (S7); Minor decreases in MSH2 levels correlate with acquired TMZ resistance in LN229 and A172 GBM cells (S8); Effects of MSH6 or MSH2 knockdown on the protein level of its dimerization partner (S9); Msh2 knockdown in GL261 glioblastoma cells (S10); Moderate decreases in Msh2 confer a growth advantage to GL261 GBM cells after TMZ, but not BCNU, exposure in vitro (S11); Distribution of patient survival in TMZ treated TCGA GBM patients and effects of MSH2 transcript levels on the survival of TMZ treated patients in the 95th percentile for patient survival after TMZ therapy (S12); Overall survival of GBM patients stratified by MSH3, MLH1 and PMS2 tumor transcript levels (S13); PMS2 transcript levels correlate with increased chromosome 7 copy number (S14).

Supplementary Tables S1-S2. O6-methylguanine adducts levels in parental and TMZR3 GBM cells 3 hours post-TMZ exposure (S1); shRNA constructs used in this study (S2).

Supplementary Methods and Discussion. Description of additional methods and procedures used in the study. Also includes Supplementary References.

Genotoxicity testing is critical for predicting adverse effects of pharmaceutical, industrial, and environmental chemicals. The comet assay is a commonly used approach for detecting DNA damage that is based on the underlying principle that damaged DNA migrates more readily than undamaged DNA when electrophoresed in agarose. We previously developed a higher-throughput version of the comet assay (Wood DK, PNAS 2010). For the “CometChip” assay, cells are loaded into an array of agarose microwells to create a cell microarray. The CometChip can be fully automated, making the assay more than 1000X faster, while improving reproducibility. While effective for detecting single-strand breaks, abasic sites, and alkali-sensitive sites, the alkaline comet assay is not effective for detection of carcinogenic bulky DNA lesions that do not impact DNA mobility and that require metabolic activation. To overcome this, we use DNA replication inhibitors (hydroxyurea and 1-β-d-arabinofuranosyl cytosine) shown to trap single-strand breaks that are formed during nucleotide excision repair, which normally removes bulky lesions. Thus, comet-undetectable bulky lesions are converted into comet-detectable single-strand breaks. Together with HepaRG™ cells that recapitulate in vivo metabolic capacity, we have thus created the “HepaCometChip,” which provides a more broadly effective approach for detection of DNA damage. In addition to genotoxicity testing, the microwell array has also been harnessed for use in a cell survival assay. For the “MicroColonyChip” (Ngo LP, Cell Reports 2019), cells are loaded into the agarose microwell array and allowed to grow to form microcolonies. Differences in cell survival can be detected by changes in the distribution of colony sizes, a novel metric for cell survival quantitation. The assay is as sensitive as the traditional “gold standard” colony-forming assay, yet it takes days instead of weeks to complete. Parallel studies of genotoxicity and cytotoxicity can thus be performed using a shared microwell platform. These tools have broad utility, including studies of microbe-induced DNA damage. Examples of S. pneumoniae and E. coli microbial product-induced double-strand breaks and interstrand crosslinks contribute to an emerging paradigm wherein pathogen-induced DNA damage has the potential to promote disease. Citation Format: Le P. Ngo, Prashant Rai, Matthew R. Wilson, Carole Swartz, John Winters, Yang Su, Jing Ge, Tze-Khee Chan, Emily P. Balskus, Vincent Chow, Les Recio, Leona D. Samson, Bevin P. Engelward. Novel cell microarray technologies for studies of DNA damage and cell survival and applications for studies of microbe-induced DNA damage [abstract]. In: Proceedings of the AACR Special Conference on Environmental Carcinogenesis: Potential Pathway to Cancer Prevention; 2019 Jun 22-24; Charlotte, NC. Philadelphia (PA): AACR; Can Prev Res 2020;13(7 Suppl): Abstract nr IA20.

Cancer cells can resist the effects of DNA-damaging therapeutic agents via utilization of DNA repair pathways, suggesting that DNA repair capacity (DRC) measurements in cancer cells could be used to identify patients most likely to respond to treatment. However, the limitations of available technologies have so far precluded adoption of this approach in the clinic. We recently developed fluorescence-based multiplexed host cell reactivation (FM-HCR) assays to measure DRC in multiple pathways. Here we apply a mathematical model that uses DRC in multiple pathways to predict cellular resistance to killing by DNA-damaging agents. This model, developed using FM-HCR and drug sensitivity measurements in 24 human lymphoblastoid cell lines, was applied to a panel of 12 patient-derived xenograft (PDX) models of glioblastoma (GBM) to predict GBM response to treatment with the chemotherapeutic DNA damaging agent temozolomide (TMZ). This work showed that, in addition to changes in O6-methylguanine DNA methyltransferase (MGMT) activity, small changes in mismatch repair (MMR), nucleotide excision repair (NER), and homologous recombination (HR) capacity contributed to acquired TMZ resistance in PDX models, and lead to reduced relative survival prolongation following TMZ treatment of orthotopic mouse models in vivo. Our data indicate that measuring the combined status of MMR, HR, NER, and MGMT provided a more robust prediction of TMZ resistance than assessments of MGMT activity alone., National Institutes of Health (U.S.) (DP1-ES022576), National Institutes of Health (U.S.) (U54-CA112967)

Endogenous formation of the mutagenic DNA adduct 1,N6-ethenoadenine (εA) originates from lipid peroxidation. Elevated levels of εA in cancer-prone tissues suggest a role for this adduct in the development of some cancers. The base excision repair pathway has been considered the principal repair system for εA lesions until recently, when it was shown that the Escherichia coli AlkB dioxygenase could directly reverse the damage. We report here kinetic analysis of the recombinant human AlkB homologue 2 (hABH2), which is able to repair εA lesions in DNA. Furthermore, cation exchange chromatography of nuclear extracts from wild-type and mABH2−/− mice indicates that mABH2 is the principal dioxygenase for εA repair in vivo. This is further substantiated by experiments showing that hABH2, but not hABH3, is able to complement the E. coli alkB mutant with respect to its defective repair of etheno adducts. We conclude that ABH2 is active in the direct reversal of εA lesions, and that ABH2, together with the alkyl-N-adenine-DNA glycosylase, which is the most effective enzyme for the repair of εA, comprise the cellular defense against εA lesions. [Cancer Res 2008;68(11):4142–9]

The Samson lab has been developing potentially high-throughput methods for measuring DNA repair capacity (DRC) in human cells. These approaches are modeled on the pioneering work of the late Professor Lawrence Grossman and rely on the transfection of plasmids containing specific types of DNA damage and then monitoring the repair of that damage by the expression of a reporter gene that is poorly expressed in the absence of repair. One of our goals is to simultaneously measure DRC for a variety of DNA repair pathways using a multiplexed approach and a collection of fluorescent proteins of different color. So far we have developed methods for measuring relative levels of nucleotide excision repair, homologous recombination, DNA mismatch repair, and MGMT mediated repair. We are currently extending this approach to encompass other DNA repair pathways. Measuring DNA repair capacity in various human cell types may help predict inter-individual differences in the ability of people to respond upon exposure to environmental agents and thus predict their cancer susceptibility. Moreover, knowing the DNA repair capacity of tumor cells for different types of DNA damage could help in choosing more effective chemotherapy regimens. Citation Format: Leona D. Samson. Developing improved methods to measure human DNA repair capacity [abstract]. In: Proceedings of the AACR Special Conference on Chemical Systems Biology: Assembling and Interrogating Computational Models of the Cancer Cell by Chemical Perturbations; 2012 Jun 27-30; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2012;72(13 Suppl):Abstract nr IA17.