Introduction
Current treatment for glioblastoma (GBM), the most common and aggressive primary malignant brain tumor in adults, consists of maximum surgical resection followed by adjuvant radiotherapy and temozolomide (TMZ) [
1]. TMZ is an alkylating agent that induces the formation of methyl adducts, most importantly at the O
6-guanine position. Methylguanine mispairs with thymine instead of cytosine during replication, which initiates DNA mismatch repair (MMR). A futile cycle of DNA mismatching and attempted repair ensues, resulting in replication fork collapse, DNA strand breaks, and apoptosis [
2,
3]. Failure to trigger DNA replication checkpoints, if MMR is deficient, can lead to apoptotic escape and drug resistance [
4,
5]. Inactivating mutations and loss of expression of MMR genes in GBM has been correlated with higher tumor proliferation rates and poorer survival outcomes [
6‐
8].
Hypomethylating agents have garnered interest as a means of restoring the expression of genes that might aid anticancer treatment. Decitabine (DAC) is a nucleoside analog that functions by irreversibly binding to DNA methyltransferases (DNMTs), depleting free enzyme, and preventing further DNA methylation during subsequent replication cycles [
9]. Due to the high frequency of mutations in DNA methylation enzymes in hematologic malignancies, which cause silencing of tumor suppressors via aberrant hypermethylation, DNMT inhibitors such as DAC have a well-established role in the treatment of patients with myelodysplastic syndrome (MDS) and acute myelogenous leukemia (AML) [
10,
11], where they exert their epigenetic effects at relatively low doses (5–20 mg/m
2/d) [
12‐
16]. In solid malignancies, where driver mutations involving methylation enzymes are uncommon, the ability of DAC to re-express genes that might reduce resistance to cytotoxic agents is of significant interest. Preclinical data showing that the MMR protein mutL homolog 1 (MLH1) can be re-expressed using DAC in ovarian and colon cancer cells to improve sensitivity to platinum agents spurred the development of several clinical trials [
17‐
19]. In advanced melanoma, low-dose DAC was tested in combination with TMZ, yielding an objective response rate of 18% with minimal toxicity [
20‐
22]. A challenge in demonstrating the efficacy of this approach has been the availability of a biomarker to rationally select patients with amenable gene methylation profiles, such as a hypermethylated
MLH1 promoter. In correlative analyses, pre- and post-treatment tissue samples often do not demonstrate the targeted methylation or gene expression change [
18,
23].
In GBM, an agent that potentiates TMZ cytotoxicity by increasing MMR activity could be particularly impactful, since TMZ remains the cornerstone of adjuvant therapy. DAC in particular holds promise given its ability to cross the blood–brain barrier to reach cerebrospinal fluid (CSF) concentrations up to 50% of plasma levels [
24]. Furthermore, several studies have identified aberrant hypermethylation in the
MLH1 promoter in up to 15% of GBM specimens [
25‐
27], suggesting that a substantial subset of patients might benefit from DAC preconditioning. Published data may underestimate the true rate of hypermethylation of MMR gene promoters due to the use of techniques that limit the number of CpGs profiled in a single assay. There have been three preclinical studies on GBM cell lines demonstrating possible synergy between DAC and TMZ [
28‐
30], but none investigated whether this might be mediated by demethylation of gene promoters causing MMR protein re-expression.
Here, using a set of prospectively derived IDH-wildtype GBM cell lines of mixed MGMT methylation status, we sought to evaluate the effects of DAC preconditioning on TMZ sensitivity and MMR protein expression. We leveraged the long-read capabilities of single molecule real-time (SMRT) bisulfite sequencing to profile a 2.5 kb segment of MLH1 promoter before and after DAC treatment, and identified several loci with potential clinical utility as predictive biomarkers of DAC response.
Methods
See Online Resource 1 for full details.
Ex-vivo treatment of GBM spheroid cell lines
For cell lines treated with TMZ after DAC preconditioning, medium containing DAC 100 nM was replenished every 24 h for 5 days. Cells were resuspended in serum-free medium containing TMZ 10 µg/mL (0.05 mM) and 100 nM DAC daily for 2 days. At the completion of concurrent treatment, cells were resuspended in serum-free medium and harvested at 4, 24, 48, and 96 h. A schematic overview of all treatment conditions is provided in Online Resource 2.
Determination of IC50
GBM cell lines were cultured in T25 flasks until 70–80% confluence, and then preconditioned with 100 nM DAC for 7 days; non-treated cells were cultured in parallel. Cells were then digested and resuspended to a final concentration of 2 × 105 cells/mL in Neurobasal Medium (Gibco, #21,103–049). 50 µL of cell suspension was added to 96-well plates (10,000 cells/well) with serial dilutions of TMZ ranging from 0 to 2.5 mM. Plates were incubated at 37 °C for 72 h. Absorbance was recorded at 490 nm. Raw data was normalized to the mean absorbance of the 0 mM TMZ wells. IC50 was determined by a nonlinear regression least squares fit for [inhibitor] vs. response (four-variable slope model) using Graphpad Prism 7.0 software.
Single-molecule real-time (SMRT) sequencing
PCR samples were barcoded and pooled as previously described [
31]. SMRT sequencing was performed according to the P5-C3 Pacific Biosciences protocol with a movie collection time of 180 min. Raw sequencing reads in FASTQ format were demultiplexed and trimmed using NGSutils [
32], and then aligned to the
MLH1 promoter sequence (hg38) with Bismark and Bowtie2 [
33,
34]. The Bismark “coverage2cytosine” script was used to generate an Excel file, from which percent methylation at each CpG site was calculated. Read depth ranged from 500-2500X per sample, depending on multiplexing conditions.
Discussion
In this study, we demonstrated that DAC 100 nM for 7 days induces genome-wide DNA hypomethylation in a set of prospectively collected, IDH-wildtype GBM cell lines grown in serum-free conditions. Existing pharmacokinetic data indicate that CSF concentrations in the 100 nM range would be potentially achievable with intravenous DAC in the well-tolerated low dose range [
24,
37]. We compared changes in the level of the MMR proteins MLH1, MSH2, and MSH6 before and after DAC treatment, and found that levels of MLH1 most strongly correlated with baseline resistance, and degree of sensitization to, TMZ. Furthermore, MLH1 knockdown was able to reverse the effects of DAC. Previous studies have established the important role MMR deficiency plays in recurrent GBM. The MutSα complex, composed of MSH2 and MSH6 heterodimers, binds to methylguanine-thymine mismatches, and then recruits the MutLα complex, composed of MLH1 and PMS2 heterodimers, to initiate base excision. Although complete deficiency of MMR, which confers the microsatellite instability phenotype, is rare, inactivating mutations acquired during TMZ and reductions in MMR protein expression are common [
38,
39]. The relative importance of deficiencies in the MutSα versus the MutLα complex in GBM is less clear. In an analysis of 43 matched pairs of pre- and post-treatment GBM samples, Felsberg et al., saw significant reductions in expression of MSH2, MSH6, and PMS2, but not MLH1 [
39]. In a mouse xenograft model of human GBM cell lines, McFaline-Figueroa et al. found that MSH2 knockdown conferred TMZ resistance more potently than MSH6 knockdown [
40]. In vitro experiments using U251 cells demonstrated that reductions in MLH1 expression drive destabilization of its binding partner PMS2, and may be more correlated with TMZ resistance than either MSH2 or MSH6 [
41,
42]. Our results are overall consistent with the preclinical studies pointing to the relative importance of MLH1.
Interestingly, we observed DAC-induced upregulation of MLH1and TMZ sensitization in both
MGMT methylated and unmethylated tumors. Of the two unmethylated tumors, one (315) was derived from an aggressive secondary gliosarcoma, and the other (306) from a GBM with a high TMZ IC
50 of 9.5 mM that decreased by half to 4.7 mM with DAC preconditioning. Identification of
MGMT promoter methylation status at the time of surgery is routinely used to guide adjuvant treatment on the premise that MGMT expression predicts TMZ responsiveness and improved survival [
43]. The prognosis for elderly patients with
MGMT unmethylated tumors is particularly poor [
44‐
46]. Because
MGMT is unmethylated in 60% of IDH-wildtype GBM, a strategy to chemosensitize GBM using DAC, so that TMZ has wider utility in this subtype, could have a large impact in the poorest prognosis patients.
One theoretical concern is that DAC might act at a hypermethylated
MGMT promoter to increase expression of MGMT and thus resistance to TMZ. Although significant TMZ desensitization was seen in three GBM cell lines in our study, including one
MGMT methylated line, no associated increase in MGMT levels was observed. Rather, DAC tended to decrease MGMT levels in TMZ sensitized cell lines, which suggests that DAC alters MGMT expression through other mechanisms. Moen et al. examined the role of gene body methylation levels in MGMT regulation and found that in the presence of an unmethylated promoter, DAC could decrease MGMT expression by demethylating a region of the gene body [
28]. They further suggested that gene body methylation status should be considered together with promoter methylation status to improve the prediction of TMZ response. Our findings of the discordant lack of MGMT expression by western blot in 4 of 7 GBMs determined by pyrosequencing to be unmethylated, and the reduction of MGMT levels by DAC in unmethylated lines, lend support to these conclusions.
Previous studies examining the promoter methylation status of MMR genes in GBM cell lines found low rates of aberrant hypermethylation and an unclear relationship between this and treatment response.
MLH1 promoter hypermethylation rates ranging from 2 to 15% have been reported using short-read pyrosequencing [
39] and older qualitative assays [
25‐
27]. Rodriguez-Hernandez et al. found that hypermethylation of the proximal
MLH1 promoter region was predictive of loss of protein expression but not for treatment response [
26], while Fukushima et al. found that hypermethylation of the distal promoter strongly predicted response to nimustine [
25]. To clarify these findings, we turned to a long-read bisulfite sequencing method capable of surveying the entire
MLH1 promoter without the need for PCR subcloning, and report the largest amplicon successfully analyzed using this method to date. Our results corroborate the finding that the proximal promoter region may be critical for MLH1 expression. With DAC, hypermethylation in desensitized lines decreased inconsistently, while the proximal promoter remained uniformly hypomethylated in sensitized lines, suggesting that hypomethylation of this region is necessary but not sufficient for MLH1 expression. This is contrary to previous findings in ovarian and colon cancer xenografts suggesting that upregulation of
MLH1 with DAC is mediated directly by its action at hypermethylated CpGs in the promoter [
17]. We speculate that DAC may act indirectly on
MLH1 in GBM by increasing the expression of proapoptotic E2F1 [
47], the action of which is blocked by a hypermethylated proximal promoter. Resistance to DAC-mediated demethylation at the proximal promoter could be due to variability among different cell lines in the rate of incorporation of DAC into DNA, which is dependent on nucleoside receptor uptake, pyrimidine metabolism, and the rate of cell cycling [
48]. Despite these lingering questions, our findings nevertheless point to the existence of baseline
MLH1methylation differences between DAC responsive and non-responsive tumors that could see utility as a biomarker for patient selection in future clinical trials.
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