Abstract LB-120: Investigation of PARP inhibitor resistance in BRCA1-mutant ovarian tumors

Patients with familial high-grade serous ovarian carcinoma (HGSOC) associated with germline BRCA1/2 mutations exhibit improved outcome and high sensitivity to double strand DNA break (DSB)-inducing agents [i.e. platinum and Poly(ADP-ribose) polymerase (PARP) inhibitors] due to an underlying defect in DNA repair via homologous recombination (HR). Importantly, a subset of patients with sporadic HGSOCs also exhibit improved outcome and responsiveness to these cytotoxic agents, possibly due to defective HR caused by mechanisms unrelated to germline mutation in BRCA-1 or 2. In this regard, in The Cancer Genome Atlas (TCGA) dataset, approximately 50% of HGSOC harbored the genetic or epigenetic alterations involving HR pathway. Interestingly, even though these tumors harbored an underlying defect in the HR pathway, a significant percentage of them unexpectedly exhibited resistance to platinum chemotherapy resulting in poor prognosis. In contrast to the relative promiscuity of platinum-based therapy, the PARP inhibitor (PARPi)s have emerged as an exciting new therapeutic opportunity for HGSOCs with BRCA mutations. However, several resistance mechanisms are emerging, including reversion mutations in the BRCA genes, and loss of 53BP1. A systematic investigation of the underlying cause of PARPi resistance is necessary to identify novel drug targets to potentially overcome resistance. The bacterial clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 system for genome editing has greatly expanded the toolbox for mammalian genetics, enabling the rapid generation of isogenic cell lines with disrupted genes. We utilized this elegant system in the form of a genome-scale lenti-viral CRISPR-Cas9 knockout (GeCKO) library targeting 18,080 genes with 64,751 unique guide sequences to screen a panel of patient-derived BRCA1-deficient HGSOC lines for resistance to clinical grade PARPi and platinum drugs. The goal was to identify specific genes and signaling pathways that influence the process of resistance in these tumors. The ‘top’ hit was DYNLL1 and another hit was its binding partner ATMIN. In our validation screen, targeted disruption of ATMIN or DYNLL1 in multiple BRCA1-mutant HGSOC lines led to increase of Cisplatin IC50 up to 200% and Olaparib IC50 up to 400% along with the restoration of HR. Analysis of TCGA revealed that ATMIN is under-expressed in about 30% ovarian cancer patients and low ATMIN or DYNLL1 expression correlated with poor prognosis specifically for patients with BRCA1-mutant ovarian carcinomas. Here we explore the mechanism by which loss of ATMIN/DYNLL1 causes restoration of HR and consequent resistance to PARPi and platinum drugs in BRCA1-mutant tumors. We found ATMIN/DYNLL1 loss lead to increased end resection and Rad51 foci in the absence of BRCA1. This increase is due to increased expression of end resection enzyme in ATMIN/DYNLL1 deficient cells. We have preliminary evidence that ATMIN/DYNLL1 impedes the expression of end resection enzymes via specific transcription factors to further restrict HR in the BRCA1-mutant cells. Our study identifies a new role for ATMIN/DYNLL1 in regulating HR and provide insight on novel mechanisms of PARPi resistance that may occur in BRCA1-mutant HGSOCs.

Citation Format: Yizhou J. He, Dipanjan Chowdhury, Khyati Meghani. Investigation of PARP inhibitor resistance in BRCA1-mutant ovarian tumors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr LB-120. doi:10.1158/1538-7445.AM2017-LB-120

Abstract 1118: Synthetic lethality of CDK12 inhibition in tumors with EWS/FLI rearrangements

THZ1 is a potent, covalent inhibitor of the transcriptional CDKs, CDK7/12/13. Chemical genomic profiling of THZ1 across >1,000 diverse cancer cell lines revealed that EWS/FLI- rearranged Ewing sarcoma cells were remarkably sensitive to this molecule. We demonstrated that THZ1 inhibits the phosphorylation of the C-terminal domain of RNA Polymerase II, decreased colony formation capacity, and induced apoptosis in a dose-dependent manner in Ewing sarcoma cell lines. Using selective CDK7 and CDK12/13 inhibitors, we revealed that the primary target of THZ1 in Ewing sarcoma is CDK12/13. Genetic suppression of CDK12, but not CDK13, induced strong anti-viability effects, confirming CDK12 as the primary target. Treatment of Ewing sarcoma cell lines with THZ531, a novel CDK12/13 selective inhibitor, preferentially repressed genes involved in DNA damage repair. Additionally, suppression of EWS/FLI rendered Ewing sarcoma cells resistant to THZ531 and partially rescued the anti-viability effects of CDK12 knockdown. These results suggest that EWS/FLI imparts vulnerability to DNA damage repair inhibition and implicate a synthetic lethal relationship between the tumor-specific expression of EWS/FLI and CDK12 inhibition. Furthermore, we demonstrated that CDK12 and PARP inhibitors are highly synergistic in vitro, inducing widespread yH2AX foci formation. Interestingly, THZ531 impairs the ability of the PARP inhibitor, olaparib, to induce RAD51 foci formation, suggesting that THZ531 specifically causes a defect in homologous recombination repair. Moreover, we observed striking synergy of THZ1 and olaparib in two mouse models of Ewing sarcoma with limited toxicity observed. These findings have important translational significance as clinical trials with PARP inhibitors as single agents in Ewing sarcoma failed to demonstrate efficacy, highlighting the need to identify combination therapies that will enhance the activity of PARP inhibition. We anticipate that CDK12 and PARP inhibitor combinations will be of therapeutic interest in other ETS-rearranged tumors, as well as tumors with defects in DNA repair.

Citation Format: Amanda L. Balboni, Bjorn Stolte, Amy Saur Conway, Gabriela Alexe, Emily Jue Wang, Nicholas Kwiatkowski, Tinghu Zhang, Brian J. Abraham, Peter Kalev, Dipanjan Chowdhury, Cyril H. Benes, Richard A. Young, Nathanael S. Gray, Kimberly Stegmaier. Synthetic lethality of CDK12 inhibition in tumors with EWS/FLI rearrangements [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1118. doi:10.1158/1538-7445.AM2017-1118

miRNA profiling in a case: Control study of African American women with uterine serous carcinoma (USC)

e17116

Background: USC is an aggressive subtype of endometrial cancer associated with worse outcomes in African American patients. We evaluated differences in tumor miRNA expression by race, clinical and tumor characteristics, and survival outcomes. Methods: FFPE tumor tissue from hysterectomy specimens was identified for 29 African American cases. Case matching was performed by computer-based random assignment in a 1:1 ratio with Caucasian controls based on age ( < 70 vs. ≥70 years), stage (FIGO I/II vs. III/IV) and histologic subtype (pure vs. mixed). RNA was extracted from 77 specimens with sufficient tumor cellularity (54 tumors and 23 matched normal endometrium). miRNA array profiling was performed by microRNA Hi-Power Labeling (Hy3/Hy5) and hybridization to miRCURY LNA microRNA Array 7th Gen (Exiqon, Denmark). Analysis was performed with R/Bioconductor using a moderated t-statistic with multiple testing correction. Validation was done using the TCGA dataset. Results: Clinical and treatment characteristics were similar for cases and controls, although use of adjuvant radiation was less common in African Americans (p = 0.03). With a median follow-up of 43 months, 17 patients had recurrent or progressive disease. DFS and OS rates were similar by race (both logrank p > 0.5). Of 968 miRNAs analyzed, 649 were differentially expressed in normal endometrium vs. tumor. When compared by race, histologic subtype, stage or presence of LVI, no differentially expressed miRNAs were identified. In patients with disease recurrence at 3 years, miR-223 was significantly upregulated (fold change 1.5; p = 0.002). In validation using a TCGA dataset of 131 patients with mixed (n = 22) or pure serous (n = 109) histology, increased miR-223 expression ( > median) was associated with worse overall survival (HR 2.47; 95%CI 0.9-6.6). After adjustment for patient age and BMI, upregulation of miR-223 was a significant risk factor for death (adjusted HR 2.94; 95%CI 1.01-8.52). Conclusions: Upregulation of miR-223 was associated with disease recurrence in a cohort of women with uterine serous carcinoma and validated by TCGA data. miRNA profiling did not identify biological differences between African American and Caucasian patients.

Abstract PR04: Mechanism for PARPi resistance: Homologous recombination without BRCA1

Approximately 15-20% of all epithelial ovarian cancers harbor germline or somatic mutations in BRCA1/2. Despite PARP inhibitor induce synthetic lethality in non-cancerous mouse embryo fibroblast cells that harbor BRCA1/2 mutations, a substantial fraction of BRCA1/2-mutated tumors patients do not respond to PARPi treatment, and a large fraction of BRCA1/2-mutated tumors patients eventually develop resistance to PARPi suggest significant frequency of acquired mutation lead to PARPi resistance preventing complete cure.

We use CRISPR based library screen identified ATMIN/DYNLL1 loss as strong candidate for PARPi and cisplatin resistance mechanism. Targeted mutation on ATMIN or its transcription target DYNLL1 lead to increase of Cisplatin IC50 up to 200% and Olaparib IC50 up to 400%. More interestingly, ATMIN/DYNLL1 loss lead to restoration of Homologous recombination in BRCA1 mutant cells. ATMIN is under-expressed in about 30% ovarian cancer patient and low ATMIN expression correlate with shorter survival. Since ATMIN is important for DNA base damage repair but not Double Strand Break repair, we hypothesis ATMIN play important role in DNA damage repair pathway choice to suppress DSB repair while promote DNA base damage repair. Cells with mutant BRCA1 and loss ATMIN/DYNLL1 may result in abnormal DSB repair activity and lead to resistance to DNA damage agent such as Olaparib and Cisplatin.

This abstract is also being presented as Poster A18.

Citation Format: Yizhou Joseph He, Khyati Meghani, Dipanjan Chowdhury. Mechanism for PARPi resistance: Homologous recombination without BRCA1 [abstract]. In: Proceedings of the AACR Special Conference on DNA Repair: Tumor Development and Therapeutic Response; 2016 Nov 2-5; Montreal, QC, Canada. Philadelphia (PA): AACR; Mol Cancer Res 2017;15(4_Suppl):Abstract nr PR04.

TIRR regulates 53BP1 by masking its histone methyl-lysine binding function

P53-binding protein 1 (53BP1) is a multi-functional double-strand break repair protein that is essential for class switch recombination in B lymphocytes and for sensitizing BRCA1-deficient tumours to poly-ADP-ribose polymerase-1 (PARP) inhibitors. Central to all 53BP1 activities is its recruitment to double-strand breaks via the interaction of the tandem Tudor domain with dimethylated lysine 20 of histone H4 (H4K20me2). Here we identify an uncharacterized protein, Tudor interacting repair regulator (TIRR), that directly binds the tandem Tudor domain and masks its H4K20me2 binding motif. Upon DNA damage, the protein kinase ataxia-telangiectasia mutated (ATM) phosphorylates 53BP1 and recruits RAP1-interacting factor 1 (RIF1) to dissociate the 53BP1-TIRR complex. However, overexpression of TIRR impedes 53BP1 function by blocking its localization to double-strand breaks. Depletion of TIRR destabilizes 53BP1 in the nuclear-soluble fraction and alters the double-strand break-induced protein complex centring 53BP1. These findings identify TIRR as a new factor that influences double-strand break repair using a unique mechanism of masking the histone methyl-lysine binding function of 53BP1.

Clear cell ovarian cancers with microsatellite instability: A unique subset of ovarian cancers with increased tumor-infiltrating lymphocytes and PD-1/PD-L1 expression

Clear cell ovarian carcinoma (CCOC) represents a distinct histologic subtype of ovarian cancer associated with significantly worse prognosis across all stages and no effective therapeutic options. Here, we report a rare but clinically important cohort of CCOCs with microsatellite instability (MSI) (MSI-CCOCs), which are highly immunogenic and may thus be very responsive to immune checkpoint blockade. CCOCs with MSI exhibit a significantly higher number of CD8⁺ TILs, higher CD8⁺/CD4⁺ ratio, and higher PD-1⁺ TILs compared with microsatellite stable (MSS) CCOCs and compared with high grade serous ovarian cancers, which are the most common histologic subtype of ovarian cancer. Of note, PD-L1 expression in tumor cells or immune cells was noted in all cases of CCOCs with MSI. These observations open an alternative therapeutic avenue for a fraction of patients with CCOC and argue for the routine testing of CCOCs for MSI, a test that is not currently routinely performed.

Abstract 2441: CDK12/13 inhibition cooperates with the Ewing sarcoma oncoprotein EWS/FLI to attenuate homologous recombination repair in Ewing sarcoma cells

A therapeutic challenge in pediatric oncology is the paucity of readily “druggable” genetic events in many of the childhood malignancies. These tumors are frequently defined by sentinel abnormalities involving transcription factors in an otherwise quiet genomic landscape. One approach to treating these tumors would involve direct targeting of the aberrant transcription factor; however, this is a drug discovery challenge. A second approach would be to identify synthetic lethal relationships in the context of the aberrant transcription factor. THZ1, a covalent and potent inhibitor of CDK7, CDK12, and CDK13, kinases involved in transcriptional regulation, recently emerged as a targeted strategy to impair aberrant transcription. Extensive profiling of THZ1 against a diverse panel of &gt;1,000 cancer cell lines revealed that the pediatric solid tumor, Ewing sarcoma, was exceptionally sensitive to this compound. We found that the anti-proliferative effects of THZ1 in Ewing sarcoma can be attributed primarily to CDK12/13 inhibition. Treatment of Ewing sarcoma cells with THZ531, a covalent and selective CDK12/13 inhibitor, decreased the phosphorylation of the C-terminal domain of RNA polymerase II, induced apoptosis, and markedly decreased colony formation capacity of Ewing sarcoma cell lines. In contrast, treatment with a selective CDK7 inhibitor had minimal effect. EWS/FLI is the transcription factor fusion protein that typically drives tumor establishment and maintenance in Ewing sarcoma tumors. Based on prior reports of this compound class inhibiting a small subset of highly expressed genes critical to tumor maintenance, we expected that these inhibitors would disrupt oncogenic EWS/FLI-driven transcription as the mechanism of inducing cell death. Surprisingly, however, global gene expression profiling revealed that THZ531 did not selectively repress EWS/FLI or EWS/FLI target genes. Rather, we observed that THZ531 preferentially repressed genes involved in DNA damage repair. Consistent with this finding, we found that THZ531 induced defects in DNA damage repair and highly synergized with DNA damaging agents that induce lesions repaired by homologous recombination (HR). Furthermore, we found that suppression of EWS/FLI attenuated sensitivity to THZ531 and the PARP inhibitor olaparib and abrogated synergy observed with this drug combination. Thus, we conclude that EWS/FLI establishes tumor cell synthetic lethality to CDK12/13 inhibitors by imparting sensitivity to DNA repair defects. This work establishes a novel mechanism of action of CDK12/13 inhibitors and gives further credence to the role of EWS/FLI in DNA damage response. Ongoing work is dedicated to the in vivo testing of THZ1 alone, and in combination with olaparib, as a novel targeted therapy for the treatment of Ewing sarcoma.

Citation Format: Amanda Balboni, Björn Stolte, Peter Kalev, Nicholas Kwiatkowski, Tinghu Zhang, Brian Abraham, Gabriela Alexe, Dipanjan Chowdhury, Richard A. Young, Nathanael S. Gray, Kimberly Stegmaier. CDK12/13 inhibition cooperates with the Ewing sarcoma oncoprotein EWS/FLI to attenuate homologous recombination repair in Ewing sarcoma cells. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 2441.

Common variation in BRCA1 may have a role in progression to lethal prostate cancer after radiation treatment

BACKGROUND

To evaluate whether single-nucleotide polymorphisms (SNPs) reflecting common variation in the tumor suppressor BRCA1 affect prostate cancer outcomes. Because radiation therapy (RT) induces DNA damage, we hypothesized that common variation in BRCA1 has a role in progression to lethal prostate cancer, particularly in patients receiving RT.

METHODS

We followed 802 men diagnosed with localized prostate cancer (cT1-T3/N0/M0) who were treated with RT in the US Health Professionals Follow-up Study (HPFS) and Physicians' Health Study (PHS), for progression to lethal prostate cancer. Six SNPs (rs3737559, rs1799950, rs799923, rs915945, rs4474733 and rs8176305) were genotyped in HPFS to capture common variation across BRCA1. rs4474733 and rs8176305 were also evaluated in the PHS cohort. Cox proportional hazards models were used to estimate per-allele hazard ratios (HR) and 95% confidence intervals (CI) stratified by primary treatment.

RESULTS

In the RT group (n=802), 71 men progressed to lethal disease during a mean follow-up of 12 years. We found that two SNPs, rs4473733 (HR: 0.65; 95% CI 0.42-0.99) and rs8176305 (HR: 2.03; 95% CI 1.33-3.10), were associated with lethal prostate cancer in men receiving RT.

CONCLUSIONS

Common variation in BRCA1 may influence clinical outcomes in patients receiving RT for localized prostate cancer by modifying the response to RT. Our findings merit further follow-up studies to validate these SNPs and better understand their functional and biological significance.

Circulating miR-29a and miR-150 correlate with delivered dose during thoracic radiation therapy for non-small cell lung cancer

BACKGROUND

Risk of normal tissue toxicity limits the amount of thoracic radiation therapy (RT) that can be routinely prescribed to treat non-small cell lung cancer (NSCLC). An early biomarker of response to thoracic RT may provide a way to predict eventual toxicities-such as radiation pneumonitis-during treatment, thereby enabling dose adjustment before the symptomatic onset of late effects. MicroRNAs (miRNAs) were studied as potential serological biomarkers for thoracic RT. As a first step, we sought to identify miRNAs that correlate with delivered dose and standard dosimetric factors.

METHODS

We performed miRNA profiling of plasma samples obtained from five patients with Stage IIIA NSCLC at five dose-points each during radical thoracic RT. Candidate miRNAs were then assessed in samples from a separate cohort of 21 NSCLC patients receiving radical thoracic RT. To identify a cellular source of circulating miRNAs, we quantified in vitro miRNA expression intracellularly and within secreted exosomes in five NSCLC and stromal cell lines.

RESULTS

miRNA profiling of the discovery cohort identified ten circulating miRNAs that correlated with delivered RT dose as well as other dosimetric parameters such as lung V20. In the validation cohort, miR-29a-3p and miR-150-5p were reproducibly shown to decrease with increasing radiation dose. Expression of miR-29a-3p and miR-150-5p in secreted exosomes decreased with radiation. This was concomitant with an increase in intracellular levels, suggesting that exosomal export of these miRNAs may be downregulated in both NSCLC and stromal cells in response to radiation.

CONCLUSIONS

miR-29a-3p and miR-150-5p were identified as circulating biomarkers that correlated with delivered RT dose. miR-150 has been reported to decrease in the circulation of mammals exposed to radiation while miR-29a has been associated with fibrosis in the human heart, lungs, and kidneys. One may therefore hypothesize that outlier levels of circulating miR-29a-3p and miR-150-5p may eventually help predict unexpected responses to radiation therapy, such as toxicity.

Association and prognostic significance of BRCA1/2-mutation status with neoantigen load, number of tumor-infiltrating lymphocytes and expression of PD-1/PD-L1 in high grade serous ovarian cancer

Immune checkpoint inhibitors (e.g., anti-PD-1 and anti-PD-L1 antibodies) have demonstrated remarkable efficacy against hypermutated cancers such as melanomas and lung carcinomas. One explanation for this effect is that hypermutated lesions harbor more tumor-specific neoantigens that stimulate recruitment of an increased number of tumor-infiltrating lymphocytes (TILs), which is counterbalanced by overexpression of immune checkpoints such as PD-1 or PD-L1. Given that BRCA1/2-mutated high grade serous ovarian cancers (HGSOCs) exhibit a higher mutational load and a unique mutational signature with an elevated number of larger indels up to 50 bp, we hypothesized that they may also harbor more tumor-specific neoantigens, and, therefore, exhibit increased TILs and PD-1/PD-L1 expression. Here, we report significantly higher predicted neoantigens in BRCA1/2-mutated tumors compared to tumors without alterations in homologous recombination (HR) genes (HR-proficient tumors). Tumors with higher neoantigen load were associated with improved overall survival and higher expression of immune genes associated with tumor cytotoxicity such as genes of the TCR, the IFN-gamma and the TNFR pathways. Furthermore, immunohistochemistry studies demonstrated that BRCA1/2-mutated tumors exhibited significantly increased CD3+ and CD8+ TILs, as well as elevated expression of PD-1 and PD-L1 in tumor-associated immune cells compared to HR-proficient tumors. Survival analysis showed that both BRCA1/2-mutation status and number of TILs were independently associated with outcome. Of note, two distinct groups of HGSOCs, one with very poor prognosis (HR proficient with low number of TILs) and one with very good prognosis (BRCA1/2-mutated tumors with high number of TILs) were defined. These findings support a link between BRCA1/2-mutation status, immunogenicity and survival, and suggesting that BRCA1/2-mutated HGSOCs may be more sensitive to PD-1/PD-L1 inhibitors compared to HR-proficient HGSOCs.

Association and prognostic significance of BRCA1/2-mutation status with neoantigen load, number of tumor-infiltrating lymphocytes and expression of PD-1/PD-L1 in high grade serous ovarian cancer

Immune checkpoint inhibitors (e.g., anti-PD-1 and anti-PD-L1 antibodies) have demonstrated remarkable efficacy against hypermutated cancers such as melanomas and lung carcinomas. One explanation for this effect is that hypermutated lesions harbor more tumor-specific neoantigens that stimulate recruitment of an increased number of tumor-infiltrating lymphocytes (TILs), which is counterbalanced by overexpression of immune checkpoints such as PD-1 or PD-L1. Given that BRCA1/2-mutated high grade serous ovarian cancers (HGSOCs) exhibit a higher mutational load and a unique mutational signature with an elevated number of larger indels up to 50 bp, we hypothesized that they may also harbor more tumor-specific neoantigens, and, therefore, exhibit increased TILs and PD-1/PD-L1 expression. Here, we report significantly higher predicted neoantigens in BRCA1/2-mutated tumors compared to tumors without alterations in homologous recombination (HR) genes (HR-proficient tumors). Tumors with higher neoantigen load were associated with improved overall survival and higher expression of immune genes associated with tumor cytotoxicity such as genes of the TCR, the IFN-gamma and the TNFR pathways. Furthermore, immunohistochemistry studies demonstrated that BRCA1/2-mutated tumors exhibited significantly increased CD3+ and CD8+ TILs, as well as elevated expression of PD-1 and PD-L1 in tumor-associated immune cells compared to HR-proficient tumors. Survival analysis showed that both BRCA1/2-mutation status and number of TILs were independently associated with outcome. Of note, two distinct groups of HGSOCs, one with very poor prognosis (HR proficient with low number of TILs) and one with very good prognosis (BRCA1/2-mutated tumors with high number of TILs) were defined. These findings support a link between BRCA1/2-mutation status, immunogenicity and survival, and suggesting that BRCA1/2-mutated HGSOCs may be more sensitive to PD-1/PD-L1 inhibitors compared to HR-proficient HGSOCs.

Serum microRNAs are early indicators of survival after radiation-induced hematopoietic injury

Accidental radiation exposure is a threat to human health that necessitates effective clinical planning and diagnosis. Minimally invasive biomarkers that can predict long-term radiation injury are urgently needed for optimal management after a radiation accident. We have identified serum microRNA (miRNA) signatures that indicate long-term impact of total body irradiation (TBI) in mice when measured within 24 hours of exposure. Impact of TBI on the hematopoietic system was systematically assessed to determine a correlation of residual hematopoietic stem cells (HSCs) with increasing doses of radiation. Serum miRNA signatures distinguished untreated mice from animals exposed to radiation and correlated with the impact of radiation on HSCs. Mice exposed to sublethal (6.5 Gy) and lethal (8 Gy) doses of radiation were indistinguishable for 3 to 4 weeks after exposure. A serum miRNA signature detectable 24 hours after radiation exposure consistently segregated these two cohorts. Furthermore, using either a radioprotective agent before, or radiation mitigation after, lethal radiation, we determined that the serum miRNA signature correlated with the impact of radiation on animal health rather than the radiation dose. Last, using humanized mice that had been engrafted with human CD34(+) HSCs, we determined that the serum miRNA signature indicated radiation-induced injury to the human bone marrow cells. Our data suggest that serum miRNAs can serve as functional dosimeters of radiation, representing a potential breakthrough in early assessment of radiation-induced hematopoietic damage and timely use of medical countermeasures to mitigate the long-term impact of radiation.

A genome-wide miRNA screen revealed miR-603 as a MGMT-regulating miRNA in glioblastomas

MGMT expression is a critical determinant for therapeutic resistance to DNA alkylating agents. We previously demonstrated that MGMT expression is post-transcriptionally regulated by miR-181d and other miRNAs. Here, we performed a genome-wide screen to identify MGMT regulating miRNAs. Candidate miRNAs were further tested for inverse correlation with MGMT expression in clinical specimens. We identified 15 candidate miRNAs and characterized the top candidate, miR-603. Transfection of miR-603 suppressed MGMT mRNA/protein expression in vitro and in vivo; this effect was reversed by transfection with antimiR-603. miR-603 affinity-precipitated with MGMT mRNA and suppressed luciferase activity in an MGMT-3'UTR-luciferase assay, suggesting direct interaction between miR-603 and MGMT 3'UTR. miR-603 transfection enhanced the temozolomide (TMZ) sensitivity of MGMT-expressing glioblastoma cell lines. Importantly, miR-603 mediated MGMT suppression and TMZ resistance were reversed by expression of an MGMT cDNA. In a collection of 74 clinical glioblastoma specimens, both miR-603 and miR-181d levels inversely correlated with MGMT expression. Moreover, a combined index of the two miRNAs better reflected MGMT expression than each individually. These results suggest that MGMT is co-regulated by independent miRNAs. Characterization of these miRNAs should contribute toward strategies for enhancing the efficacy of DNA alkylating agents.

A functional screen identifies miRs that induce radioresistance in glioblastomas

The efficacy of radiotherapy in many tumor types is limited by normal tissue toxicity and by intrinsic or acquired radioresistance. Therefore, it is essential to understand the molecular network responsible for regulating radiosensitivity/resistance. Here, an unbiased functional screen identified four microRNAs (miR1, miR125a, miR150, and miR425) that induce radioresistance. Considering the clinical importance of radiotherapy for patients with glioblastoma, the impact of these miRNAs on glioblastoma radioresistance was investigated. Overexpression of miR1, miR125a, miR150, and/or miR425 in glioblastoma promotes radioresistance through upregulation of the cell-cycle checkpoint response. Conversely, antagonizing with antagomiRs sensitizes glioblastoma cells to irradiation, suggesting their potential as targets for inhibiting therapeutic resistance. Analysis of glioblastoma datasets from The Cancer Genome Atlas (TCGA) revealed that these miRNAs are expressed in glioblastoma patient specimens and correlate with TGFβ signaling. Finally, it is demonstrated that expression of miR1 and miR125a can be induced by TGFβ and antagonized by a TGFβ receptor inhibitor. Together, these results identify and characterize a new role for miR425, miR1, miR125, and miR150 in promoting radioresistance in glioblastomas and provide insight into the therapeutic application of TGFβ inhibitors in radiotherapy.

IMPLICATIONS

Systematic identification of miRs that cause radioresistance in gliomas is important for uncovering predictive markers for radiotherapy or targets for overcoming radioresistance.

Phosphorylated RPA recruits PALB2 to stalled DNA replication forks to facilitate fork recovery

Phosphorylation of replication protein A (RPA) by Cdk2 and the checkpoint kinase ATR (ATM and Rad3 related) during replication fork stalling stabilizes the replisome, but how these modifications safeguard the fork is not understood. To address this question, we used single-molecule fiber analysis in cells expressing a phosphorylation-defective RPA2 subunit or lacking phosphatase activity toward RPA2. Deregulation of RPA phosphorylation reduced synthesis at forks both during replication stress and recovery from stress. The ability of phosphorylated RPA to stimulate fork recovery is mediated through the PALB2 tumor suppressor protein. RPA phosphorylation increased localization of PALB2 and BRCA2 to RPA-bound nuclear foci in cells experiencing replication stress. Phosphorylated RPA also stimulated recruitment of PALB2 to single-strand deoxyribonucleic acid (DNA) in a cell-free system. Expression of mutant RPA2 or loss of PALB2 expression led to significant DNA damage after replication stress, a defect accentuated by poly-ADP (adenosine diphosphate) ribose polymerase inhibitors. These data demonstrate that phosphorylated RPA recruits repair factors to stalled forks, thereby enhancing fork integrity during replication stress.

EGFR-mediated chromatin condensation protects KRAS-mutant cancer cells against ionizing radiation

Therapeutics that target the epidermal growth factor receptor (EGFR) can enhance the cytotoxic effects of ionizing radiation (IR). However, predictive genomic biomarkers of this radiosensitization have remained elusive. By screening 40 non-small cell lung cancer cell (NSCLC) lines, we established a surprising positive correlation between the presence of a KRAS mutation and radiosensitization by the EGFR inhibitors erlotinib and cetuximab. EGFR signaling in KRAS-mutant NSCLC cells promotes chromatin condensation in vitro and in vivo, thereby restricting the number of DNA double-strand breaks (DSB) produced by a given dose of IR. Chromatin condensation in interphase cells is characterized by an unexpected mitosis-like colocalization of serine 10 phosphorylation and lysine 9 trimethylation on histone H3. Aurora B promotes this process in a manner that is codependent upon EGFR and protein kinase C α (PKCα). PKCα, in addition to MEK/ERK signaling, is required for the suppression of DSB-inducible premature senescence by EGFR. Blockade of autophagy results in a mutant KRAS-dependent senescence-to-apoptosis switch in cancer cells treated with IR and erlotinib. In conclusion, we identify EGFR as a molecular target to overcome a novel mechanism of radioresistance in KRAS-mutant tumor cells, which stands in contrast to the unresponsiveness of KRAS-mutant cancers to EGFR-directed agents in monotherapy. Our findings may reposition EGFR-targeted agents for combination with DSB-inducing therapies in KRAS-mutant NSCLC.

MicroRNAs down-regulate homologous recombination in the G1 phase of cycling cells to maintain genomic stability

Homologous recombination (HR)-mediated repair of DNA double-strand break (DSB)s is restricted to the post-replicative phases of the cell cycle. Initiation of HR in the G1 phase blocks non-homologous end joining (NHEJ) impairing DSB repair. Completion of HR in G1 cells can lead to the loss-of-heterozygosity (LOH), which is potentially carcinogenic. We conducted a gain-of-function screen to identify miRNAs that regulate HR-mediated DSB repair, and of these miRNAs, miR-1255b, miR-148b*, and miR-193b* specifically suppress the HR-pathway in the G1 phase. These miRNAs target the transcripts of HR factors, BRCA1, BRCA2, and RAD51, and inhibiting miR-1255b, miR-148b*, and miR-193b* increases expression of BRCA1/BRCA2/RAD51 specifically in the G1-phase leading to impaired DSB repair. Depletion of CtIP, a BRCA1-associated DNA end resection protein, rescues this phenotype. Furthermore, deletion of miR-1255b, miR-148b*, and miR-193b* in independent cohorts of ovarian tumors correlates with significant increase in LOH events/chromosomal aberrations and BRCA1 expression.

DOI:http://dx.doi.org/10.7554/eLife.02445.001

The DNA in a cell is damaged thousands of times every day. One of the most serious types of damage involves something breaking both of the strands in the double helix. Such a double-strand break can delete genes or even kill the cell. In fact, conventional cancer therapy kills cancer cells by causing irreparable double-strand breaks. Conversely, a normal cell that is constantly exposed to DNA damaging agents can become a tumor if double-strand breaks are incorrectly repaired. An efficient and accurate double-strand break repair system needs to be in place to prevent this transformation. Therefore, an in-depth understanding of double-strand break repair and the factors involved are important for both gaining insight into the cause of cancer and to improve cancer therapy.

Cells have evolved several different ways to detect and repair double-strand breaks. A method called homologous recombination, for example, uses an undamaged DNA molecule as a template that can be copied to make new DNA. Since it needs a readily available DNA template, this method only works in phases of the cell growth cycle where there are many copies of DNA—that is, in the post-DNA replication phases. In particular, homologous recombination does not work during the pre-replication, G1 phase. If homologous recombination is attempted during G1, it will block the other methods employed by cells to repair broken strands of DNA.

An important challenge is to understand how homologous recombination is restricted to particular parts of the cell cycle. Although certain proteins associated with the early stages of double-strand repair are thought to determine the type of DNA repair that occurs, the details of this process are not fully understood.

One group of molecules that are thought to be involved are microRNAs, which normally limit the number of proteins produced from certain genes. However, since a single microRNA molecule can be associated with several proteins, and since a single protein can be associated with several microRNA molecules, it has proved difficult to establish the exact effects of a specific microRNA molecule.

Choi et al. now show that seven microRNA molecules can control homologous recombination, and three microRNAs in particular restrict homologous recombination during the G1 phase of the cell cycle. If these microRNAs are inhibited during the G1 phase, which allows homologous recombination to start, and counter-intuitively more double-stranded breaks are seen. However, if a gene involved in starting homologous repair–called CtIP—is silenced while the microRNAs are inhibited, then the DNA breaks are repaired. Exactly, how the microRNA molecules produce different effects during different phases of the cell cycle will be need to be investigated by future studies.

DOI:http://dx.doi.org/10.7554/eLife.02445.002

Dephosphorylation enables the recruitment of 53BP1 to double-strand DNA breaks

Excluding 53BP1 from chromatin is required to attenuate the DNA damage response during mitosis, yet the functional relevance and regulation of this exclusion are unclear. Here we show that 53BP1 is phosphorylated during mitosis on two residues, T1609 and S1618, located in its well-conserved ubiquitination-dependent recruitment (UDR) motif. Phosphorylating these sites blocks the interaction of the UDR motif with mononuclesomes containing ubiquitinated histone H2A and impedes binding of 53BP1 to mitotic chromatin. Ectopic recruitment of 53BP1-T1609A/S1618A to mitotic DNA lesions was associated with significant mitotic defects that could be reversed by inhibiting nonhomologous end-joining. We also reveal that protein phosphatase complex PP4C/R3β dephosphorylates T1609 and S1618 to allow the recruitment of 53BP1 to chromatin in G1 phase. Our results identify key sites of 53BP1 phosphorylation during mitosis, identify the counteracting phosphatase complex that restores the potential for DDR during interphase, and establish the physiological importance of this regulation.

Evaluation of ophthalmic manifestations in patients with intracranial tumours

The present study was done to observe the ophthalmic manifestations in patients with intracranial tumor. This was a prospective, purposive, consecutive, observational study conducted in patients with radiologically proven intracranial tumors in the department of Ophthalmology with collaboration of Department of Neuro-surgery of Bangabandhu Sheikh Mujib Medical University from January 2006 to December 2010. All cases had tissue histopathology confirmation post-operatively. The most common type of intracranial tumor was pituitary adenoma (58.04%), followed by craniopharyngioma (20.53%), posterior fossa tumour (12.50%) [medulloblestoma, ependymoma], meningioma (8.04%) [sphenoidalwing meningioma, petroclavel meningioma, oligodendroglioma] and others (0.89%) [nasopharyngial carcinoma, esthesio - astrocytoma]. Common neuro-ophthalmological findings were visual blur (91.07%), visual field defect (71.42%), optic disc changes (50%), pupillary light reaction defect (48.21%) and colour vision defect (46.42%). The study shows, pituitary adenoma is the most common tumor that impairs the visual pathway structures followed by craniopharyngioma, posterior fossa tumour & meningioma. Furthermore, decreased visual acuity, visual field defect, abnormal optic discs, relative afferent pupillary defect and ophthalmoplegia etc. are the common neuro-ophthalmic features that should be carefully examined for early detection of intracranial tumors.