The ERCC1 and ERCC4 genes encode the two subunits of the ERCC1–XPF nuclease. This enzyme plays an important role in repair of DNA damage and in maintaining genomic stability. ERCC1–XPF nuclease nicks DNA specifically at junctions between double-stranded and single-stranded DNA, when the single-strand is oriented 5′ to 3′ away from a junction. ERCC1–XPF is a core component of nucleotide excision repair and also plays a role in interstrand crosslink repair, some pathways of double-strand break repair by homologous recombination and end-joining, as a backup enzyme in base excision repair, and in telomere length regulation. In many of these activities, ERCC1–XPF complex cleaves the 3′ tails of DNA intermediates in preparation for further processing. ERCC1–XPF interacts with other proteins including XPA, RPA, SLX4 and TRF2 to perform its functions. Disruption of these interactions or direct targeting of ERCC1–XPF to decrease its DNA repair function might be a useful strategy to increase the sensitivity of cancer cells to some DNA damaging agents. Complete deletion of either ERCC1 or ERCC4 is not compatible with viability in mice or humans. However, mutations in the ERCC1 or ERCC4 genes cause a remarkable array of rare inherited human disorders. These include specific forms of xeroderma pigmentosum, Cockayne syndrome, Fanconi anemia, XFE progeria and cerebro-oculo-facio-skeletal syndrome.

Nucleotide excision repair (NER) in mammalian cells requires the xeroderma pigmentosum group A protein (XPA) as a core factor. Remarkably, XPA and other NER proteins have been detected by chromatin immunoprecipitation at some active promoters, and NER deficiency is reported to influence the activated transcription of selected genes. However, the global influence of XPA on transcription in human cells has not been determined. We analyzed the human transcriptome by RNA sequencing (RNA-Seq). We first confirmed that XPA is confined to the cell nucleus even in the absence of external DNA damage, in contrast to previous reports that XPA is normally resident in the cytoplasm and is imported following DNA damage. We then analyzed four genetically matched human cell line pairs deficient or proficient in XPA. Of the ∼14,000 genes transcribed in each cell line, 325 genes (2%) had a significant XPA-dependent directional change in gene expression that was common to all four pairs (with a false discovery rate of 0.05). These genes were enriched in pathways for the maintenance of mitochondria. Only 27 common genes were different by more than 1.5-fold. The most significant hits were AKR1C1 and AKR1C2, involved in steroid hormone metabolism. AKR1C2 protein was lower in all of the immortalized XPA-deficient cells. Retinoic acid treatment led to modest XPA-dependent activation of some genes with transcription-related functions. We conclude that XPA status does not globally influence human gene transcription. However, XPA significantly influences expression of a small subset of genes important for mitochondrial functions and steroid hormone metabolism. The results may help explain defects in neurological function and sterility in individuals with xeroderma pigmentosum.

Background: Proton relative biological effectiveness (RBE) is known to depend on physical factors of the proton beam, such as its linear energy transfer (LET), as well as on cell-line specific biological factors, such as their ability to repair DNA damage. However, in a clinical setting, proton RBE is still considered to have a fixed value of 1.1 despite the existence of several empirical models that can predict proton RBE based on how a cell's survival curve (linear-quadratic model [LQM]) parameters α and β vary with the LET of the proton beam. Part of the hesitation to incorporate variable RBE models in the clinic is due to the great noise in the biological datasets on which these models are trained, often making it unclear which model, if any, provides sufficiently accurate RBE predictions to warrant a departure from RBE = 1.1. Purpose: Here, we introduce a novel model of proton RBE based on how a cell's intrinsic radiosensitivity varies with LET, rather than its LQM parameters. Methods and materials: We performed clonogenic cell survival assays for eight cell lines exposed to 6 MV x-rays and 1.2, 2.6, or 9.9 keV/µm protons, and combined our measurements with published survival data (n = 397 total cell line/LET combinations). We characterized how radiosensitivity metrics of the form D SF% , (the dose required to achieve survival fraction [SF], e.g., D 10% ) varied with proton LET, and calculated the Bayesian information criteria associated with different LET-dependent functions to determine which functions best described the underlying trends. This allowed us to construct a six-parameter model that predicts cells' proton survival curves based on the LET dependence of their radiosensitivity, rather than the LET dependence of the LQM parameters themselves. We compared the accuracy of our model to previously established empirical proton RBE models, and implemented our model within a clinical treatment plan evaluation workflow to demonstrate its feasibility in a clinical setting. Results: Our analyses of the trends in the data show that D SF% is linearly correlated between x-rays and protons, regardless of the choice of the survival level (e.g., D 10% , D 37% , or D 50% are similarly correlated), and that the slope and intercept of these correlations vary with proton LET. The model we constructed based on these trends predicts proton RBE within 15%-30% at the 68.3% confidence level and offers a more accurate general description of the experimentalThis is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

Small molecule inhibitors are currently in preclinical and clinical development for the treatment of selected cancers, particularly those with existing genetic alterations in DNA repair and DNA damage response (DDR) pathways. Keen interest has also been expressed in combining such agents with other targeted antitumor strategies such as radiotherapy. Radiotherapy exerts its cytotoxic effects primarily through DNA damage–induced cell death; therefore, inhibiting DNA repair and the DDR should lead to additive and/or synergistic radiosensitizing effects. In this study we screened the response to X-ray or proton radiation in cell lines treated with DDR inhibitors (DDRis) targeting ATM, ATR, DNA-PKcs, Rad51, and PARP, with survival metrics established using clonogenic assays. We observed that DDRis generate significant radiosensitization in cancer and primary cells derived from normal tissue. Existing genetic defects in cancer cells appear to be an important consideration when determining the optimal inhibitor to use for synergistic combination with radiation. We also show that while greater radiosensitization can be achieved with protons (9.9 keV/μm) combined with DDRis, the relative biological effectiveness is unchanged or in some cases reduced. Our results indicate that while targeting the DDR can significantly radiosensitize cancer cells to such combinations, normal cells may also be equally or more severely affected, depending on the DDRi used. These data highlight the importance of identifying genetic defects as predictive biomarkers of response for combination treatment.

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We assessed whether adding sodium borocaptate (BSH) or 4borono-L-phenylalanine (BPA) to cells irradiated with proton beams influenced the biological effectiveness of those beams against prostate cancer cells to investigate if the alpha particles generated through proton-boron nuclear reactions would be sufficient to enhance the biological effectiveness of the proton beams. Methods: We measured clonogenic survival in DU145 cells treated with 80.4ppm BSH or 86.9-ppm BPA, or their respective vehicles, after irradiation with 6-MV X-rays, 1.2-keV/μm (low linear energy transfer [LET]) protons, or 9.9-keV/μm (high-LET) protons. We also measured γH2AX and 53BP1 foci in treated cells at 1 and 24 h after irradiation with the same conditions. Results: We found that BSH radiosensitized DU145 cells across all radiation types. However, no difference was found in relative radiosensitization, characterized by the sensitization enhancement ratio or the relative biological effectiveness, for vehicle-versus BSH-treated cells. No differences were found in numbers of γH2AX or 53BP1 foci or γH2AX/53BP1 colocalized foci for vehicle-versus BSH-treated cells across radiation types. BPA did not radiosensitize DU145 cells nor induced any significant differences when comparing vehicle-versus BPA-treated cells for clonogenic cell survival or γH2AX and 53BP1 foci or γH2AX/53BP1 colocalized foci. Conclusions: Treatment with 11 B, at concentrations of 80.4 ppm from BSH or 86.9 ppm from BPA, had no effect on the biological effectiveness of proton beams in DU145 prostate cancer cells. Our results agree with published theoretical calculations indicating that the contribution of alpha particles from such reactions to the total absorbed dose and biological effectiveness is negligible. We also found that BSH radiosensitized DU145 cells to X-rays, low-LET protons, and high-LET protons but that the radiosensitization was not related to DNA damage. K E Y W O R D Salpha particles, proton-boron capture therapy, proton-boron nuclear reaction, relative biological effectiveness, sensitization enhancement ratio 6098

Purpose Triple negative breast cancers (TNBC) are more often found among BRCA gene mutation carriers; even among non-mutation carriers, TNBCs are thought to carry a phenotype of BRCAness. Inhibitors of Poly(adenosine diphosphate-ribose) polymerase (PARPi) have improved survival outcomes for both advanced and early stage breast cancer associated with a BRCA mutation, as well as BRCA mutated ovarian and prostate cancers. Radiotherapy (RT) is a widely used treatment to locally control cancers, but it is unclear how different types of RT, including clinical x-rays and protons, interact with PARPi and how these affect antitumor immunity. Protons induce more clustered DNA lesions, including clustered double and single strand breaks (DSBs and SSBs) and clustered base damages, than x-rays due to their higher ionization density. If not properly repaired, DSBs can generate micronuclei (MN), which activate the cyclic GMP-AMP synthase (cGAS) and stimulator of interferon (IFN) genes (STING) (cGAS-STING) pathway, leading to antitumor immunity. Residual DNA damage also induces cellular senescence, which is a known tumor suppressor mechanism. In this study we investigated the effects of combining a PARPi with x-rays or protons on clonogenic cell survival, residual DNA damage, senescence, cGAS co-localization with MN and delay in tumor growth in the context of BRCA1 mutation. Methods In vitro, BRCA1 deficient (HCC1937 and MDA-MB-436) and proficient (HCC1937-BRCA and MDA-MB-436-BRCA) breast cancer cell lines were treated with a PARPi (Olaparib, 0.1 - 5.0 μM) and irradiated with 6 MV x-rays or protons (9.9 keV/um) with doses from 0.5 to 5 Gy. HCC1937-BRCA was gifted from Dr. Stecklein (The University of Kansas Cancer Center) and MDA-MB-436-BRCA was gifted from Dr. Johnson (Fox Chase Cancer Center). We then quantified clonogenic cell survival, gH2AX and 53BP1 foci at 24 h after irradiation, MN number and MN-cGAS co-localization (cGAS+ MN) at 24 and 74 h after irradiation, and RT-induced senescence. In vivo, we used a preclinical TNBC mouse model (4T1 tumors on the leg of BALB/c mice) to assess survival and tumor growth delay on animals treated with DMSO, PARPi alone (Olaparib, 100 mg/kg), DMSO+x-rays, and PARPi+x-rays. Experiments with protons are ongoing. PARPi was administrated via oral gavage 2 h prior to irradiation (1 × 11 Gy). Results Survival fraction was lower after protons compared to x-rays (RBED10%>1) in HCC1937-BRCA, HCC1937 and MDA-MB-436 cells. Regardless of the radiation type, survival fraction was lower for HCC1937 compared to HCC1937-BRCA cells. PARPi treatment appears to result in greater radiosensitization of cells exposed to protons than those exposed to x-rays as assessed by clonogenic cell survival. The number of MN per nucleus was higher in HCC1937 than HCC1937-BRCA at 24 and 72 h after protons and x-rays at both 2 and 5 Gy, and this effect that was amplified with PARPi vs. without PARPi. Moreover, the number of cGAS+ MN was greater after protons than x-rays for HCC1937 but not HCC1937-BRCA at 24 and 72 h. The proportion of senescent cells for HCC1937-BRCA was higher (1.4 fold) after PARPi+protons compared to PARPi+x-rays. In vivo, x-rays lead to a delay in tumor growth, which was higher for the PARPi+x-rays group compared to PARPi alone or DMSO+x-rays groups. Conclusion In vitro, a PARPi treatment in BRCA1 mutated cell lines leads to a greater sensitivity to radiation compared to their counterparts with recovered BRCA1 function. This sensitivity is higher after protons compared to x-rays (survival fraction and number of micronuclei). In vivo, PARPi treatment combined with x-rays lead to higher delay in tumor growth compared to x-rays alone. These preliminary data are promising results on the effect of radiation combined with PARPi on BRCA1 mutated models. Citation Format: Mariam Ben Kacem, Scott J. Bright, Broderick X Turner, David B Flint, Mandira Manandhar, David Martinus, Gabriel O Sawakuchi, Simona F Shaitelman. Parp inhibition sensitizes brca deficient cancer cell lines and tumors to clinical x-ray and proton irradiation [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr P2-06-01.

Background: Mutant KRAS is a key stratification factor in determining colorectal cancer (CRC) treatment. Nearly 50% of CRC tumors have KRAS mutations and these patients are unlikely to respond to anti-EGFR therapy. 5-fluorouracil (5-FU)-based chemotherapy is the preferred treatment for CRC patients with KRAS mutations; however, response rates remain very low for patients with advanced disease. Further, a sub-set of patients treated with 5-FU-based regimens suffers from serious side effects resulting from RNA-directed effects that do not contribute to the anti-cancer activity. We are developing polymeric fluoropyrimidines, such as CF10, to treat CRC more effectively and with reduced side effects. CF10 is >300-fold more potent than 5-FU across the NCI 60 cell line screen with particularly strong potency to KRAS-mutant CRC cells. We investigate the role of KRAS mutation on CF10 and 5-FU response as part of an overall effort to determine if CF10-based regimens can more effectively treat CRC patients for whom 5-FU-based regimens are currently the preferred treatment option. Methods: HKe3-wtKRAS and HKe3-mtKRAS were generated from HCT-116 human CRC cells (ATCC) by transfection with the pMSCVpuro vector encoding HA-tagged mutant or wild-type KRAS. Cytotoxicity was determined using an Alamar blue assay. Thymidylate synthase (TS) inhibition was evaluated by detecting ternary complex formation by Western blot and using a TS activity assay. Topoisomerase 1 cleavage complex (Top1cc) was evaluated using a RADAR assay and by immunofluorescence. DNA double strand breaks were detected by IF for γH2AX. Results: CF10 is highly potent to CRC cells regardless of KRAS mutation status. In isogenic cell lines that differ only in KRAS, CF10 is more potent to KRAS-mutant relative to wild type cells. The improved potency of CF10 relative to 5-FU and increased sensitivity of KRAS-mutant cells is enhanced for cells grown in 3D culture. CF10 cytotoxicity is mediated by TS inhibition and Top1cc formation that induces DNA DSBs and activates apoptosis. In vivo, CF10 displays significantly improved anti-tumor activity relative to 5-FU in HCT-116 orthotopic tumors and causes minimal systemic toxicity. Conclusions. KRAS mutation confers increased sensitivity to the DNA-directed fluoropyrimidine CF10. The overall mechanism of CF10 cytotoxicity to CRC cells is similar in both KRAS-WT and KRAS-MT CRC cells and involves TS inhibition, and misincorporation of FdU into DNA followed by generation of Top1-mediated DNA DSBs. Our studies indicate FP polymers are likely to be effective in CRC regardless of KRAS-mutation. The increased sensitivity of KRAS-mutant CRC to CF10 together with the very low systemic toxicity indicates that CRC patients currently being treated with 5-FU-based therapy could more effectively be treated with CF10-based regimens. Citation Format: William H. Gmeiner, Mandira Manandhar, Amanda M. Hinds, Julija Holmes, Pierre Vidi, Toshiyuki Tsunoda, Senji Shirasawa. Enhanced potency of the polymeric fluoropyrimidine CF10 to KRAS-mutant colorectal cancer cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 2079.