DNA Repair-deficient Research Articles

RHNO1: at the crossroads of DNA replication stress, DNA repair, and cancer.

The DNA replication stress (DRS) response is a crucial homeostatic mechanism for maintaining genome integrity in the face of intrinsic and extrinsic barriers to DNA replication. Importantly, DRS is often significantly increased in tumor cells, making tumors dependent on the cellular DRS response for growth and survival. Rad9-Hus1-Rad1 Interacting Nuclear Orphan 1 (RHNO1), a protein involved in the DRS response, has recently emerged as a potential therapeutic target in cancer. RHNO1 interacts with the 9-1-1 checkpoint clamp and TopBP1 to activate the ATR/Chk1 signaling pathway, the crucial mediator of the DRS response. Moreover, RHNO1 was also recently identified as a key facilitator of theta-mediated end joining (TMEJ), a DNA repair mechanism implicated in cancer progression and chemoresistance. In this literature review, we provide an overview of our current understanding of RHNO1, including its structure, function in the DRS response, and role in DNA repair, and discuss its potential as a cancer therapeutic target. Therapeutic targeting of RHNO1 holds promise for tumors with elevated DRS as well as tumors with DNA repair deficiencies, including homologous recombination DNA repair deficient (HRD) tumors. Further investigation into RHNO1 function in cancer, and development of approaches to target RHNO1, are expected to yield novel strategies for cancer treatment.

DNA repair-deficient premature aging models display accelerated epigenetic age.

Several premature aging mouse models have been developed to study aging and identify interventions that can delay age-related diseases. Yet, it is still unclear whether these models truly recapitulate natural aging. Here, we analyzed DNA methylation in multiple tissues of four previously reported mouse models of premature aging (Ercc1, LAKI, Polg, and Xpg). We estimated DNA methylation (DNAm) age of these samples using the Horvath clock. The most pronounced increase in DNAm age could be observed in Ercc1 mice, a strain which exhibits a deficit in DNA nucleotide excision repair. Similarly, we detected an increase in epigenetic age in fibroblasts isolated from patients with progeroid syndromes associated with mutations in DNA excision repair genes. These findings highlight that mouse models with deficiencies in DNA repair, unlike other premature aging models, display accelerated epigenetic age, suggesting a strong connection between DNA damage and epigenetic dysregulation during aging.

LepR+ niche cell–derived AREG compromises hematopoietic stem cell maintenance under conditions of DNA repair deficiency and aging

AbstractThe cross talk between extrinsic niche-derived and intrinsic hematopoietic stem cell (HSC) factors controlling HSC maintenance remains elusive. Here, we demonstrated that amphiregulin (AREG) from bone marrow (BM) leptin receptor (LepR+) niche cells is an important factor that mediates the cross talk between the BM niche and HSCs in stem cell maintenance. Mice deficient of the DNA repair gene Brca2, specifically in LepR+ cells (LepR-Cre;Brca2fl/fl), exhibited increased frequencies of total and myeloid-biased HSCs. Furthermore, HSCs from LepR-Cre;Brca2fl/fl mice showed compromised repopulation, increased expansion of donor-derived, myeloid-biased HSCs, and increased myeloid output. Brca2-deficient BM LepR+ cells exhibited persistent DNA damage–inducible overproduction of AREG. Ex vivo treatment of wild-type HSCs or systemic treatment of C57BL/6 mice with recombinant AREG impaired repopulation, leading to HSC exhaustion. Conversely, inhibition of AREG by an anti–AREG-neutralizing antibody or deletion of the Areg gene in LepR-Cre;Brca2fl/fl mice rescued HSC defects caused by AREG. Mechanistically, AREG activated the phosphoinositide 3-kinases (PI3K)/AKT/mammalian target of rapamycin (mTOR) pathway, promoted HSC cycling, and compromised HSC quiescence. Finally, we demonstrated that BM LepR+ niche cells from other DNA repair–deficient and aged mice also showed persistent DNA damage–associated overexpression of AREG, which exerts similar negative effects on HSC maintenance. Therefore, we identified an important factor that regulates HSCs function under conditions of DNA repair deficiency and aging.

LepR+ Niche Cell-Derived AREG Compromises Hematopoietic Stem Cell Maintenance Under Conditions of DNA Repair Deficiency and Aging

The maintenance of the rare hematopoietic stem cell (HSC) population in the bone marrow (BM) and preservation of their functional properties is supported by a highly specialized microenvironment inside the BM, the HSC niche. However, the crosstalk between extrinsic niche-derived and intrinsic HSC factors controlling hematopoiesis remain elusive. Using three niche-specific conditional knockout mouse models, here we demonstrate that epidermal growth factor (EGF)-like molecule, amphiregulin (AREG) from bone marrow (BM) leptin receptor (LepR+) stromal cells is an important factor that mediates the crosstalk between BM niche and HSCs in stem cell maintenance. Mice deficient for the DNA repair gene Brca2 specifically in LepR+ cells (LepR-Cre;Brca2fl/fl) exhibit increased frequencies of total and myeloid-biased HSCs. Furthermore, HSCs from LepR-Cre;Brca2fl/flmice show compromised repopulation, increased expansion of donor-derived myeloid-biased HSCs and myeloid output in the transplanted recipients. Brca2-deficient BM LepR+ cells exhibit persistent DNA damage-inducible overproduction of stromal AREG. Ex vivo treatment of WT HSCs or systemic treatment of C57BL/6 mice with recombinant AREG impairs repopulation, leading to HSC exhaustion. Conversely, inhibition of AREG by anti-AREG neutralizing antibody or deletion of the Areg gene in LepR-Cre;Brca2fl/flmice rescues the HSC defects caused by AREG. Mechanistically, AREG activates the PI3K/AKT/mTOR pathway, promotes HSC cycling and compromises HSC quiescence. Finally, we demonstrate that BM LepR+ niche cells from other DNA repair-deficient and aged mice also show persistent DNA damage-associated overexpression of AREG, which exerts similar negative effects on HSC maintenance. We have therefore identified an important niche factor negatively regulating HSCs function under conditions of DNA repair deficiency and aging, and underscored the therapeutic potential of AREG intervention in improving HSC function.

Preclinical Characterization of AZD5305, A Next-Generation, Highly Selective PARP1 Inhibitor and Trapper.

We hypothesized that inhibition and trapping of PARP1 alone would be sufficient to achieve antitumor activity. In particular, we aimed to achieve selectivity over PARP2, which has been shown to play a role in the survival of hematopoietic/stem progenitor cells in animal models. We developed AZD5305 with the aim of achieving improved clinical efficacy and wider therapeutic window. This next-generation PARP inhibitor (PARPi) could provide a paradigm shift in clinical outcomes achieved by first-generation PARPi, particularly in combination. AZD5305 was tested in vitro for PARylation inhibition, PARP-DNA trapping, and antiproliferative abilities. In vivo efficacy was determined in mouse xenograft and PDX models. The potential for hematologic toxicity was evaluated in rat models, as monotherapy and combination. AZD5305 is a highly potent and selective inhibitor of PARP1 with 500-fold selectivity for PARP1 over PARP2. AZD5305 inhibits growth in cells with deficiencies in DNA repair, with minimal/no effects in other cells. Unlike first-generation PARPi, AZD5305 has minimal effects on hematologic parameters in a rat pre-clinical model at predicted clinically efficacious exposures. Animal models treated with AZD5305 at doses ≥0.1 mg/kg once daily achieved greater depth of tumor regression compared to olaparib 100 mg/kg once daily, and longer duration of response. AZD5305 potently and selectively inhibits PARP1 resulting in excellent antiproliferative activity and unprecedented selectivity for DNA repair deficient versus proficient cells. These data confirm the hypothesis that targeting only PARP1 can retain the therapeutic benefit of nonselective PARPi, while reducing potential for hematotoxicity. AZD5305 is currently in phase I trials (NCT04644068).

Abstract 794: Pan-cancer proteogenomic analysis reveals functional mechanisms underlying DNA repair deficiencies

Abstract Emerging classifiers that leverage recent advances in the characterization of mutational signatures have identified a broader range of cancer patients with DNA repair deficiencies, many of whom do not harbor mutations or epigenetic silencing of canonical DNA repair genes. Investigating the various mechanisms underlying dysfunctional DNA damage response (DDR) and heterogeneity across patients will be crucial to understand disparate responses to therapy, including to PARP1 inhibitors and to immunotherapy. In this study, we integrate genomic, transcriptomic, proteomic, and post-translational modification (PTM) data across 11 cancer types to elucidate the diverse functional mechanisms of DNA repair deficiencies and their therapeutic implications through an in-depth proteogenomic analysis. We first characterized the landscape of mutational signatures in 1110 patients by applying SignatureAnalyzer, a tool that uses a Bayesian non-negative matrix factorization method to discover patterns of somatic mutations. Our analysis identified 144 homologous recombination-deficient (HRD) and 60 mismatch repair-deficient (MMRD) patients. Multi-omic (mRNA, protein, PTMs) signature based hierarchical clustering revealed two distinct clusters of HRD patients defined by either (i) acute or (ii) chronic hypoxic states. The acute hypoxia cluster exhibited typical HRD phenotypes, including a preference for non-homologous end joining (NHEJ) and enrichment in PARP1 activity, as well as phosphorylation patterns driven by DNA-PKcs, ATM, and ATR. In contrast, tumors under chronic hypoxia exhibited a halting of replication and silencing of DDR, suggesting that patients with these tumors may respond poorly to common HRD treatments that exploit alternative error-prone repair and PARP1 activation. Notably, these tumors were enriched in signatures representative of highly active kinases involved in cellular stress responses, potentially providing additional avenues for therapy. Additional analysis of both HRD and MMRD tumors revealed groups of highly immunogenic DNA repair-deficient tumors that may respond well to some types of immunotherapy given their increased mutagenesis. Moreover, differences in inflammation-related kinase activities offer further insight into the interaction between faulty DDR and the innate immune response (e.g., alterations in the cGAS-STING DNA sensing pathway). Overall, our multi-omic signature analysis provides insights into the mechanisms underlying DDR and its crosstalk with other cancer-related pathways that remain unexplained by evaluating genomic and transcriptomic data alone. Our characterization of the heterogeneity within the population of patients with DNA repair deficiency shows promise for improved prediction of treatment response, as well as identifying additional potential therapeutic targets. Citation Format: Yo Akiyama, Yifat Geffen, Shankara Anand, Tomer Yaron, Jared L. Johnson, Emily Huntsman, David Heiman, Chet Birger, Karl Clauser, Özgün Babur, Mendy Miller, Karsten Krug, D R Mani, Lewis C. Cantley, Steven A. Carr, PanCancer Oncogenic Drivers and Pathways Group, Clinical Proteomic Tumor Analysis Consortium (CPTAC), Francois Aguet, Li Ding, Gad Getz. Pan-cancer proteogenomic analysis reveals functional mechanisms underlying DNA repair deficiencies [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 794.

Improved pathologic complete response rates for triple-negative breast cancer in the I-SPY2 Trial.

591 Background: The I-SPY2 Trial evaluates multiple investigative agents in neoadjuvant breast cancer therapy with the primary endpoint of estimated pathologic complete response (pCR) rate. As a platform phase 2 trial it utilizes an adaptive design to compare new regimens with control chemotherapy (weekly paclitaxel followed by AC). Methods: Specific regimens are assigned based on clinically relevant signatures, including triple negative breast cancer (TNBC). Drug regimens graduate from the trial when the predicted pCR rate in any signature meets the pre-specified threshold of 85% probability of success in a hypothetical 300-patient, 1:1 randomized, phase 3 trial. The strong correlation between pCR rate and event free survival has been reported. To establish the benefit of administering investigational agents in combination with control weekly paclitaxel x 12 in TNBC, we report estimated pCR rates for the first 7 investigational agents. Results: TNBC accounted for 37% (363/987) of enrolled patients. Only veliparib and carboplatin (VC) and pembrolizumab (Pembro) met the graduation criteria for TNBC. However, compared to control chemotherapy, each drug tested in TNBC resulted in a numerically superior pCR rate compared to control. These findings imply that stratification of TNBC by response-predictive biomarkers may lead to improved pCR rates. For example, we have used gene expression profiling to further refine TNBC classification into Immune enhanced (Immune+), Immune-/DNA Repair Deficient (DRD)+, and Immune-/DRD- classes. TNBC identified as immune enhanced (63%) have an 89% pCR rate to pembrolizumab, while VC is less effective with pCR rate of 71%. Similarly, Immune-/DRD+ (11%) identifies TNBCs with a 80% pCR rate to VC, while pembrolizumab’s pCR rate in this group is only 33%. For tumors that are neither immune enhanced or DRD-positive (Immune-/DRD-; 25%) show numerically improved pCR rates for neratinib (20%), MK2206 (25%), ganitumab (24%), and ganetespib (22%) compared to control (12%). pCR rates for VC (10%) and pembrolizumab (20%) in this group were similar to drugs that did not graduate. For TNBC, many agents in I-SPY2 showed numerically improved pCR rates compared to conventional chemotherapy even when they did not meet our specified definition of graduation. Conclusions: Further refinement of TNBC signatures should yield improved therapeutic strategies while also sparing women unnecessary systemic therapy. Clinical trial information: NCT01042379. [Table: see text]

Olaparib combined with abiraterone versus olaparib alone for patients with DNA-repair deficient metastatic castration-resistant prostate cancer after progressing on abiraterone: A multicenter, real-world study.

e17021 Background: Accumulated evidence reports that olaparib has antitumor activity for patients with DNA-repair deficient (DRD) metastatic castration-resistant prostate cancer (mCRPC). Olaparib monotherapy also has significantly longer survival outcomes in patients with DRD mCRPC after progressing on a novel hormonal therapy (NHT) than physician’s choice of another subsequent NHT. In addition, clinical trials indicate that olaparib combined with abiraterone is more effective than abiraterone alone for mCRPC patients irrespective of DRD status. However, the efficacy of olaparib combined with abiraterone in patients with DRD mCRPC after progressing on abiraterone has not been studied. Therefore, we conducted a multicenter, real-world study to compare olaparib combined with abiraterone versus olaparib alone for patients with DRD mCRPC. Methods: A total of 89 mCRPC patients from three Chinese hospitals were retrospectively studied between October 2017 and November 2021. All the patients had disease with progression after abiraterone and with DRD status by a 50-gene panel targeted next-generation sequencing (NGS), including pathogenic, suspected pathogenic, or variants of unknown significance (VUS) in the DNA damage repair (DDR) genes. 35 patients received olaparib combined with abiraterone and 54 olaparib alone. The primary end point included progression-free survival (PFS) and overall survival (OS) which were calculated using Kaplan-Meier methods, and compared using Cox proportional hazards model. The safety was also evaluated. Results: There was no difference in the basline characteristics between the two groups. The median follow-up time was 9 months (range 1-48 months). The median PFS and OS were significantly higher in patients receiving olaparib combined with abiraterone than in those receiving olaparib alone respectively (PFS: 6 vs. 3 months; OS: 24 vs. 12 months, both p < 0.01). Moreover, olaparib combined with abiraterone had a better adjusted hazard ratio of 0.385 (95% CI 0.230-0.643, p < 0.001) and 0.359 (95% CI 0.175-0.737, p = 0.005) as compared to monotherapy in PFS and OS respectively. Some drug-related adverse events, such as nausea and anemia, were reported, and the serious adverse events were rare, which were similar to those previously reported. Conclusions: Olaparib combined with abiraterone had better PFS and OS compared with olaparib alone in Patients with DRD mCRPC after progressing on abiraterone, suggesting a potential synergistic effect of olaparib with abiraterone in clinical settings. Both the combination therapy and monotherapy were relatively well tolerated in the mCRPC patients and the adverse events were within acceptable limits. The results need to be further confirmed by a large-scale prospective randomized controlled trial.

Increased risk of internal tumors in DNA repair-deficient xeroderma pigmentosum patients: analysis of four international cohorts

BackgroundXeroderma pigmentosum (XP) is a rare, autosomal, recessive DNA repair-deficiency disorder with a frequency of 1–3 per million livebirths in Europe and USA but with higher frequencies in isolated islands or in countries with a high level of consanguinity. XP is characterized by high incidence of skin cancers on sun-exposed sites. Recent improvement in life expectancy of XP patients suggests an increased risk of frequently aggressive and lethal internal tumors. Our purpose was to quantify relative risks of internal tumor development for XP patients by tumor type, XP-subtype, patients’ ages and ethnicity through comparison with the US general population.MethodsWe analyzed four independent international well-characterized XP cohorts (from USA, UK, France and Brazil) with a total of 434 patients, where 11.3% developed internal tumors and compared them to the American general population. We also compiled, through PubMed/Medline, a dataset of 89 internal tumors in XP patients published between 1958 and 2020.ResultsIn the combined 4-XP cohort, relative risk of internal tumors was 34 (95% confidence interval (CI) 25–47) times higher than in the general population (p-value = 1.0E−47) and tumor arose 50 years earlier. The XP-C group was at the highest risk for the 0–20 years old-patients (OR = 665; 95% CI 368–1200; p-value = 4.3E−30). The highest risks were observed for tumors of central nervous system (OR = 331; 95% CI 171–641; p-value = 2.4E−20), hematological malignancies (OR = 120; 95% CI 77–186; p-value = 3.7E−36), thyroid (OR = 74; 95% CI 31–179; p-value = 1.2E−8) and gynecological tumors (OR = 91; 95% CI 42–193; p-value = 3.5E−12). The type of mutation on the XPC gene is associated with different classes of internal tumors. The majority of French XP-C patients (80%) are originated from North Africa and carried the XPC delTG founder mutation specific from the South Mediterranean area. The OR is extremely high for young (0–20 years) patients with more than 1300-fold increase for the French XPs carrying the founder mutation.ConclusionBecause the age of XP population is increasing due to better sun-protection and knowledge of the disease, these results are of particular importance for the physicians to help in early prevention and detection of internal tumors in their XP patients. Few preventive blood analyses or simple medical imaging may help to better detect early cancer appearance in this population.

Targeting resistant prostate cancer, with or without DNA repair defects, using the combination of ceralasertib (ATR inhibitor) and olaparib (the TRAP trial).

88 Background: Men with metastatic, castration resistant prostate cancer (mCRPC) harboring DNA repair defects (̃20%) achieve a radiographic progression free survival of 7.4 months with PARP inhibitors (PARPi). Preclinical studies combining a PARPi (olaparib) and DNA damage checkpoint inhibitor (ATR inhibitor, ceralasertib) show synergy, providing the rationale to test this combination in men with mCRPC, including where single agent olaparib has been shown to be active. Methods: Two cohorts were accrued to a trial combining ceralasertib with olaparib in men a) with or b) without DNA repair defects. All patients progressed on ≥1 prior mCRPC therapy with no prior PARPi or platinum chemotherapy. The primary endpoint was disease response (confirmed PSA decline ≥50% and/or RECIST response), while disease progression was defined per Prostate Cancer Working Group 3 definition. Each cohort is analyzed independently for disease endpoints, while both groups were combined for toxicity assessments. Results: The 12 person DNA repair-deficient (DRDef) cohort allowed patients with germline BRCA2 loss (n = 4), somatic BRCA2 loss (n = 1) and ATM loss (n = 1 germline, n = 5 somatic and n = 1 somatic with unknown germline). 35 men without BRCA2/BRCA1 or ATM genomic loss were accrued to the DNA repair-proficient (DRPro) cohort. These men had next-generation sequencing (NGS) on contemporary biopsies (prior to enrolment without intervening therapy, 12), prior NGS on metastatic tissue (10), prior NGS on primary prostatic tissue (n = 3), or cell-free analyses (5). Five patients have incomplete cell-free analyses. At data cutoff (October 2021), in the DRDef cohort, the response rate by confirmed ≥50% PSA decline was 4/10 (40%) including 3 of 4 BRCA2 patients, and another is awaiting sufficient follow up; 1 of 6 ATM-deficient patients responded and another is awaiting sufficient follow up. All 4 DRDef responders remain on therapy (median of 8 months). For patients in the DRPro cohort who have completed therapy and response assessment (n = 21), 3 responded, one with a duration of 12 months, two with 6 months. An updated analysis will be presented. Conclusions: This analysis suggests potential activity of the doublet for DRDef (BRCA2 mainly) and DRPro mCRPC. Ongoing biomarker analysis (e.g. ATM IHC, contemporaneous cell-free DNA analysis rather than archived tissue) may help guide selection of patients most likely to benefit. Clinical trial information: NCT03787680.

Immune checkpoint inhibitor sensitivity of DNA repair deficient tumors.

Faithful DNA replication is necessary to maintain genome stability and implicates a complex network with several pathways depending on DNA damage type: homologous repair, nonhomologous end joining, base excision repair, nucleotide excision repair and mismatch repair. Alteration in components of DNA repair machinery led to DNA damage accumulation and potentially carcinogenesis. Preclinical data suggest sensitivity to immune checkpoint inhibitors in tumors with DNA repair deficiency. Here, we review clinical studies that explored the use of immune checkpoint inhibitor in patient harboring tumor with DNA repair deficiency.

DNA Damage-Induced Neurodegeneration in Accelerated Ageing and Alzheimer's Disease.

DNA repair ensures genomic stability to achieve healthy ageing, including cognitive maintenance. Mutations on genes encoding key DNA repair proteins can lead to diseases with accelerated ageing phenotypes. Some of these diseases are xeroderma pigmentosum group A (XPA, caused by mutation of XPA), Cockayne syndrome group A and group B (CSA, CSB, and are caused by mutations of CSA and CSB, respectively), ataxia-telangiectasia (A-T, caused by mutation of ATM), and Werner syndrome (WS, with most cases caused by mutations in WRN). Except for WS, a common trait of the aforementioned progerias is neurodegeneration. Evidence from studies using animal models and patient tissues suggests that the associated DNA repair deficiencies lead to depletion of cellular nicotinamide adenine dinucleotide (NAD+), resulting in impaired mitophagy, accumulation of damaged mitochondria, metabolic derailment, energy deprivation, and finally leading to neuronal dysfunction and loss. Intriguingly, these features are also observed in Alzheimer’s disease (AD), the most common type of dementia affecting more than 50 million individuals worldwide. Further studies on the mechanisms of the DNA repair deficient premature ageing diseases will help to unveil the mystery of ageing and may provide novel therapeutic strategies for AD.

Analysis of mutational signatures in C. elegans: Implications for cancer genome analysis

Genome integrity is constantly challenged by exogenous and endogenous insults, and mutations are associated with inherited disease and cancer. Here we summarize recent studies that utilized C. elegans whole genome next generation sequencing to experimentally determine mutational signatures associated with mutagen exposure, DNA repair deficiency or a combination of both and discuss the implications of these results for the understanding of cancer genome evolution.The experimental analysis of wild-type and DNA repair deficient nematodes propagated under unchallenged conditions over many generations revealed increased mutagenesis in approximately half of all DNA repair deficient strains, its rate, except for DNA mismatch repair, only being moderately increased. The exposure of wild-type and DNA repair defective strains to selected genotoxins, including UV-B and ionizing radiation, alkylating compounds, aristolochic acid, aflatoxin-B1, and cisplatin enabled the systematic analysis of the relative contributions of redundant repair modalities that mend DNA damage. Combining genotoxin exposure with DNA repair deficiency can manifest as altered mutation rates and/or as a change in mutational profiles, and reveals how different DNA alterations induced by one genotoxin are repaired by separate DNA repair pathways, often in a highly redundant way.Cancer genomes provide a snapshot of all mutational events that happened prior to cancer detection and sequencing, necessitating computational models to deduce mutational signatures using mathematical best fit approaches. While computationally deducing signatures from cancer genomes has been tremendously successful in associating some signatures to known mutagenic causes, many inferred signatures lack a clear link to a known mutagenic process. Moreover, analytical signatures might not reflect any distinct mutagenic processes. Nonetheless, combined effects of mutagen exposure and DNA damage-repair deficiency are also present in cancer genomes, but cannot be as easily detected owing to the unknown histories of genotoxic exposures and because biallelic in contrast to monoallelic DNA repair deficiency is rare. The impact of damage-repair interactions also manifests through selective pressure for DNA repair gene inactivation during cancer evolution. Using these considerations, we discuss a theoretical framework that explains why minute mutagenic changes, possibly too small to manifest as change in a signature, can have major effects in oncogenesis.Overall, the experimental analysis of mutational processes underscores that the interpretation of mutational signatures requires considering both the primary DNA lesion and repair status and imply that mutational signatures derived from cancer genomes may be more variable than currently anticipated.

BRCA Mutations, Homologous DNA Repair Deficiency, Tumor Mutational Burden, and Response to Immune Checkpoint Inhibition in Recurrent Ovarian Cancer.

Homologous DNA repair-deficient (HRD) ovarian cancers (OCs), including those with BRCA1/2 mutations, have higher levels of genetic instability, potentially resulting in higher immunogenicity, and have been suggested to respond better to immune checkpoint inhibitors (ICIs) than homologous DNA repair-proficient OCs. However, clinical evidence is lacking. The study aimed to evaluate the associations between BRCA1/2 mutations, HRD, and other genomic parameters and response to ICIs and survival in OC. This is a single-institution retrospective analysis of women with recurrent OC treated with ICIs. BRCA1/2 mutation status and clinicopathologic variables were abstracted from the medical records. Targeted and whole-exome sequencing data available for a subset of patients were used to assess tumor mutational burden (TMB), HRD, and fraction of genome altered (FGA). ICI response was defined as lack of disease progression for ≥ 24 weeks. Associations of BRCA1/2 status and genomic alterations with progression-free survival (PFS) and overall survival (OS) were determined using Cox proportional hazards models. Of the 143 women treated with ICIs, 134 had known BRCA1/2 mutation status. Deleterious germline or somatic BRCA1/2 mutations were present in 31 women (24%). There was no association between presence of BRCA1/2 mutations and response (P = .796) or survival. Genomic analysis in 73 women found no association between TMB (P = .344) or HRD (P = .222) and response, PFS, or OS. There were also no significant differences in somatic genetic alterations between responders and nonresponders. High FGA was associated with an improvement in PFS (P = .014) and OS (P = .01). TMB, BRCA1/2 mutations, and HRD are not associated with response or survival, cautioning against their use as selection criteria for ICI in recurrent OC. FGA should be investigated further as a biomarker of response to immunotherapy in OC.

Association of plasma DNA repair deficient (DRD) status with clinical outcome of metastatic castration-resistant prostate cancer (mCRPC) patients (pts) treated with abiraterone acetate (AA) plus prednisone/dexamethasone (+P/D).

5066 Background: Somatic DRD deficiency in 15-30% of mCRPC pts have been observed and inhibition of enzyme poly ADP ribose polymerase (PARP) could prove beneficial. We aimed to define DRD status using plasma from pts treated on AA and evaluate associations with prospectively-collected outcome measures. Methods: Plasma DNA samples (128 baseline [BL], 134 cycle 2 day 1 [C2D1], 46 progression [PROG]) from chemotherapy-naïve mCRPC pts in a phase 2 study (NCT01867710) evaluating AA+P/D were subjected to custom target-capture next-generation sequencing. DRD assay was optimized and validated to detect pathogenic point mutations, small insertions/deletions, and copy number alternations (DRD+) in 8 DRD genes: BRCA1, BRCA2, FANCA, ATM, CHEK2, HDAC2, BRIP1, and PALB2. Analysis for genomic aberrations was a secondary exploratory objective. Associations with overall survival (OS), progression-free survival (PFS), and radiographic PFS (rPFS) were assessed using Cox regression models and Kaplan Meier analyses. Results: 11.7% of BL and 17.4% of PROG were DRD+. Bi-allelic was observed in 73.3% of BL DRD+ samples. Shorter PFS was observed in BL DRD+ vs DRD- (5.3 vs 15.5 mo; HR: 2.32; 95%CI:1.39-4.28; P < 0.002). Median PFS for BL DRD biallelic + vs DRD biallelic- was 5.1 vs 15.4 mo (HR: 2.49; 95% CI: 1.23-4.38; P < 0.0095). For multivariate analysis using DRD+, ALP, and LDH as covariates, DRD+ (HR: 2.1; 95% CI: 1.18-3.75; P < 0.012) and high ALP (HR: 1.66; 95% CI: 1.08-2.56; P < 0.021) were strongly associated with worse PFS. Median OS for BL DRD+ vs DRD- was 28.8 vs 41.3 mo (HR: 1.67; 95%CI:0.88-3.18; P = 0.116). Median rPFS for BL DRD+ vs DRD- was 16.2 vs 20.9 mo (HR: 1.64; 95%CI:0.83-3.21; P = 0.152). Of 39 Pts with BL, C2D1 and PROG samples, 3 were DRD+ (7.7%) at all 3 timepoints, 3 (7.7%) only at BL, 3 (7.7%) only at PROG (bi-allelic), 2 (5.1%) had extra deletion at PROG. Conclusions: Patients with mCRPC harboring DRD+ have worse outcomes with AA and represent a population with an unmet medical need.

DNA repair deficiency association with prognosis in pancreatic cancer: A single-institution experience.

e15798 Background: Understanding survival outcomes of various pathogenic mutations helps guide treatment decision making for patients. Classic pancreatic cancer mutations such as KRAS and TP53 have well documented survival outcomes while other mutations leading to DNA repair deficiency do not have well understood survival outcomes. Methods: We retrospectively evaluated survival outcomes of 70 pancreatic cancer patients who had their cancers genetically profiled by NGS methods. Patients with DNA repair deficiency harbored mutations in genes such as BRCA1 (1 Pts), BRCA2 (8 Pts), ATM (5 Pts), NBN (1 Pt), and BRIP1 (1 Pt). We compared baseline characteristics, tumor stage and clinical outcomes between patients with DNA repair deficiency versus DNA repair proficient cancer patients. Comparative survival analysis between the two groups was performed using Kaplan-Meir methods. Results: Baseline characteristics for all patients are recorded in (Table). Median OS is 24 months for DNA repair proficient group and 20 months for DNA repair deficient group. A comparison of Kaplan-Meir survival curves between the two groups yielded a p-value of 0.72. This is most likely due to sample size and different chemotherapy regimens which make it hard to retrospectively compare patient groups. Conclusions: Patients with mutated DNA repair genes did not have significantly worse survival. We are designing a clinical trial utilizing a PARP inhibitor, for these patients in order to better control for all factors in order to better ascertain any survival differences between the two groups. PARP inhibitor will create multiple single strand breaks which cancer cells deficient in DNA repair genes cannot repair and thus trigger cancer cell death[Table: see text]

NAD+ supplementation normalizes key Alzheimer’s features and DNA damage responses in a new AD mouse model with introduced DNA repair deficiency

Emerging findings suggest that compromised cellular bioenergetics and DNA repair contribute to the pathogenesis of Alzheimer's disease (AD), but their role in disease-defining pathology is unclear. We developed a DNA repair-deficient 3xTgAD/Polβ+/- mouse that exacerbates major features of human AD including phosphorylated Tau (pTau) pathologies, synaptic dysfunction, neuronal death, and cognitive impairment. Here we report that 3xTgAD/Polβ+/- mice have a reduced cerebral NAD+/NADH ratio indicating impaired cerebral energy metabolism, which is normalized by nicotinamide riboside (NR) treatment. NR lessened pTau pathology in both 3xTgAD and 3xTgAD/Polβ+/- mice but had no impact on amyloid β peptide (Aβ) accumulation. NR-treated 3xTgAD/Polβ+/- mice exhibited reduced DNA damage, neuroinflammation, and apoptosis of hippocampal neurons and increased activity of SIRT3 in the brain. NR improved cognitive function in multiple behavioral tests and restored hippocampal synaptic plasticity in 3xTgAD mice and 3xTgAD/Polβ+/- mice. In general, the deficits between genotypes and the benefits of NR were greater in 3xTgAD/Polβ+/- mice than in 3xTgAD mice. Our findings suggest a pivotal role for cellular NAD+ depletion upstream of neuroinflammation, pTau, DNA damage, synaptic dysfunction, and neuronal degeneration in AD. Interventions that bolster neuronal NAD+ levels therefore have therapeutic potential for AD.

Global Gene Expression Response in Mouse Models of DNA Repair Deficiency after Gamma Irradiation.

In the event of an improvised nuclear device or "dirty bomb" in a highly populated area, potentially hundreds of thousands of people will require screening to ensure that exposed individuals receive appropriate treatment. For this reason, there is a need to develop tools for high-throughput radiation biodosimetry. Gene expression represents an emerging approach to biodosimetry and could potentially provide an estimate of both absorbed dose and individual radiation-induced injury. Since approximately 2-4% of humans are thought to be radiosensitive, and would suffer greater radiological injury at a given dose than members of the general population, it is of interest to explore the potential impact of such sensitivity on the biodosimetric gene expression signatures being developed. In this study, we used wild-type mice and genetically engineered mouse models deficient in two DNA repair pathways that can contribute to radiation sensitivity to estimate the maximum effect of differences in radiosensitivity. We compared gene expression in response to a roughly equitoxic (LD50/30) dose of gamma rays in wild-type C57BL/6 (8 Gy) and DNA double-strand break repair-deficient Atm-/- (4 Gy) and Prkdcscid (3 Gy) mutants of C57BL/6. Overall, 780 genes were significantly differentially expressed in wild-type mice one day postirradiation, 232 in Atm-/- and 269 in Prkdcscid. Upstream regulators including TP53 and NFκB were predicted to be activated by radiation exposure in the wild-type mice, but not in either of the DNA repair-deficient mutant strains. There was also a significant muting of the apparent inflammatory response triggered by radiation in both mutant strains. These differences impacted the ability of gene expression signatures developed in wild-type mice to detect potentially fatal radiation exposure in the DNA repair-deficient mice, with the greatest impact on Atm-/- mice. However, the inclusion of mutant mice in gene selection vastly improved performance of the classifiers.

Abstract 2748: Targeting DNA repair deficient cancers with the cell-penetrating autoantibody 3E10

Abstract There is growing evidence that many solid tumors have defective DNA repair pathways and cell cycle checkpoints. This has spurred development of therapeutics to specifically target cancer cells with defective DNA repair, but few have been successful outright due to problems such as general toxicity. One novel anti-cancer agent of interest to us is 3E10, a unique cell-penetrating, anti-DNA autoantibody. This molecule is non-toxic to normal cells on its own but has deleterious effects on cells with DNA repair deficiencies. Specifically, 3E10 has been shown to be synthetically lethal in BRCA2-deficient human cancer cells, to be synergistic with radiation and other commonly used DNA damaging therapies, and to reduce the efficiency of Rad51 mediated strand exchange and thus homologous recombination (HR). The goal of this project is to better understand how 3E10 can be used as a new paradigm for cancer treatment. New evidence suggests that 3E10 inhibits Exo1 exonuclease activity. Additionally, preliminary data shows that 3E10 physically interacts with Rad51, ultimately inhibiting Rad51 nuclear localization and foci formation. Additionally, a point mutation in 3E10 that confers increased DNA binding mediates increased cell death in BRCA2-deficient human cancer cells. Furthermore, studies investigating the potential therapeutic effect of 3E10 in patient derived primary melanoma cell lines show that 3E10 is synthetically lethal with PTEN deficiency. This data suggests that 3E10 inhibits HR by binding to DNA at double strand breaks and occupying sites normally processed by core repair machinery, as well as by physically interacting with Rad51. Overall, 3E10 holds great promise as a novel therapeutic agent for various cancers, including PTEN deficient melanomas. Reference: Hansen, J. et al. Targeting cancer with a lupus autoantibody. Science Translational Medicine 4, (2012) Citation Format: Audrey L. Turchick, Peter M. Glazer. Targeting DNA repair deficient cancers with the cell-penetrating autoantibody 3E10. [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 2748.

Genome instability in Alzheimer disease

Alzheimer’s disease (AD) is a progressive neurodegenerative disorder and the most common form of dementia. Autosomal dominant, familial AD (fAD) is very rare and caused by mutations in amyloid precursor protein (APP), presenilin-1 (PSEN-1), and presenilin-2 (PSEN-2) genes. The pathogenesis of sporadic AD (sAD) is more complex and variants of several genes are associated with an increased lifetime risk of AD. Nuclear and mitochondrial DNA integrity is pivotal during neuronal development, maintenance and function. DNA damage and alterations in cellular DNA repair capacity have been implicated in the aging process and in age-associated neurodegenerative diseases, including AD. These findings are supported by research using animal models of AD and in DNA repair deficient animal models. In recent years, novel mechanisms linking DNA damage to neuronal dysfunction have been identified and have led to the development of noninvasive treatment strategies. Further investigations into the molecular mechanisms connecting DNA damage to AD pathology may help to develop novel treatment strategies for this debilitating disease. Here we provide an overview of the role of genome instability and DNA repair deficiency in AD pathology and discuss research strategies that include genome instability as a component.