bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract B45: A genome-scale screen identifies the microcephaly gene, ZNF335, as a regulator of DNA end resection
Authors: Young Jordan , Bashkurov Mikhail , McEwan Andrea , Sun Thomas , Datti Alessandro , Durocher Daniel 
Published: April 2017

Abstract
Homologous recombination (HR) is an essential DNA double-strand break (DSB) repair pathway that is of critical importance during the S and G2 phases of the mammalian cell cycle. The limiting step in the HR pathway is the generation of single-stranded DNA (ssDNA) by resection of DNA ends at the DSB site. We have established a high-throughput immunofluorescence-based assay that monitors DNA end resection by plate-based laser scanning cytometry. Employing this assay we screened a genome-scale siRNA library that targeted approximately 18,500 genes. Remarkably, the top hits in our screen were known regulators of resection including CtIP and all three subunits of the MRN complex. I will present ongoing work on one of the hits from the screen, the zinc finger protein ZNF335. The ZNF335 gene was recently found to be mutated in a syndrome that causes some of the worst cases of neonatal microcephaly ever observed. Numerous genome instability syndromes have been documented to display microcephaly as a clinical feature, including Seckel syndrome, which can be caused by mutations in the known resection genes CtIP and DNA2. We first validated the results of the screen by demonstrating that ZNF335 promotes resection and repair by HR. We determined that the four C-terminal zinc finger domains of ZNF335 are necessary and sufficient for its function in resection. Depletion of ZNF335 inhibits phosphorylation of CHK1 at a characterized ATR consensus site, suggesting that ZNF335 is needed for activation of ATR following a DSB. We examined the recruitment of known resection factors to DSB sites and determined that the localization of CtIP and BLM were impaired in cells depleted of ZNF335. Our data suggests that ZNF335 plays an important role in promoting resection and ATR activation in response to DSBs.
Citation Format: Jordan Young, Mikhail Bashkurov, Andrea McEwan, Thomas Sun, Alessandro Datti, Daniel Durocher. A genome-scale screen identifies the microcephaly gene, ZNF335, as a regulator of DNA end resection [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 B45.
Abstract IA03: Targeting the DNA damage response to generate new medicines for cancer treatment
Authors: O'Connor Mark J. 
Published: April 2017

Abstract
Cancers are characterized by high levels of genomic instability and endogenous DNA damage. Traditional cancer therapies include radiotherapy and DNA-damaging chemotherapy, but these treatments are associated with significant damage to normal tissue. These unwanted side effects may be reduced by using targeted treatment approaches that preferentially affect tumor cells with specific mutations. The DNA damage response (DDR) in cancer cells differs in at least three aspects to those of normal cells, namely the loss of one or more DDR pathway or capability, increased levels of replication stress and higher levels of endogenous DNA damage. In addition, an analysis of DDR associated genes suggests that there are more than 450 gene products involved in various aspects of DDR, many of which are performing enzymatic activities that could be targeted by small molecule inhibitors. DDR therefore represents both a hallmark of cancer and a weakness that can be exploited for new cancer therapies. Both the opportunities and challenges associated with translating inhibitors of DDR into new medicines for cancer patients will be presented.
Citation Format: Mark J. O'Connor. Targeting the DNA damage response to generate new medicines for cancer treatment [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 IA03.
Abstract IA08: Synthetic viability due to BRCA2 and PARP1 loss
Authors: Sharan Shyam K. 
Published: April 2017

Abstract
It is very well established that BRCA1 and BRCA2 deficient cells are hypersensitive to PARP inhibitors (PARPi) due to synthetic lethality. Because Parp1 parylates proteins involved in a wide range of biological processes, we hypothesized that inhibiting PARP activity may have detrimental effect on cells that are HR proficient and do not undergo synthetic lethality. We have demonstrated that although Brca2 null ES cells are not viable, they can survive after ES cells expressing a conditional allele of Brca2 are treated with olaparib prior to Cre-mediated deletion of the conditional allele. We also found that while Parp1 loss does not rescue the HR defect, surprisingly, it rescues the MRE11-mediated degradation of stalled replication forks associated with BRCA2 loss. Interestingly, we found that reducing MRE11 activity/levels also rescues the lethality of Brca2ko/ko ES cells. Similar to the ES cells, we observe fork protection in mouse B-cells deficient in Parp1 and Brca2 as well as in human MCF10A cells.
This unexpected functional interaction between BRCA2 and PARP1 that results in synthetic viability can have profound clinical implications: use of PARP inhibitors for cancer prevention in BRCA-mutation carriers is being explored based on the assumption that PARPi would be innocuous in normal cells. Our findings raise concerns that when patients are treated with PARPi, not only are the tumor cells killed, but normal cells can also be affected. In BRCA-mutation carriers, the majority of the cells that lose the wild-type allele undergo cell cycle arrest or apoptosis unless they acquire additional mutations in genes (the identity of which are unknown) that bypass such a response. Our work provides strong evidence that Parp1 inhibition contributes to the viability of BRCA2 deficient cells, a key step in the transformation of a normal cell to pre-neoplastic state. We have genetic evidence to show that Parp1 deficiency can contribute to tumorigenesis in mice. We found a significant increase in tumorigenesis in Brca2 conditional knockout mice (cko/cko) with K14Cre on a Parp1 heterozygous background compared to those on a Parp1 wild-type background.
Citation Format: Shyam K. Sharan. Synthetic viability due to BRCA2 and PARP1 loss [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 IA08.
Abstract IA09: Replication fork stability confers chemoresistance in BRCA-deficient cells
Authors: Chaudhuri Arnab Ray , Callen Elsa , Ding Xia , Gogola Ewa , Duarte Alexandra A. , Lee Ji-Eun , Wong Nancy , Lafarga Vanessa , Calvo Jennifer A. , Panzarino Nicholas J. , John Sam , Day Amanda , Crespo Anna Vidal , Shen Binghui , Starnes Linda M. , Ruiter Julian R. de , Daniel Jeremy A. , Konstantinopoulos Panagiotis A. , Cortez David , Cantor Sharon B. , Fernandez-Capetillo Oscar , Ge Kai , Jonkers Jos , Rottenberg Sven , Sharan Shyam K. , Nussenzweig André 
Published: April 2017

Abstract
Brca1- and Brca2-deficient cells have reduced capacity to repair DNA double strand breaks (DSBs) by homologous recombination (HR) and consequently are hypersensitive to DNA damaging agents including cisplatin and poly(ADP-ribose) polymerase (PARP) inhibitors. Here we show that loss of the MLL3/4 complex protein PTIP protects Brca1/2-deficient cells from DNA damage and rescues the lethality of Brca2-deficient embryonic stem cells. However, PTIP deficiency does not restore HR activity at DSBs. Instead, its absence inhibits the recruitment of the MRE11 nuclease to stalled replication forks, which in turn, protects nascent DNA strands from extensive degradation. More generally, acquisition of PARPi and cisplatin resistance is associated with replication fork (RF) protection in Brca2-deficient tumor cells that do not develop Brca2-reversion mutations. Disruption of multiple proteins including PARP1 and CHD4 leads to the same end point of RF protection, highlighting the complexities by which tumor cells evade chemotherapeutic interventions and acquire drug resistance.
Citation Format: Arnab Ray Chaudhuri, Elsa Callen, Xia Ding, Ewa Gogola, Alexandra A. Duarte, Ji-Eun Lee, Nancy Wong, Vanessa Lafarga, Jennifer A. Calvo, Nicholas J. Panzarino, Sam John, Amanda Day, Anna Vidal Crespo, Binghui Shen, Linda M. Starnes, Julian R. de Ruiter, Jeremy A. Daniel, Panagiotis A. Konstantinopoulos, David Cortez, Sharon B. Cantor, Oscar Fernandez-Capetillo, Kai Ge, Jos Jonkers, Sven Rottenberg, Shyam K. Sharan, André Nussenzweig. Replication fork stability confers chemoresistance in BRCA-deficient cells [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 IA09.
Abstract IA20: Phosphorylation of BRCA1 by CHK2 mediates resection activity and recruitment of BRCA2
Authors: Powell Simon N. 
Published: April 2017

Abstract
There is genetic evidence that Chk2, BRCA1 and BRCA2 are functioning in the same pathway of DNA repair, but the links between the proteins are poorly understood. We have previously shown that BRCA1's regulation of homologous recombination (HR) is dependent on Chk2-mediated phosphorylation of BRCA1 at serine 988 (BRCA1-S988). We also found that BRCA1 regulates BRCA2 recruitment in response to DNA damage, which is also dependent on the phosphorylation of BRCA1 at Serine-988. Furthermore, in HCT116/Chk2-/- cells and in MCF7 cells with depleted Chk2, the same effects on HR and BRCA2 recruitment has been found as found in cells expressing the BRCA1-S988A protein. However, in both cases, BRCA1 is recruited to chromatin and into nuclear foci, so the effect of Chk2 is not affecting the recruitment of BRCA1. BRCA1-S988A shows a defect in RPA phosphorylation in response to replication stress and DNA damage. After global DNA damage with X-rays, MRE11 foci form at double-strand breaks, and in S and G2 phases of the cell cycle, an association with CTIP is observed transiently. In the presence of BRCA1-S988A, MRE11 co-localized with CTIP persists for much longer, and results in reduced single-stranded DNA bound by RPA. In response to a site-specific DSB induced by I-SceI nuclease, BRCA1-S988A can localize to the vicinity of the break, but not directly at the broken end, as observed by chromatin immuno-precipitation. A physical assay of resection, which distinguishes single-stranded DNA from double-stranded DNA by its susceptibility to restriction enzyme digestion, shows that BRCA1-S988A expressing cells have an initiation of resection, but a failure to extend resection up to 2 kb observed in wild-type cells. The recruitment of Exo1 is being investigated. Therefore, these results demonstrate that BRCA1-S988 plays key role in regulating the extent of resection, which in turn impedes the recruitment of BRCA2 to sites of resected DSB. Chk2 inhibition may exacerbate the defect in HR, particularly in cells with a partial or mild HR-deficiency, which is found quite commonly in human tumor cells, suggesting that combination of Chk2 and PARP inhibitors may be a useful combination DNA repair based therapy.
Citation Format: Simon N. Powell. Phosphorylation of BRCA1 by CHK2 mediates resection activity and recruitment of BRCA2 [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 IA20.
Abstract IA22: The role of ATM in tumor and endothelial cells in mediating the response of cancer to radiation therapy
Authors: Kirsch David 
Published: April 2017

Abstract
Fibroblasts isolated from patients with ataxia telangiectasia are exquisitely sensitive to ionizing radiation and mice lacking the gene mutated in ataxia telangiectasia (ATM) are sensitive to total-body irradiation. Kinase inhibitors of ATM can sensitize tumor cells to radiation, but these inhibitors may also sensitize normal tissues to radiation toxicity. Endothelial cell damage can contribute to the development of long-term side effects after radiation therapy, but whether endothelial cell death plays an important role in tumor response to radiation therapy has remained unclear. To clarify the role of endothelial cells in the response of cancer to radiation therapy, we employed dual recombinase technology using both FlpO and Cre recombinases to generate primary sarcomas in mice with endothelial cell-specific deletion of Atm. Deletion of Atm in proliferating tumor endothelial cells increased endothelial cell death after radiation therapy and enhanced the response of primary sarcomas to radiation as measured by tumor growth delay. However, deletion of Atm from endothelial cells failed to enhance sarcoma eradication as no difference was observed when a higher radiation dose was utilized with local control as the endpoint. In contrast, deletion of Atm from tumor cells increased sarcoma eradication by radiation therapy. These results demonstrate that tumor cells, rather than endothelial cells, are critical targets that regulate sarcoma eradication by radiation therapy. Interestingly, Atm deletion in quiescent endothelial cells of the heart did not sensitize mice to radiation-induced myocardial necrosis. However, in mice lacking p53 in endothelial cells, which are sensitized to radiation-induced injury to the heart, deletion of ATM in addition to p53 further enhanced radiation sensitivity following whole-heart irradiation. Taken together, these genetic experiments suggest that targeting ATM during radiotherapy may provide a therapeutic gain for tumors lacking p53 function particularly when the tumor is located at an anatomic site where the adjacent normal tissue is quiescent. To test this model in mice using a pharmacological approach, we treated mice with BEZ235, which is a small molecule inhibitor of several PI3-kinase family kinases including ATM. BEZ235 sensitized primary sarcomas to radiation therapy, but only enhanced radiation-induced heart disease when p53 was deleted from endothelial cells. These results suggest that inhibiting ATM kinase during radiation therapy is a viable strategy for radiosensitization of some tumors.
Citation Format: David Kirsch. The role of ATM in tumor and endothelial cells in mediating the response of cancer to radiation therapy [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 IA22.
Abstract PR01: Mechanisms of regulation of the tumor suppressor PALB2
Authors: Couturier Anthony , Buisson Rémi , Pauty Joris , Rodrigue Amélie , Joshi Niraj , Caron Marie-Christine , Coulombe Yan , Zou Lee , Masson Jean-Yves 
Published: April 2017

Abstract
One typical mechanism to promote genomic instability, a hallmark of cancer, is to inactivate tumor suppressors, such as PALB2. It has recently been reported that mutations in PALB2 increase the risk of breast cancer by 8-9 fold. PALB2 was identified BRCA2 interacting protein, essential for BRCA2 anchorage to nuclear structures and for its function in double-strand break repair. Inherited mutations in PALB2 are associated with a predisposition for ovarian, breast and pancreatic cancers. The basis of the tumorigenic potential of PALB2 is thought to be related to functions in homologous recombination.
Therefore, the regulation of PALB2 during the DNA damage response and the effect of cancer-causing mutation is of high interest. Two mechanisms of regulation of PALB2 will be presented. The first mechanism regulates PALB2 localization to DNA damage sites in S-phase through ATR-mediated phosphorylation. We have found specific phosphorylated residues in PALB2 that promote BRCA1-PALB2 interaction after DNA damage.
To date, predicting the functional consequences of PALB2 mutations has been challenging as they lead to different aggressive phenotypes. We performed a structure-function analysis of PALB2 using PALB2 truncated mutants (R170fs, L531fs, Q775X and W1038X), and uncovered a second PALB2 regulation mechanism. Our data explains the tumorigenesis associated with some PALB2 mutations, a concept that also applies to other WD40-containing proteins.
This abstract is also being presented as Poster B11.
Citation Format: Anthony Couturier, Rémi Buisson, Joris Pauty, Amélie Rodrigue, Niraj Joshi, Marie-Christine Caron, Yan Coulombe, Lee Zou, Jean-Yves Masson. Mechanisms of regulation of the tumor suppressor PALB2 [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 PR01.
Abstract PR07: Identifying factors mediating response and resistance to chemotherapy through a chemical-genetic interaction map
Authors: Hu Hsien-Ming , Bandyopadhyay Sourav 
Published: April 2017

Abstract
Nearly every cancer patient, especially those with highly lethal and aggressive tumor types, is treated with cytotoxic chemotherapy. Currently, the selection of chemotherapy is based on average responses over a large number of patients. This belies our understanding of DNA repair that has demonstrated that the inability of a tumor cell to properly repair particular types of DNA damage has a dramatic influence on cell survival. Here, we report the generation of a quantitative chemical-genetic interaction map to chart the influence of knockdown of 625 genes on sensitivity to 30 FDA approved chemotherapeutic agents in breast epithelial cells. The resulting map highlights key genes which, when mutated or deleted in tumor cells, can dramatically induce sensitivity or resistance to particular DNA damaging agents. Interrogation of this map reveals new DNA repair factors that are recurrently deleted in breast and ovarian cancers, provides a platform for prediction of cancer cell line responses from genomic data and provides the basis for the prioritization of new drug combinations. Our data reveal that the loss of ARID1A, a key component of the SWI/SNF chromatin remodeling complex, drives resistance to cisplatin as well as PARP inhibition. Mechanistically, we uncover that ARID1A functions as a suppressor of DNA repair by homologous recombination (HR) and that its loss via mutation or deletion rescues HR in a BRCA1 independent fashion. Together, our data indicates a plethora of potential biomarkers for chemotherapy response and provides an opportunity for computational integration of chemical-genetic networks with patient genomic data to predict optimal chemotherapeutic regimes.
This abstract is also being presented as Poster A14.
Citation Format: Hsien-Ming Hu, Sourav Bandyopadhyay. Identifying factors mediating response and resistance to chemotherapy through a chemical-genetic interaction map [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 PR07.
Abstract PR18: Somatic ERCC2 mutations, nucleotide excision repair (NER) function, and cisplatin response in muscle-invasive bladder cancer (MIBC)
Authors: Mouw Kent , Lazaro Jean-Bernard , Damish Alexis , Reznichenko Elizaveta , Frazier Zoe , Liu David , Kim Jaegil , Polak Paz , Garraway Levi , Getz Gad , Rosenberg Jonathan , Allen Eliezer Van , D'Andrea Alan 
Published: April 2017

Abstract
ERCC2 is a core member of the nucleotide excision repair (NER) pathway, a highly conserved and remarkably versatile DNA repair pathway responsible for repairing intrastrand DNA adducts created by genotoxic agents such as UV irradiation and platinum-based chemotherapies. Recent large-scale genomic efforts have shown that somatic ERCC2 missense mutations are present in approximately 20% of all primary muscle-invasive bladder cancers (MIBC). We previously showed that ERCC2 mutations are associated with treatment response and overall survival in MIBC patients treated with cisplatin-based chemotherapy. Initial functional studies on a subset of the observed ERCC2 mutations suggest that the mutations confer loss of normal cellular NER capacity. However, sequencing of additional MIBC cohorts has revealed that mutations occur across the ERCC2 gene, and the functional effects of the majority of these mutations remain unknown. In order to understand the functional landscape of ERCC2 mutations in MIBC, we have developed a high-throughput fluorescence-based assay to test the functional consequences of mutations in ERCC2 and other NER genes on cellular NER capacity. We apply this approach to all observed ERCC2 mutations across three published MIBC cohorts and find that the majority of ERCC2 mutations result in complete or near-complete loss of cellular NER. In addition, by correlating our functional results with available clinical data, we find interesting examples of cases in which ERCC2 status and cisplatin response are decoupled, highlighting the importance of using functional data to complement genomic and clinical endpoints in the search for reliable predictive biomarkers.
This abstract is also being presented as Poster A29.
Citation Format: Kent Mouw, Jean-Bernard Lazaro, Alexis Damish, Elizaveta Reznichenko, Zoe Frazier, David Liu, Jaegil Kim, Paz Polak, Levi Garraway, Gad Getz, Jonathan Rosenberg, Eliezer Van Allen, Alan D'Andrea. Somatic ERCC2 mutations, nucleotide excision repair (NER) function, and cisplatin response in muscle-invasive bladder cancer (MIBC) [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 PR18.
Diagnostic Comparison of CT Scans and Colonoscopy for Immune-Related Colitis in Ipilimumab-Treated Advanced Melanoma Patients
Authors: Garcia-Neuer Marlene , Marmarelis Melina E. , Jangi Sushrut R. , Luke Jason J. , Ibrahim Nageatte , Davis Meredith , Weinberg Janice , Donahue Hilary , Bailey Nancy , Hodi F. Stephen , Buchbinder Elizabeth L. , Ott Patrick A. 
Published: April 2017

Abstract
Colitis can be a life-threatening toxicity for patients treated with immune checkpoint blockade antibodies. With the anticipated widespread use of these reagents, the timely and accurate diagnosis of immune-related colitis becomes increasingly important. To better understand the clinical presentation of colitis from ipilimumab and to assess the use of CT scans of the abdomen/pelvis as a diagnostic tool, we retrospectively analyzed patients with advanced melanoma who received ipilimumab at our institution. Ninety nine (33%) of 303 patients developed diarrhea during therapy, and 46 patients (15%) received corticosteroids for colitis. Of the patients with diarrhea, 48 (48%) underwent colonoscopy and 46 (46%) underwent both CT and colonoscopy. In the 34 patients (34%) with a CT and biopsy, CT was highly predictive of colitis on biopsy (positive predictive value 96%), and the absence of CT findings was predictive of a negative biopsy (negative likelihood ratio 0.2). In patients who had symptoms and CT evaluation, CT was highly predictive of the need for steroids to reach resolution of symptoms (positive predictive value 92%, positive likelihood ratio 7.3). We conclude that CT is a fast, reliable, and noninvasive mode of diagnosing colitis, whereas colonoscopy and biopsy may not be needed to establish that diagnosis. Cancer Immunol Res; 5(4); 286–91. ©2017 AACR.