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Advanced non-small-cell lung cancer (NSCLC) patients with EGFR T790M-positive tumours benefit from osimertinib, an epidermal growth factor receptor-tyrosine kinase inhibitor (EGFR-TKI). Here we show that the size of the EGFR T790M-positive clone impacts response to osimertinib. T790M subclonality, as assessed by a retrospective NGS analysis of 289 baseline plasma ctDNA samples from T790M‐positive advanced NSCLC patients from the AURA3 phase III trial, is associated with shorter progression-free survival (PFS), both in the osimertinib and the chemotherapy-treated patients. Both baseline and longitudinal ctDNA profiling indicate that the T790M subclonal tumours are enriched for PIK3CA alterations, which we demonstrate to confer resistance to osimertinib in vitro that can be partially reversed by PI3K pathway inhibitors. Overall, our results elucidate the impact of tumour heterogeneity on response to osimertinib in advanced stage NSCLC patients and could help define appropriate combination therapies in these patients., A recent clinical trial shows that a proportion of lung cancer patients carrying the EGFR T790M mutation develop resistance to osimertinib. In this study, the authors show that T790M subclonality is associated with worse clinical outcome likely through co-occurring PIK3CA alterations, which can be targeted by PI3K pathway inhibitors.

The Genotype-Tissue Expression (GTEx) Project was supported by the Common Fund of the Office of the Director of the National Institutes of Health. Additional funds were provided by the NCI, NHGRI, NHLBI, NIDA, NIMH, and NINDS. Donors were enrolled at Biospecimen Source Sites funded by NCI\SAIC-Frederick, Inc. (SAIC-F) subcontracts to the National Disease Research Interchange (10XS170), Roswell Park Cancer Institute (10XS171), and Science Care, Inc. (X10S172). The Laboratory, Data Analysis, and Coordinating Center (LDACC) was funded through a contract (HHSN268201000029C) to The Broad Institute, Inc. Biorepository operations were funded through an SAIC-F subcontract to Van Andel Institute (10ST1035). Additional data repository and project management were provided by SAIC-F (HHSN261200800001E). The Brain Bank was supported by a supplements to University of Miami grants DA006227 and DA033684 and to contract N01MH000028. Statistical Methods development grants were made to the University of Geneva (MH090941 & MH101814), the University of Chicago (MH090951, MH090937, MH101820, MH101825), the University of North Carolina-Chapel Hill (MH090936 & MH101819), Harvard University (MH090948), Stanford University (MH101782), Washington University St Louis (MH101810), and the University of Pennsylvania (MH101822). The data used for the analyses described in this manuscript were obtained from: [insert, where appropriate] the GTEx Portal on 01/12/2015 and/or dbGaP accession number phs000424.vN., J.B.'s laboratory is partially funded by the Spanish Ministry of Health PI12/00070 supported by FEDER funds, and the Spanish Research Network on Rare diseases (CIBERER). C.B-B is granted by the PI12/00070. M.A.B.'s laboratory is funded with the Spanish Ministry of Science and Innovation, projects SAF2008-05384 and 2007-A-200950 (TELOMARKER), European Research Council Advanced grant GA#232854, the Körber Foundation, Fundación Botín and Fundación Lilly. MU is supported by the Spanish Ministry of Health PI14/00459 with FEDER funds.

In this report, we have tried to gain molecular insight into a single nucleotide polymorphism (SNP) in the NEIL2 gene previously identified as "cancer risk modifier" for BRCA2 mutation carriers. To that end, we studied the role of this SNP (rs804271) on NEIL2 transcriptional regulation, oxidative DNA damage and genome instability in two independent set of samples: The first one was a series of eighty-six BRCA1 and BRCA2 mutation carriers and eighty non-carrier controls in which we evaluated the effect of the SNP on NEIL2 gene expression and oxidative DNA damage accumulation. The second was a set of twenty lymphoblastoid cell lines (LCLs), thirteen BRCA1 mutation carriers and seven non-carriers control, that were used to analyze the correlation between NEIL2 mRNA and/or protein levels, the oxidative and the double stranded break (DSB) DNA damage levels. Our results suggest that an excessive production of NEIL2 enzyme, associated with the SNP, may have a deleterious effect modifying cancer risk susceptibility in BRCA2 mutation carriers. We hypothesize that due to the SNP impact on NEIL2 transcriptional upregulation, a cascade of events may converge in the accumulation of oxidative DNA damage and its posterior conversion into DSBs for this specific group of patients. We thank Alicia Barroso her technical assistance. Also to Dr. Thomas Helleday, (Karolinska Institutet, Stockholm, Sweden) that kindly provided NEIL2 and UNG purified enzymes. The Genotype-Tissue Expression (GTEx) Project was supported by the Common Fund of the Office of the Director of the National Institutes of Health. Additional funds were provided by the NCI, NHGRI, NHLBI, NIDA, NIMH, and NINDS. Donors were enrolled at Biospecimen Source Sites funded by NCI/SAIC-Frederick, Inc. (SAIC-F) subcontracts to the National Disease Research Interchange (10XS170),Roswell Park Cancer Institute (10XS171), and Science Care, Inc. (X10S172). The Laboratory, Data Analysis, and Coordinating Center (LDACC) were funded through a contract (HHSN268201000029C) to The Broad Institute, Inc. Biorepository operations were funded through an SAIC-F subcontract to the Van Andel Institute (10ST1035). Additional data repository and project management were provided by SAIC-F (HHSN261200800001E). The Brain Bank was supported by supplements to University of Miami grants DA006227 & DA033684 and to contract N01MH000028. Statistical Methods development grants were made to the University of Geneva (MH090941 & MH101814), the University of Chicago (MH090951, MH090937, MH101820, MH101825), the University of North Carolina - Chapel Hill (MH090936 & MH101819), Harvard University (MH090948), Stanford University (MH101782), Washington University St Louis (MH101810), and the University of Pennsylvania (MH101822). The data used for the analyses described in this manuscript were obtained from: [insert, where appropriate] the GTEx Portal on 01/12/2015 and/or dbGaP accession number phs000424.v7.p2 on 01/10/2017. Sí

BRCA1 germline mutations increase the lifetime risk of developing breast and ovarian cancers. However, taking into account the differences in disease manifestation among mutation carriers, it is probable that different BRCA1 mutations have distinct haploinsufficiency effects and lead to the formation of different phenotypes. Using lymphoblastoid cell lines derived from heterozygous BRCA1 mutation carriers and non-carriers, we investigated the haploinsufficiency effects of various mutation types using qPCR, immunofluorescence, and microarray technology. Lymphoblastoid cell lines carrying a truncating mutation showed significantly lower BRCA1 mRNA and protein levels and higher levels of gamma-H2AX than control cells or those harboring a missense mutation, indicating greater spontaneous DNA damage. Cells carrying either BRCA1 mutation type showed impaired RAD51 foci formation, suggesting defective repair in mutated cells. Moreover, compared to controls, cell lines carrying missense mutations displayed a more distinct expression profile than cells with truncating mutations, which is consistent with different mutations giving rise to distinct phenotypes. Alterations in the immune response pathway in cells harboring missense mutations point to possible mechanisms of breast cancer initiation in carriers of these mutations. Our findings offer insight into how various heterozygous mutations in BRCA1 could lead to impairment of BRCA1 function and provide strong evidence of haploinsufficiency in BRCA1 mutation carriers.

In this report, we have tried to gain molecular insight into a single nucleotide polymorphism (SNP) in the NEIL2 gene previously identified as “cancer risk modifier” for BRCA2 mutation carriers. To that end, we studied the role of this SNP (rs804271) on NEIL2 transcriptional regulation, oxidative DNA damage and genome instability in two independent set of samples: The first one was a series of eighty-six BRCA1 and BRCA2 mutation carriers and eighty non-carrier controls in which we evaluated the effect of the SNP on NEIL2 gene expression and oxidative DNA damage accumulation. The second was a set of twenty lymphoblastoid cell lines (LCLs), thirteen BRCA1 mutation carriers and seven non-carriers control, that were used to analyze the correlation between NEIL2 mRNA and/or protein levels, the oxidative and the double stranded break (DSB) DNA damage levels. Our results suggest that an excessive production of NEIL2 enzyme, associated with the SNP, may have a deleterious effect modifying cancer risk susceptibility in BRCA2 mutation carriers. We hypothesize that due to the SNP impact on NEIL2 transcriptional upregulation, a cascade of events may converge in the accumulation of oxidative DNA damage and its posterior conversion into DSBs for this specific group of patients.

BRCA1-deficient cells show defects in DNA repair and rely on other members of the DNA repair machinery, which makes them sensitive to PARP inhibitors (PARPi). Although carrying a germline pathogenic variant in BRCA1/2 is the best determinant of response to PARPi, a significant percentage of the patients do not show sensitivity and/or display increased toxicity to the agent. Considering previously suggested mutation-specific BRCA1 haploinsufficiency, we aimed to investigate whether there are any differences in cellular response to PARPi olaparib depending on the BRCA1 mutation type. Lymphoblastoid cell lines derived from carriers of missense pathogenic variants in the BRCA1 BRCT domain (c.5117G > A, p.Gly1706Glu and c.5123C > A, p.Ala1708Glu) showed higher sensitivity to olaparib than cells with truncating variants or wild types (WT). Response to olaparib depended on a basal PARP enzymatic activity, but did not correlate with PARP1 expression. Interestingly, cellular sensitivity to the agent was associated with the level of BRCA1 recruitment into γH2AX foci, being the lowest in cells with missense variants. Since these variants lead to partially stable protein mutants, we propose a model in which the mutant protein acts in a dominant negative manner on the WT BRCA1, impairing the recruitment of BRCA1 into DNA damage sites and, consequently, increasing cellular sensitivity to PARPi. Taken together, our results indicate that carriers of different BRCA1 mutations could benefit from olaparib in a distinct way and show different toxicities to the agent, which could be especially relevant for a potential future use of PARPi as prophylactic agents in BRCA1 mutation carriers.

Variants of Uncertain Significance (VUS) are genetic variants whose association with a disease phenotype has not been established. They are a common finding in sequencing-based genetic tests and pose a significant clinical challenge. The objective of this study was to assess the use of functional data to classify variants according to pathogenicity. We conduct functional analysis of a large set of BRCA1 VUS combining a validated functional assay with VarCall, a Bayesian hierarchical model to estimate the likelihood of pathogenicity given the functional data. The results from the functional assays were incorporated into a joint analysis of 214 BRCA1 VUS to predict their likelihood of pathogenicity (breast cancer). We show that applying the VarCall model (1.0 sensitivity; lower bound of 95% confidence interval (CI)=0.75 and 1.0 specificity; lower bound of 95% CI=0.83) to the current set of BRCA1 variants, use of the functional data would significantly reduce the number of VUS associated with the C-terminal region of the BRCA1 protein by ~87%. We extend this work developing yeast-based functional assays for two other genes coding for BRCT domain containing proteins, MCPH1 and MDC1. Analysis of missense variants in MCPH1 and MDC1 shows that structural inference based on the BRCA1 data set can aid in prioritising variants for further analysis. Taken together our results indicate that systematic functional assays can provide a robust tool to aid in clinical annotation of VUS. We propose that well-validated functional assays could be used for clinical annotation even in the absence of additional sources of evidence.

Although the majority of breast cancers affect women, approximately 1% of cases occur in men. At present comparatively little is known about the molecular mechanisms that influence male breast cancer predisposition and tumorigenicity. This is largely due to the current unavailability of an established cell line model in which to study male breast cancer. Development of in vitro models of the disease is therefore warranted, not least because growing evidence indicates that it is sufficiently different from female breast cancer such that extrapolating knowledge from one to the other may be misleading. Here we report the establishment and characterisation of a male breast cancer cell line derived from a primary tumor arising in a 61-year old male patient. We used 3T3-J2 mouse fibroblast co-culture in the presence of a ROCK inhibitor to conditionally reprogram epithelial cells from freshly resected tumor tissue. Once established, the cell line showed a rapid proliferation rate and growth in full conditioned media without the support of mouse fibroblasts. Immunohistochemical profiling demonstrated expression of epithelium-specific antigens AE1/AE3, breast epithelial marker CK7 and confirmed estrogen receptor positivity in concordance with the primary tumor. Germline sequencing detected no pathogenic germline predisposition mutations in either BRCA1 or BRCA2. There was no evidence of somatic mutation in any of the established female breast cancer driver genes. Somatic whole genome sequencing of early and late passages indicated a paucity of structural aberration and little evidence for obvious accumulation of gross genetic alterations. In conclusion, we have established a novel in vitro model for studying male breast cancer. That the cell line genome displays minimal evidence of significant acquired genetic changes arising due to reprogramming suggests that it will be of value in future studies of the biology of male breast cancer. Citation Format: Tereza Vaclova, Sarah Maguire, Matthew Pugh, Peter Barry, Nick Orr. Molecular and genomic characterization of a newly established male breast cancer cell line [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 816. doi:10.1158/1538-7445.AM2017-816

Oxidative stress is a source of DNA damage which can lead to genomic instability and telomere shortening. The OGG1 glycosidase plays an important role in the Base Excision Repair (BER) pathway that counteracts the oxidative DNA damage caused by endogenous cell stress. Recently, we have demonstrated that a single nucleotide polymorphism (SNP) in the OGG1 gene can modify cancer risk in carriers of germline mutations in the BRCA1 and BRCA2 genes1. Hence, we aimed to explore the possible role of this variant in DNA damage and telomere shortening to explain the association of this cancer risk variant. We used 2 independent set of samples with a heterogeneous BRCA mutational status. First of all, a familiar breast and ovarian cancer (FBOC) set of 154 BRCA patients (BRCA1, BRCA2 and BRCAX) and 68 controls, were used to measure the mRNA OGG1 expression levels in blood and the leukocyte telomere length (TL). Second, we used a panel of 23 Lymphoblastoid Cell Lines (LCL) from patients harboring germline mutations in BRCA1 and non-carrier controls to validate previous results regarding OGG1 mRNA expression levels and telomere shortening. Additionally we measured gammaH2AX intensity levels in LCL to evaluate the role of the SNP on DNA damage. In the FBOC series, we found that the carriers of the variant had significant decreased expression levels of the OGG1 transcript compared with the non-carriers (p = 0.013). Regarding TL studies, we found that the variant may exert a synergistic effect together with BRCA1/2 mutations on telomere shortening (p Using the LCL panel we were able to detect OGG1 mRNA down regulation due to the presence of the variant and a significant telomere shortening exclusively in the BRCA1 defective cells harboring the OGG1 SNP after 55 passages. The DNA damage studies, confirmed significant higher intensity levels of gammaH2AX in the damaged LCL harboring the SNP compared to those not harboring it (p These results, may explain the molecular insights behind this modifier variant. Under the prism of a deleterious interaction, in cells harboring mutations in BRCA genes, the presence of the SNP itself, seems to affect OGG1 mRNA down regulation. This could lead to a defective performance of the BER pathway that may lead to genome instability, characterized by higher gammaH2AX intensity in damaged cells and telomere shortening when both genetic events are present, and as consequence, higher cancer risk. 1. Osorio A, et al (2014) PLoS Genet Funding: J.B's laboratory, INNPRONTA 2012, Spanish Ministry of Health (PI12/00070) and (CIBERER). C.B is granted by PI12/00070 M.A.B.'s laboratory, Spanish Ministry of Science and Innovation (SAF2008-05384;2007-A-200950) (TELOMARKER), ERCA (GA#232854) Citation Format: Carlos Benitez-Buelga, Tereza Vaclova, María Sofia Ferreira, Nora Soberon, María Antonia Blasco, Ana Osorio, Javier Benitez. Molecular insights into OGG1 gene, a modifier of cancer risk in BRCA1 and BRCA2 mutations carriers. [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 2547.

Carrying an inherited mutation in BRCA1 or BRCA2 genes significantly increases individual´s lifetime risk to develop breast or ovarian cancer. However, there are considerable differences in disease manifestation among mutation carriers, suggesting the existence of other factors which could modify the risk of cancer development. Since BRCA1 is an important component of DNA repair, BRCA1-deficient cells have to rely on other members of the DNA repair machinery. This makes them sensitive to drugs which target specific repair pathways, such as inhibitors of poly (ADP-ribose) polymerase (PARP). Several PARP inhibitors are currently being tested in preclinical or clinical trials, either as a monotherapy or in combination with chemo- or radiotherapy. Taking into account the promising results in patients with germline mutation in BRCA1 or BRCA2 genes, we aimed to investigate which BRCA1 mutation carriers, depending on the mutation type, might benefit from treatment with PARP inhibitors the most. In addition, we were also interested in identifying markers of sensitivity/resistance to PARP inhibitors. We have used lymphoblastoid cell lines (LCLs) derived from lymphocytes of healthy women heterozygous for different BRCA1 mutations and healthy women from the same families with no mutation. In total, 23 LCLs were characterized according to their DNA repair capacity, growth rate, gene/miRNA expression and sensitivity to PARP inhibitors. Our preliminary results have shown significantly higher sensitivity to PARP inhibitor olaparib in cells harbouring missense mutation in comparison to cells with truncating or no mutation. The ongoing functional studies on these BRCA1 missense variants indicate that these mutations could act in a dominant negative manner. Importantly, the observed differences in sensitivity to olaparib among mutation carriers could be also relevant for recently proposed use of PARP inhibitors as prophylactic agent for mutation carriers. Our ongoing work may help us to better understand the mechanisms of action of PARP inhibitors and lead to improvement of therapeutic strategies for BRCA1-associated cancers with extension to other tumors. Citation Format: Tereza Vaclova, Nicholas T. Woods, Fernando Setién, José María García Bueno, José Antonio Macías, Alicia Barroso, Miguel Urioste, Manel Esteller, Alvaro N.A. Monteiro, Javier Benítez, Ana Osorio. Implications of the type of BRCA1 germline mutation in the treatment of patients with hereditary breast cancer. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 5483. doi:10.1158/1538-7445.AM2014-5483

Germ-line mutations in the BRCA1 and BRCA2 genes confer a high lifetime risk of developing breast and other cancers. However, remarkable differences exist regarding disease manifestation in mutation carriers, suggesting the existence of other genetic modifier factors. Given that both BRCA1 and BRCA2 are involved in the repair of double-strand breaks (DSBs) mainly by Homologous Recombination, SNPs in genes involved in DNA repair are good candidates to be tested as phenotypic modifiers. The Base Excision Repair (BER) pathway could be particularly interesting given the relation of synthetic lethality that exists between one of the components of this pathway, PARP1, and both BRCA1 and BRCA2. To test our hypothesis we have performed a comprehensive analysis of the 18 genes involved in BER, in a series of 2000 BRCA1 and BRCA2 mutation carriers from the Spanish Consortium for the Study of Hereditary Breast Cancer, the Istituto Nazionale Tumori and the National Centre for Scientific Research “Demokritos”. For this purpose we have used a tagging SNP approach in which we have evaluated the common genetic variation in the 18 genes using the VeraCode GoldenGate 144 SNP Genotyping Kit. Preliminary results have showed statistically significant associations with cancer risk in BRCA1 and/or BRCA2 mutation carriers for 46 SNPs (p Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 90. doi:1538-7445.AM2012-90