bluuebunny/crossref_metadata_2025_split huggingface dataset:
Preclinical testing of the PARP inhibitor ABT-888 in microsatellite instable colorectal cancer
Authors: Vilar Sanchez E. , Chow A. , Raskin L. , Iniesta M. D. , Mukherjee B. , Gruber S. B. 
Published: August 2020

11028 Background: Microsatellite instability (MSI) represents approximately 15% of colorectal cancer (CRC) cases. MSI due to hypermethylation or mutation in DNA mismatch repair genes leads to genetic instability and a mutator phenotype. Genetic instability is particularly high at repetitive sequences such as those located in MRE11, RAD50, CtIP and MBC. Each of these genes are implicated in the double strand break (DSB) repair pathway. PARP inhibitors induce single strand breaks that remain unrepaired and then will be converted to DSB during DNA replication. Our objective was to assess the preclinical activity of a novel PARP inhibitor ABT-888 in MSI cell lines deficient in the DSB repairing pathway and compare it to Microsatellite Stable (MSS) lines. Methods: We used the systems biology tool “Connectivity Map” to synthesize data from 5 different published studies of expression profiling of MSI CRC phenotype and to identify target compounds. We assessed the mutational status of MRE11, RAD50, CtIP and MBC in a panel of 10 CRC cell lines displaying either MSI or MSS, and measured the expression of MRE11 by quantitative RT-PCR. We tested the cytotoxic activity of single-agent ABT-888 for 6 days in MSS and MSI cell lines, stratified by mutational status. Flow cytometry was performed after 24 hours. Results: Systems biology studies identified PARP inhibitors as a candidate compound relevant for MSI CRC. Mutational status of MRE11 was perfectly correlated with MSI status. ABT-888 shows a preferential activity on those MSI cell lines harboring mutations in both MRE11 and RAD50 genes compared to MSS cell lines (wild-type for both genes). A significant correlation exists between MRE11 expression levels and cytotoxicity to ABT-888 at 10 μM (R2=0.915, P<0.001). Flow cytometry analyses show a G1 arrest following to the treatment with ABT-888 that is higher in MSI cell lines with mutations in MRE11 and RAD50 compared to MSS cell lines. Conclusions: This is the first report of the preclinical activity of a PARP inhibitor in CRC models. MSI colorectal tumors deficient in DSB repair show a higher sensitivity to PARP inhibition. Further clinical investigation of ABT-888 as a single agent or in combination with other chemotherapy drugs inducing DSB is warranted in MSI CRC with mutations in MRE11 and RAD50. No significant financial relationships to disclose.
Detection of BRAF kinase mutations in melanoma, ovarian, and prostate carcinomas: Evidence for tumor heterogeneity in clinical samples
Authors: Litterman A. J. , Yancovitz M. , Shapiro R. , Berman R. , Pavlick A. , Daarvishian F. , Blank S. , Lee P. , Osman I. , Polsky D. 
Published: August 2020

11031 Background: Several studies have provided evidence that solid tumors are polyclonal malignancies, an observation which may contribute to difficulties in achieving durable treatment responses. In some patients, molecularly targeted therapies may be compromised due to heterogeneity among tumor subclones. In this study we compared conventional DNA sequencing with a fluorescent-based mutant-specific PCR (MS-PCR) assay to detect the BRAF hotspot mutation V600E in a large panel of patient tumors, including paired primary and metastatic tumors from individual patients. Methods: BRAF MS-PCR and conventional sequencing were performed on DNA from 304 tumors (112 melanoma, 110 ovarian, 82 prostate) to determine the presence of the BRAFV600E hot-spot mutation. Among the melanomas were 18 matched primary and metastatic specimens, and 40 metastatic specimens from 19 patients, each of whom had 2 or more metastases. Results: DNA sequencing detected mutations in 5/110 (4.5%) ovarian tumors, 1/82 (1.2%) prostate tumors, and 36/112 (32%) melanomas. In contrast, the MS-PCR assay detected mutations in 12/110 (11%) ovarian tumors, 15/82 (18%) prostate tumors and 85/112 (76%) melanomas. The presence of contaminating normal tissue was scored for each melanoma sample, but excess normal tissue did not influence the results using either methodology. In all cases mutations detected by sequencing were also detected by MSPCR. Among 18 patients with matched primary and metastatic melanoma, 8/18 (44%) had discordant results including 2 patients with mutant primary tumors and wild-type metastases; among the 19 patients with multiple metastases 5/19 (26%) had discordant (both wild-type and mutant) tumors. Conclusions: Using a highly sensitive BRAF mutation detection method, we observed substantial evidence for heterogeneity within clinical tumor specimens. This was especially true in melanoma samples, where multiple specimens from individual patients differed with respect to the presence of the mutant BRAF allele. These results suggest that failures of molecularly targeted therapies, such as those directed against mutant BRAF, may be due in part to a lack of clonality among the tumors under treatment. No significant financial relationships to disclose.
Quantitative determination of predictive cancer biomarkers in formalin-fixed, paraffin-embedded tissue using a new, fully automated method for RNA isolation
Authors: Müller B. M. , Kronenwett R. , Hennig G. , Weber K. , Bohmann K. , Winzer K. J. , Kristiansen G. , Petry C. , Dietel M. , Denkert C. 
Published: August 2020

11032 Background: Personalized cancer therapy depends on the evaluation of tissue-based biomarkers in routine tumor samples. As many new biomarkers are measured on the mRNA level, standardized procedures for mRNA analysis in formalin-fixed, paraffin-embedded (FFPE) tissue are needed. In this study, we present a novel, standardized, and fully automated method for fast isolation of total RNA from FFPE tissue sections. Methods: Tissue samples (n = 501) from 167 breast carcinomas which had been stored between 2 months and 21 years were investigated. Total RNA was extracted from tissue sections using a new method based on silica-coated iron oxide beads in combination with a specific liquid-handling robot. Novel and unique features of the method are an automated extraction-integrated deparaffinization step and a bead-based negative selection step to eliminate any undigested tissue. Yield of RNA was assessed using the Ribogreen assay. mRNA fragment lengths were estimated by reverse transcription PCR (RT-PCR) for G6PDH. Expression of the breast cancer biomarkers ESR1, PGR and HER2 was measured by kinetic RT-PCR (kPCR) and compared with immunohistochemistry (IHC). Results: RNA was successfully isolated from all samples, with a mean yield of 1.4 μg/sample (range: 0.1–7.8 μg) and fragment lengths of at least 150 bp in 99% of samples. PCR analyses could be performed in all samples. Investigating three sections of each tumor, we observed a low section-to-section variability of kPCR results (root of mean squared errors of relative ESR1, PGR or HER2 expression in three sections: 0.2–0.5 Ct values). Comparing kPCR results with IHC, we detected a good concordance between both methods, with agreements of 98.4% (standard error [SE]: 2.7%) for ESR1, 84.4% (SE: 5.3%) for PGR and 89.9% (SE: 8.9%) for HER2. Conclusions: This novel RNA extraction method is a major technical improvement for implementation of reproducible, high-throughput and cost-efficient testing of cancer biomarkers in the clinical routine and in gene-expression research studies using archived FFPE material in molecular labs. [Table: see text]
Thymidilate synthase (TS), thymidine phosphorylase (TP), dihydropyrimidine dehydrogenase (DPD), and dihydrofolate reductase (DHFR) as predictive markers of capecitabine efficacy in breast cancer patients
Authors: Audet R. , Shen C. , Edgerton S. , Lay L. , Vang Nielsen K. , Thor A. D. , Chang J. C. , Miller K. D. , Sledge G. W. , Leyland-Jones B. 
Published: August 2020

11033 Background: The efficacy of 5-FU and the pro-drug capecitabine (C) is mediated through the thymidylate synthase pathway and may be affected by expression of key enzymes in this pathway. The expression and/or gene copy number of TS, TP, DPD and DHFR was assessed and correlated with time-to progression (TTP) and progression-free survival (PFS). Methods: Adult female patients with pathologically confirmed breast cancer and locally advanced or metastatic disease were treated with C 1000 mg/m2 BID days 1–14 of a 21-day cycle. Formalin-fixed, paraffin-embedded (FFPE) specimens from C-treated patients were processed for RNA extraction. Total RNA was isolated from 32 FFPE tissue samples containing at least 70% tumor cells and RNA levels for TS, TP, DPD and DHFR were quantified using real time RT-PCR and Affymetrix GeneChip microarrays. Custom made TS and TP FISH probes (Dako, Glostrup, Denmark) were used to evaluate gene copy number and gene to reference ratios in at least 60 morphologically intact non-overlapping nuclei. Markers were correlated with TTP and PFS using Cox proportional hazard models in 24 patients. Results: Higher TS gene copy number was significantly associated with a decrease in PFS (HR 1.46, 95% CI 1.08 to 1.96, p=0.014) and TTP (HR 1.49, 95% CI 1.05 to 2.13, p=0.028). However, the association between TS RNA levels (expressed as Ct values) and PFS (HR 0.82, 95% CI 0.61 to 1.11, p=0.198) or TTP (HR 0.74, 95% CI 0.49 to 1.14, p=0.172) failed to reach statistical significance. RNA levels, determined by Affymetrix, were significantly correlated with RT-PCR for TS (r= -0.5073, p=0.0004) and DHFR (r=-0.50994, p=0.003). Neither TP gene copy number nor RNA levels were significantly associated with PFS (HR 099, and HR 0.93) or TTP (HR 1.07 and HR 1.029), respectively. The association between RNA levels and PFS or TTP did not reach statistical significance for both DPD (HR 1.17 and HR 1.13) and DHFR (HR 0.68 and HR 0.63), respectively. Conclusions: These data indicate that TS gene copy number, assessed by FISH with proper standardization, might be a useful and easily accessible marker for C sensitivity in human breast cancer and warrants further investigation. [Table: see text]
Cell-free miR-10b and miR-21 as diagnostic biomarkers for malignant effusions
Authors: Xie L. , Chen X. , Qian X. , Wei J. , Ding Y. , Zhang C. , Liu B. 
Published: August 2020

11035 Background: Numerous studies have proved the roles of tissue microRNAs (miRNAs) as biomarkers in cancer diagnosis. Cell-free miRNAs from plasma or serum have been shown to be good biomarkers in the diagnosis of cancers. Here we tried to explore the potential application of cell-free miRNAs as diagnostic biomarkers to discriminate malignant effusions from benign. Methods: To obtain a molecular signature for malignant effusions, a stem-loop real-time PCR was adopted to measure the expression of 23 tumor-related miRNAs. After a pre-screening for discarding low amount miRNAs in 10 samples (5 benign/5 malignant) and a proper internal control was identified, the expression levels of 7 miRNAs were further compared among 74 malignant effusion samples (35 gastric cancer-related ascites and 39 lung cancer-related plural effusions) and 30 benign effusions. miRNAs specifically associated with malignant effusions were derived from a training group (20 malignant/10 benign) and tested in a validation group (54 malignant/20 benign). All samples were confirmed by both pathological and clinical diagnosis. Results: miR-215 was employed as the reference RNA for its abundance and consistence. The expression of miR-10b was significantly different between benign and malignant effusions (P< 0.001). Furthermore, it was showed that miR-10b can distinguish malignant plural effusions with high accuracy (areas under the curve (AUC) of receiver operating characteristic (ROC) curve 0.98, 95% CI, 0.90 to 1.0, P< 0.001), and miR-21 can be used to discriminate malignant ascites (AUC of ROC curve 0.71, 95% CI, 0.56 to 0.83, P= 0.018). Conclusions: In the present study, we demonstrated that cell-free miRNA can serve as a novel diagnostic biomarker in distinguishing malignant from benign effusions. No significant financial relationships to disclose.
Concordant HER2 status between malignant CSF cells and primary breast carcinoma tissue
Authors: Kwon Y. , Ro J. , Lee K. S. , Park I. H. 
Published: August 2020

1104 Background: Leptomeningeal diseases (LMD) from breast cancer are detected in up to 19% of patients with brain metastasis and their prognosis is extremely poor. Diagnosis of leptomeningeal disease requires positive cerebrospinal fluid (CSF) cytology. However, it is not known whether HER2 status of malignant CSF cells coincides with that of original breast carcinoma cells. We intended to determine whether CSF cytology specimen is suitable for evaluating HER2 status by fluorescence in situ hybridization (FISH) in LMD to provide the basis for HER2 targeted intrathecal therapy. Methods: Both formalin-fixed paraffin-embedded (FFPE) breast carcinoma tissue and liquid based CSF cytology specimen were tested for HER2 status in 16 patients who developed LMD at National Cancer Center between Dec 2004 and Jul 2008. We evaluated HER2 gene amplification by FISH on destained CSF cytology slides which contained minimum 20 malignant cells per slide, and compared with HER2 status by immunohistochemistry (IHC) in FFPE breast carcinoma tissue. HER2 was determined positive when FISH ratio > 2.2 or IHC 3+ according to ASCO/CAP guideline. Results: Concordance rate of HER2 status between CSF cytology by FISH and FFPE tissue by IHC was 100% as shown in the table. Conclusions: When CSF cytology specimen was appropriately prepared yielding adequate cellularity without dry artifact, CSF cytology was suitable for evaluating HER2 status by FISH in LMD. Intrathecal HER2 targeted therapy could be attempted when FFPE breast carcinoma tissue is HER2 positive in view of highly concordant HER2 status by our data. Supported by NCC Grant No 0610240- 3. [Table: see text] No significant financial relationships to disclose.
Influence of loco-regional radiation therapy on subsequent cancer risk among BC pts with p53 germline mutations
Authors: Rahal A. , Caron O. , Bourgier C. , Frebourg T. , Bressac de Paillerets B. , Barreau L. , Pachet C. , Mathieu M. , Marsiglia H. , Delaloge S. 
Published: August 2020

11043 Background: The management of breast cancer (BC) patients (pts) with germline p53 mutations, a rare genetic condition, is not the object of specific recommendations. Preclinical data and preliminary clinical observations suggest a theoretically major radio-sensitivity and high risk of secondary radio-induced malignancies. It remains discussed whether the knowledge of a germline p53 mutation may influence treatment (trt) choices and have prognostic importance. We reviewed our cohort of BC diagnosed as first tumor in pts with germline p53 mutations within the past 11 years, with an attempt to describe secondary malignancies occurring after trt of primary tumor. Patients and Methods: 9 pts have been diagnosed and treated in our institution within the past 11 years for BC as first tumor in the context of a documented germline p53 mutation. Their tumor characteristics, treatment and follow-up data were extracted from prospectively-registered medical records. Results: Median age at diagnosis of primary BC was 32 (22–48). 7/9 pts had a family history compatible with Li Fraumeni syndrome, while 2 had no family history. No pt had previous knowledge of her p53 mutation. Primary tumors were ductal carcinoma in situ (4), infiltrating ductal carcinoma (4), phyllode tumor (1). 3 pts had conservative surgery and 6/9 underwent mastectomy (M). 6 received loco-regional radiation therapy (RT). None had prophylactic contra lateral mastectomy. Loco-regional (LRR) and contra-lateral relapses are listed in the Table , as well as incidence of second primaries within or outside radiation field. Second primaries were sarcoma in 3/4 cases and 1 was papillary thyroid carcinoma. Conclusions: Because of high risk of second breast primary and probably very high risk of radio-induced breast cancer, BC pts with germline p53 mutations should be advised bilateral prophylactic mastectomy and avoidance of radiation therapy. In this context, the knowledge of the mutation might be of great importance. [Table: see text] No significant financial relationships to disclose.
Determination of factors predicting for estrogen receptor positive (ER+) breast cancers in BRCA1 mutation carriers
Authors: Comander A. H. , Gallagher B. M. , Krag K. , Wang Y. , Li H. , Gelman R. , Collins L. C. , Schnitt S. J. , Garber J. E. , Tung N. 
Published: August 2020

11045 Background: Most breast cancers that occur in BRCA1 mutation carriers tend to lack ER, progesterone receptors and Her2/neu. Foulkes et al.(Clin Can Res 2004; 10: 2029) reported an increase in BRCA1-associated ER+ tumors with increasing age. Little is known about the clinical factors that predict for ER status in this population. Understanding these factors and whether ER+ cancers are sporadic may have important implications for chemoprevention and treatment strategies. Methods: BRCA1mutation carriers who developed an invasive breast cancer from 1973–2008 were identified through the Cancer Risk and Prevention programs at 4 Boston-area hospitals. Clinical characteristics were abstracted from medical and research records. ER status was obtained from pathology reports, and ER staining was repeated when data was missing or when ER was listed as “weak”. Logistic regression was used to model ER positivity for the first invasive breast cancer. Potential predictors included menopausal status, age at cancer diagnosis, prior use of hormone replacement therapy, Ashkenazi-Jewish descent, age at first live birth, tobacco use, and alcohol use. Results: 170 BRCA1 mutation carriers were identified; 56 with ER+ and 114 with ER- first invasive cancers. Menopausal status was found to be a significant predictor of ER status; 18/56 (32%) with ER+ breast cancer were postmenopausal vs.14/114 (12%) with ER- cancer (odds ratio = 0.30, p = 0.002). Age >= 50 was significant in univariate analysis, 14/ 56 (25%) ER+ vs. 11/ 114 (10%) ER- cancers (p=0.01), but not in multiple regression. Conclusions: While most breast cancers in BRCA1 carriers are ER-, we found postmenopausal BRCA1carriers significantly more likely to develop an ER+ tumor than premenopausal carriers. As mutation carriers are likely to become surgically menopausal before age 50, and menopause and age are correlated, additional data will be needed to sort out the relative contribution of each factor to ER status. An understanding of this issue could have important implications for chemoprevention strategies. Molecular analysis of the ER+ breast cancers in our BRCA1+ cohort is underway to investigate whether ER+ breast cancers are manifestations of the BRCA1 mutation or sporadic. No significant financial relationships to disclose.
Use of genome-wide scan in women with breast cancer to identify common germline variants that may be associated with recurrence
Authors: Comen E. A. , Lautenberger J. , McGee K. , Kirchhoff T. , Dean M. , Hudis C. , Norton L. , Offit K. , Gold B. , Robson M. 
Published: August 2020

11049 Background: Studies of normal DNA variation have identified several common single nucleotide polymorphisms (SNPs) associated with susceptibility to breast cancer. It is not known whether common SNPs are associated with breast cancer outcomes. Methods: Subjects were Ashkenazi Jewish women with familial breast cancer and without BRCA mutations. Subjects were genotyped on an Affymetrix 500K SNP platform in the first phase of a genome-wide association study seeking susceptibility loci (Gold et. al, Proc Natl Acad Sci 2008;105:4340). Clinical variables and outcomes for these women were abstracted from medical records. Using a Cox proportional hazards model, we assessed associations between clinical outcomes and the 111 SNPs that were most significantly associated with susceptibility in the case-control study and heterozygous in the subset of affected patients. Dominant, codominant, and recessive models were explored. A secondary analysis assessed associations with recurrence of 48,562 additional SNPs that were not strongly associated with susceptibility. Results: The 173 subjects were a median of 51 years of age at diagnosis (range 27–74). Median follow-up for surviving subjects was 85.5 months. Most cancers (74.6%) were T1/T2; 62% were N0. Most were ER positive (81.5%), HER2 negative (87.5%). For the entire group, the 5- and 10-year freedom from recurrence was 84% and 72%, respectively. The 5- and 10-year overall survival was 94% and 86%, respectively. Minor alleles at rs6439927 (within CLSTN2,calsyntenin2, a post-synaptic calcium-binding membrane protein, MAF 27%) and rs7943562 ( linked to GALNTL4, an N-acetylgalactosaminyltransferase, MAF 47%) were most strongly associated with disease recurrence (log likelihood ratio chi square P=0.003 and P=0.002, respectively). No additional SNPs from the secondary analysis achieved genome-wide significance. Conclusions: Genome-wide SNP genotyping of women with breast cancer identified two novel loci that may be associated with disease recurrence. Further studies in larger cohorts will be performed to replicate these findings. No significant financial relationships to disclose.
Effect of the epidermal growth factor receptor antibody panitumumab on triggering of ADCC
Authors: Valerius T. , Dechant M. , Lammerts van Bueren J. J. , Schneider-Merck T. , Berger S. , Beyer T. , Gramatzki M. , Bleeker W. K. , Parren P. W. , van de Winkel J. G. 
Published: August 2020

11055 Targeted therapy against the epidermal growth factor receptor (EGF-R) has been introduced into clinical practice for several solid tumors. Thus far, EGF-R- directed antibodies have received approval for the treatment of advanced colorectal and head and neck cancer. Recent studies demonstrated an association between Fcg receptor polymorphisms and clinical outcome. Here, we investigated effector mechanisms of the human IgG2 antibody pantitumumab and zalutumumab—a human IgG1 antibody against EGF-R, currently in phase III clinical evaluation. Both antibodies had similar binding characteristics, but differed in induction of antibody- dependent cellular cytotoxicity (ADCC). Zalutumumab induced potent MNC-mediated ADCC via FcgRIII (CD16), which was poorly triggered by panitumumab. Interestingly, not only zalutumumab but also panitumumab recruited neutrophils for ADCC. Neutrophil- mediated killing is triggered via FcgRIIa (CD32), and is potentially affected by its 131R/H polymorphism. Thus, panitumumab- mediated ADCC was more effective by neutrophils from FcgRIIa-131H homozygous individuals than from -131R individuals. ADCC induced by the IgG1 antibody zalutumumab was not affected by this polymorphism. In an experimental metastasis model in mice, both zalutumumab and panitumumab prevented establishment of metastases at low antibody concentrations which allowed the induction of ADCC but not the inhibition of signalling. Our results may implicate neutrophil- mediated ADCC in the in vivo mechanisms of action of EGF-R- directed antibodies, and suggest that heterogeneity in clinical responses due to the FcgRIIa-131R/H polymorphism can be expected for panitumumab. [Table: see text]