bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract P2-07-03: High-throughput germline mutation screening for hereditary breast cancer in southern Chinese patients by massively parallel DNA sequencing
Authors: Kwong A , Au CH , Law FB , Ho DN , Ip BK , Wong AT , Shin VY , Chan TL , Ma ES 
Published: August 2014

Abstract
Introduction: Breast cancer is the most common malignancy and 3rd leading cause of deaths among the female population in Hong Kong. Since the establishment of The Hong Kong Hereditary Breast Cancer Family Registry in 2007, 1344 patients with breast and/or ovarian cancer who met the selection criteria were recruited for genetic testing in Hong Kong. Since 2011 we started to employ next-generation DNA sequencing (NGS) to expedite the analysis workflow and expand the panel of genes for sequencing.
Aim: To evaluate the workflow of NGS in mutation screening of BRCA1, BRCA2, TP53 and PTEN genes, and compared with the sequence data obtained by Sanger sequencing.
Methods: We sequenced BRCA1, BRCA2, TP53 and PTEN genes in peripheral blood samples of 410 patients, 53 positive controls and 107 healthy local individuals using 454 GS Junior System. Generation of barcoded amplicon libraries was streamlined by microfluidic PCR using Fluidigm Access Array System. Sequencing data were analyzed by an in-house developed fully automatic bioinformatics pipeline, which mainly consists of GS Amplicon Variant Analyzer, SAMtools and Ensembl Variant Effect Predictor. All putative mutations identified were validated by Sanger sequencing. Furthermore, the frequency of BRCA1, BRCA2 and PTEN missense variants of unknown significance (VUS) identified in the cohort were compared among 107 healthy local individuals and 1000 Genomes project samples. The VUS were also subjected to a panel of in silico prediction methods including PolyPhen and SIFT.
Results: Among 410 patients, there were 7 in BRCA1, 6 in BRCA2 and 1 in TP53 mutations found, including 1 novel recurrent BRCA2 (c.7007G&gt;T) and 1 novel founder BRCA2 (c.5164_5165delAG) mutations. Based on multiple criteria, 12 in BRCA1, 12 in BRCA2 and 1 in PTEN VUS could be prioritized for further investigation. The bioinformatics pipeline was extensively evaluated with Sanger-validated controls. The evaluation determined minimum sequencing coverage needed in this sequencing platform for accurate analysis. The pipeline accuracy was demonstrated by successful detecting mutations from 53 positive controls, including single nucleotide variants, insertions and deletions in different sequence context.
Conclusion: BRCA1, BRCA2, TP53 and PTEN mutation screening of 410 patients were expedited by high-throughput DNA sequencing. This method could detect 14 positive cases, including recurrent mutations, in a shorter period of time when compared with Sanger full gene sequencing. High-risk patients who are negative for the gene panel may need further investigation other than screening for BRCA1/2. The in-house developed bioinformatics pipeline was validated to detect various types of mutations and potentially become a conventional platform for genetic screening.
Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P2-07-03.
Abstract P2-07-05: Prevalence of germline BRCA1 and BRCA2 mutations in triple-negative breast cancer patients unselected for family history
Authors: Scott RJ , Wong-Brown M , Meldrum CJ , Avery-Kiejda K 
Published: August 2014

Abstract
Triple-negative breast cancer (TNBC) is a histological classification of a breast cancer subtype that is negative for the estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor receptor 2 (HER2). TNBCs represent an important subtype of breast cancer as they have a lower recurrence-free and overall survival compared to receptor-positive disease, regardless of disease staging at time of diagnosis. It has been suggested that TNBCs may harbour mutations in genes involved in the BRCA-associated DNA repair pathway (i.e. BRCAness). Recent studies have shown that up to 20% of tumours classified as TNBC present with BRCA mutations.
Additionally, TNBCs are over-represented in patients who harbour BRCA1 or BRCA2 mutations and are predominantly associated with early onset breast cancer. This suggests a link between the BRCA-associated DNA repair pathway and TNBC.
Genomic DNA was obtained from a series of 347 consecutively-collected patients with histopathologically-diagnosed TNBC, irrespective of family history. BRCA1 and BRCA2 coding sequence (including the intron/exon boundaries) was amplified using Fluidigm 48.48 Access Arrays (184 primer sets designed to cover the coding regions of both BRCA1 and BRCA2 genes) were used to prepare the libraries. The libraries were paired-end sequenced on Illumina MiSeq and the data analyzed with NextGENe 2nd Generation Sequencing Software.
Overall the number of pathogenic BRCA mutations detected was 30 (8.6%): 18 (5.2%) in BRCA1 and 12 (3.4%) in BRCA2. The proportion of pathogenic mutations observed in our cohort is not too dissimilar to the number of mutations detected in a familial breast cancer setting, which in our experience is approximately 12%.
Investigation of the family histories of the TNBC patients revealed that 13/30 (43.3%) had a confirmed family history of disease. Examination of the families revealed that the disease spectrum was as expected for hereditary breast and ovarian cancer. The age of diagnosis of breast cancer in the TNBC BRCA mutation carriers (Mean = 51, SD = 16) was significantly different (p = .03) to those with wild-type BRCA (Mean = 58, SD15) suggesting a different disease trajectory.
This study confirms that there a substantial proportion of BRCA1 and BRCA2 mutation carriers reside in populations of patients diagnosed with TNBC. This adds to the growing body of evidence suggesting that breast cancer with a triple-negative phenotype should be considered as an additional criterion for genetic testing of both BRCA genes.
Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P2-07-05.
Abstract P2-08-03: Patterns of somatic mutations in metaplastic carcinoma of the breast
Authors: O'Toole SA , Yu B , Ng CC , Selinger CI , Cooper WA , Carmalt H , Mak C , Chan C , Lee S , Karim R , Beith J , Cooper C 
Published: August 2014

Abstract
Introduction
Metaplastic carcinoma of the breast (MCB) is a heterogeneous group of malignant tumors comprising less than 1% of all breast carcinomas encompassing tumors with purely epithelial, as well as epithelial and mesenchymal components, which may be entirely metaplastic or admixed with carcinoma. There is no agreed upon optimal treatment regime for these tumors, which overall have a worse prognosis than similar stage invasive ductal carcinoma (IDC). Research into MCB has been limited by the rarity of this tumor; however as the majority of these tumors do not express ER, PR or Her2 (triple negative) and response to traditional chemotherapy is limited, there is a need for further research to identify predictive biomarkers and new targets for treatment. We report our findings of multigene mutation profiling in a series of 21 MCB.
Methods
DNA was extracted from tumors of twenty one patients with MCB, genotyped using the Oncocarta v1.0 kit a sensitive, high throughput mass spectrometry based assay which detects a panel of 238 specific mutations in 19 oncogenes including KRAS, BRAF, PIK3CA, MET, AKT1 & ERBB2 and processed on the Sequenom compact MassARRAY platform. In the case with heterologous differentiation, separate cores were taken from the spindle cell, osteo- and chrondrosarcomatous areas.
Results
Histological review revealed three pure spindle cell cases with the remainder showing mixed patterns of spindle, squamous and IDC, no special type. A single case showed heterologous osteosarcomatous and chondrosarcomatous differentiation. Ten mutations were detected in these 21 MCB. PIK3CA gene mutations (six H1047L and one E545K mutation) were seen in seven patients; and KRAS gene mutations (two G12V and one G12A) were observed in three patients. No mutations were detected in the case with heterologous elements in the separate areas of spindle, osteo- and chondrosarcomatous differentiation.
Conclusions
PIK3CA mutations were seen in 33% and KRAS mutations were seen in 14% of MCB cases in this series. Given the general lack of effective chemotherapies in MCB, these findings suggest that the PI3K pathway may be a promising therapeutic target worthy of further investigation. We plan to also undertake detailed mutational analyses using next generation sequencing to identify further potential therapeutic targets in these rare and difficult to treat malignancies.
Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P2-08-03.
Abstract P2-09-22: Synthesis of nitroxyl radical-containing nanoparticles with pH-sensitive behavior and their application for cancer therapy
Authors: Yu A , Wang H , Zhang T , Wang Y 
Published: August 2014

Abstract
Extensive research has documented that redox dysregulation is a causative involvement in tumor progression, and reactive oxygen species (ROS) are involved in cancer initiation and progression. ROS are mutagenic and may promote cancer. Early studies observed that the increased ROS production was in response to oncogenic activity. It is now widely accepted that redox chemotherapeutics represents a novel class of promising anticancer agents. Small molecule nitroxides are stable free radicals which are able to scavenge radicals and act as radical chain reaction terminators. Nitroxyl radical, 2, 2, 6, 6-tetramethyl-piperidine-1-oxyl (TEMPO), is capable of reacting with ROS and shows chemotherapeutic efficacy in various cancer cell lines and xenograft models. However, low-molecular-weight TEMPO derivatives are hard to utilize in the clinic, owing to a preferential renal clearance and side effects such as antihypertensive effect.
To address these issues, we have designed and developed nitroxyl radical-containing nanoparticles with pH-sensitive behavior using the first generation PAMAM (G1 PAMAM) partially modified with 3,4,5,6-tetrahydrophthalic anhydride (THPA) and PROXYL. The synthesis of the modified PAMAM was carried out by a two-step reaction. Firstly, part of the primary amine end group of PAMAM dendrimers reacted with anhydride THPA to produce a THPA-modified PAMAM. The b-carboxylic acid amides between G1 PAMAM and THPA are acid-sensitive. Therefore, the THPA-modified PAMAM are stable and negatively charged at physiological pH, thus preventing blood serum aggregation. However, the THPA-modified PAMAM degrades at acidic pH, converting its surface to positive charge which is benefit for cellular uptake. Secondly, the THPA-modified PAMAM reacted subsequently with 3-carboxy-PROXYL whose carboxyl group was activated by N-hydroxysuccinimide. The EPR signal of the product was analyzed by EPR measurement and confirmed the PROXYL group covalently conjugated onto THPA-modified PAMAM. The obtained THPA-PROXYL-modified PAMAM was denoted as TP-PAMAM. Experimental results showed that TP-PAMAM was stable at pH 7.4, and hydrolyzed at pH 6.0. The rate of hydrolysis was increased with pH decreasing. In vitro studies indicated that cell proliferation of MDA-MB-231 was greatly inhibited by TP-PAMAM compared to low-molecular-weight TEMPO. This may due to the fact that cellular uptake is easy for nanoparticles with pH-sensitive behavior. Therefore, the nitroxyl radical conjugated onto the pH-sensitive nanoparticles scavenges ROS more effectively. As a result, these new nitroxyl radical-containing nanoparticles have a significantly high therapeutic efficacy in the application for cancer therapy. Hence, engineered nitroxyl radical-containing nanoparticles with pH-sensitive behavior may enable therapeutic selectivity and to overcome drug resistance and metastatic cancer.
Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P2-09-22.
Abstract P2-11-21: Ipsilateral breast tumor recurrence in patients with operable breast cancer who undergo breast-conserving treatment after receiving neoadjuvant chemotherapy: Validation of the MD Anderson prognostic index
Authors: Rouzier R , Bailleux M , Guinebretiere J-M , Delalande B , Lasry S , Lerebours F , Stevens D 
Published: August 2014

Abstract
BACKGROUND:
A prognostic index, the MD Anderson Prognostic Index (MDAPI), has been developed to help refine selection criteria for breast-conserving therapy after neoadjuvant chemotherapy. This score is based on initial nodal status N2/3, residual pathologic tumor size&gt;2cm, a multifocal pattern of residual disease, and lymphovascular space invasion and ranged from 0 to 4. The objective of the current study was to validate the MDAPI for ipsilateral breast tumor recurrence.
METHODS:
Our study was a single-center retrospective analysis of a large prospectively collected breast cancer database. We identified data from 355 patients who received neoadjuvant chemotherapy and underwent breast-conserving therapy between 2002 and 2010. Predictive factors of ipsilateral breast tumor recurrence and the usefulness of the MDAPI were analyzed. Discrimitaion of models was also calculated.
RESULTS:
The median follow-up was 65 months, and the 5-year ipsilateral breast tumor recurrence-free survival rate was 90.7%. 5-year IBTR-free survival were 91.3% and 87.4% in MDAPI 0/1 and MDAPI 2+ categories (p = 0.07). (Multivariate analysis demonstrated that MDAPI (p = 0.01), Ki67 (p = 0.0004) and HER2 status (p = 0.0006) were associated significantly with ipsilateral breast tumor recurrence-free survival. Concordance index of the MDAPI was fair (0.6) but adding HER2 and ki67 status in the model improved concordance index : 0.75.
CONCLUSIONS:
The MDAPI was barely adaptable to the study patients in terms of predicting ipsilateral breast tumor recurrence. Biological factors such as ki67 and HER2 status should be included in the prognostic model.
Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P2-11-21.
Abstract P2-18-04: No further axillary dissection in sentinel lymph node-negative breast cancer after neoadjuvant chemotherapy in patients with initial cytologically-proven axillary node metastasis
Authors: Lee HC , Lee JH , Kim MK , Kil WH , Kim J , Lee JE , Kim SW , Nam SJ , Kim SM , Bae SY , Lee SK , Kim J 
Published: August 2014

Abstract
Background
In patients with fine needle aspiration (FNA)-proven axillary lymph node metastasis at diagnosis (cN+), the current standard surgical procedure is axillary lymph node dissection (ALND) at definitive surgery after neoadjuvant chemotherapy (NAC). However, growing evidences suggest that SLNB after NAC is feasible and may demonstrate acceptable performance in selected patients. We performed sentinel lymph node biopsy in patients treated with cytologically-confirmed axillary lymph nodes metastases at presentation, who converted to a clinically negative axillary status after NAC (ycN0).
Patients and methods
We retrospectively evaluated 240 patients with invasive breast cancer with ultrasound-guided FNA-proven axillary nodal metastases at the time of diagnosis. All patients received NAC and underwent surgery at Samsung medical center between October 2007 and May 2013. Among these patients, 75 patients underwent SLNB. These patients converted to clinically node-negative disease (ycN0) after NAC on breast MRI or PET/CT scan. A combined detection technique was used with radioisotope and blue dye for the detection of SLN. Patients with negative SLN on frozen pathology and low clinical suspicion of metastasis during operation were not performed further ALND.
Results
The detection rate of SLNB was 93.3% (70/75), and median number of retrieved sentinel lymph nodes was 3.0 (range 1-8). False negative rate was 6.7% (1/15). Of these 75 patients, 35 (46.6%) patients had positive sentinel lymph nodes (ypN+) and underwent ALND. Thirty-five (46.6%) patients had tumor-free sentinel lymph nodes (ypN0sn) and 20 patients of them were followed without subsequent ALND. In these SLN-negative patients without further ALND, 9 patients were HER2-enriched subtypes and 9 patients, TNBC subtypes. Only two of them were Luminal B subtypes. The median follow-up period was 12.0 months (range 0-26 months) with 2 events; 1 regional recurrence in ipsilateral supraclavicular node and 1 systemic recurrence in brain on postoperative 7 months and 5 months, respectively. There has not occurred an ipsilateral axillary recurrence so far.
Conclusions Although the follow-up was not long enough to conclude, this study tried to demonstrate that SLNB after NAC was feasible and further ALND may not be necessary in patients with SLN-negative disease (ypN0sn).
Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P2-18-04.
Abstract P3-01-07: Metformin has an additive effect to cisplatin in triple negative breast cancer cells with high lactate dehydrogenase B (LDHB) expression
Authors: Harada N , Varghese V , Tharayil IA , Kenny L 
Published: August 2014

Abstract
Background;
Glycolysis is one of the major metabolic pathways in cancer cells. The conversion of glucose to lactate in the presence of oxygen is a critical aerobic pathway that allows cancer cells to proliferate rapidly and the amount of lactate produced is correlated with tumor aggressiveness. Moreover, the increase in glycolysis is partially mediated by hypoxia-inducible transcription factor (HIF-1) and a metabolic enzyme, lactate dehydrogenase B (LDHB). However, the mechanism behind this metabolic shift is not well understood. Metformin reduces the overall risk of cancer incidence by 31%, improves cancer-related mortality and enhances response to chemotherapy in diabetic patients pre-operatively. This study aimed to evaluate metabolism in triple negative breast cancer.
Methods;
Breast cancer cell lines (estrogen receptor positive MCF7 and triple negative MDA-MB 231 and MDA-MB468) were analysed for protein expression by western blotting and mRNA expression by qRT-PCR with or without cisplatin and metformin. To study the biological mechanism, we evaluated cell growth using proliferation assay in the presence of metformin and cisplatin. The contribution of LDHB to glycolysis was evaluated using MDA-MB-231 and MDA-MB468 cell lines.
Results;
We first examined the basal expression levels of LDHB and HIF1a in these cancer cell lines. LDHB expression was high in MDA-MB 231, and HIF1α was high in MDA-MB468. Both metformin and cisplatin treatment resulted in the down-regulation of LDHB and HIF1α in MDA-MB231, metformin led to downregulation of LDHB in MDA-MB 468, while MCF7 demonstrated no significant changes. Inhibition of cell proliferation was dose-dependent and significant at low concentrations of cisplatin and metformin in only MDA-MB468 but not in MCF7 and MDA-MB231. The combination of cisplatin in with metformin had an added inhibitory effect on cell proliferation in these MD-MB231 cells.
Conclusion;
These studies suggest that combination treatment of metformin and cisplatin have potent anticancer activity in LDHB highly expressed triple negative breast cancer cells. Identification of a new targeted therapeutic approach could contribute to the new therapy to the breast cancer patients.
Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P3-01-07.
Abstract P3-04-08: A proteo-probe for nucleotide excision repair in breast cancers
Authors: Dreze M , Calkins AS , Echelman DJ , Schnorenberg MR , Fell GL , Fisher DE , Iglehart JD , Lazaro J-B 
Published: August 2014

Abstract
The response of tumor cells to DNA damaging agents is often compromised, a weakness readily exploited for therapeutic purposes. Despite the general use of genotoxic treatments, the nature and extent of DNA damage in tumor cells is generally under-investigated, or remains unknown. We postulate DNA repair deficient breast tumor cells exhibit significantly more DNA damage after genotoxic treatments, compared to repair proficient cells.
We present a technology to detect specific DNA damage and monitor repair as a basis to categorize cancers into homogenous groups of malignancies. We rely on the use of biochemically purified DNA damage recognition complexes as ready-to-use reagents, or “proteo-probes” for DNA damage.
We developed a proteo-probe based on a purified DDB2 protein complex. DDB2 is a DNA damage recognition protein part of the nucleotide excision repair (NER) that recognizes and repairs bulky DNA adducts caused for example by UV irradiation or cisplatin. We show the DDB2 proteo-probe binds to nuclei of UV-irradiated cells. We followed the DDB2 proteo-probe signal over time, and observed a decrease concordant with the completion of NER. We then successfully distinguished repair proficient cells from genetically characterized NER-deficient cells obtained from patients. We conclude the DDB2 proteo-probe can be used to detect activation of NER by UV-induced DNA damage, and subsequent repair in situ.
It has been proposed that some breast cancers carry NER deficiencies. We screened a panel of cancer cell lines using the DDB2 proteo-probe and discovered obvious NER deficient (NER-D) cell lines. In addition, we correlated NER activity with cisplatin sensitivity. We further determined whether NER deficiency in breast cancer cell lines was caused by loss-of-function of NER genes through complementation.
The classification of breast cancer cell lines based on NER activity presented here suggests more investigation is needed about NER in breast cancers. Ultimately, we envision NER deficiencies could be used to select breast cancer patients for DNA-repair targeted therapy.
Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P3-04-08.
Abstract P3-06-03: Oral bisphosphonates and survival of breast and colon malignancies
Authors: Rennert G , Rennert HS , Pinchev M , Flugelman A , Kershenbaum A , Landsman K , Hadad R , Shulman K , Gruber SB 
Published: August 2014

Abstract
Bisphosphonates are traditionally used for treatment of osteoporosis and more recently for treatment and prevention of bone metastases in various malignancies. The use of 2nd-generation oral bisphosphonates has been reported to reduce the risk of developing breast and colon cancer but their influence on cancer survival has not been studied.
Methods Two large cohorts of consecutively diagnosed cases with breast or colorectal cancer were studied for the association between use of 2nd-generation oral bisphosphonates and cancer survival. Using computerized prescription records, sustained use of alendronate/risedronate was assessed in postmenopausal women with newly diagnosed breast (n = 2,843) or colorectal cancer (n = 1,706). Overall survival and cancer-specific survival were evaluated using time dependent analysis.
Results Postmenopausal women with breast cancer previously unexposed to bisphosphonates who used 2nd-generation bisphosphonates after diagnosis for at least one year had a significantly better survival than non-users, adjusted for age, tumor stage and grade (Overall survival: HR = 0.53, 0.33-0.86, breast cancer-specific survival: HR = 0.26, 0.10-0.71, p = 0.009). A similar advantageous hazard ratio was found in users with ER positive, ER negative and HER2neu positive tumors. A similar significantly better survival was noted for colorectal cancer after adjustment for age, tumor stage and grade (Overall survival: HR = 0.53, 0.33-0.85, colorectal cancer-specific survival: HR = 0.44, 0.21-0.88, p = 0.02). Women who used bisphosphonates before diagnosis did not exhibit a significant survival benefit. Pharmacogenetic studies of F(D)PPS (Farnesyl Pyrophosphate Synthase), a gene coding a key step in the mevalonate pathway revealed direct correlation between a minor homozygous status and survival in bisphosphonate users.
Conclusions The use of 2nd-generation bisphosphonates initiated after diagnosis was associated with a significant improvement in overall and in cancer-specific survival of postmenopausal women with breast or colon cancers.
Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P3-06-03.