bluuebunny/crossref_metadata_2025_split huggingface dataset:
Combining semiconductor-based sequencing with amplicon-based cancer gene panels: A rapid next-gen approach to clinical cancer genotyping.
Authors: Corless Christopher L. , Neff Tanaya , Heinrich Michael C. , Beadling Carol 
Published: March 2020

10591 Background: Bringing next-gen sequencing into clinical (CLIA-licensed) laboratories is an important step in the advancement of personalized cancer care. We have validated a new sequencing approach on the Ion Torrent (IT) PGM using the AmpliSeq Cancer Panel, which covers hotspot regions across 46 commonly mutated cancer genes. Methods: The AmpliSeq panel is comprised of 190 primer pairs that are co-amplified in a single tube to generate amplicons for sequencing. In our testing only 10ng of input DNA was used. Initial PCR was for 20 cycles, after which the amplicons were ligated with sequencing/barcode adapters, amplified for an additional 7 cycles, and then subjected to emulsion PCR. The resulting nanospheres were sequenced on an IT 316 chip. Results: We sequenced 44 samples of FFPE-derived tumor DNA that were previously genotyped on a mass spectroscopy (MS)-based panel. Samples were barcoded and sequenced in batches of 4, yielding an average of 2034 reads per amplicon (range: 95-5162) and an average read length of 76bp. Overall, 95.4% of reads were on target, and 79% of reads were AQ20 or better; 95% of the 190 amplicons had over 500 reads. All 42 known point mutations were accurately identified by the variant caller software. Seventeen in/dels from 4 to 63 bp in length were at least partially visible upon manual inspection of the read alignments, but some were not accurately called by the software. In addition, 22 new mutations were identified in gene regions not covered on our MS-based panel. We demonstrated sensitivity to the level of 5% mutant allele, and the correlation between allelic ratios measured by MS and IT sequencing was excellent (r2=0.81). Two DNA samples from laser-captured tumor worked well with the AmpliSeq Panel. Conclusions: Combining solid-state sequencing with a highly multiplexed PCR method for library construction is a rapid (48 hr) approach for next-gen sequencing of clinical cancer samples. The process is highly scalable and larger, cancer-specific amplicon panels are in development. Automated identification of in/dels remains a challenge in next-gen sequencing output.
The components of progression as explanatory variables for overall survival in the RECIST database.
Authors: Litière Saskia , De Vries Elisabeth , Seymour Lesley , Sargent Daniel J. , Shankar Lalitha , Bogaerts Jan ,   on behalf of the RECIST Working Group
Published: March 2020

10602 Background: Progressive disease (PD) according to RECIST 1.1 (Eisenhauer et al, 2009) is defined as one or more of (1) PD of measurable target lesions, (2) the presence of a new lesion (NL) or (3) the unequivocal PD of non-target disease (NT-PD). We explored the impact of these components, varying over time, on predicting overall survival (OS) in the RECIST database residing at EORTC (Bogaerts et al, 2009). Methods: Data was selected from 12 randomized clinical trials (3530 patients with breast, lung or colorectal cancer). A maximum of 5 target lesions was used to determine the sum of diameters. The following were calculated or assigned at each measurement time t: best response (BR) was best % improvement from baseline up to t (0% if no improvement - 100% if complete response (CR)); tumor growth (TG) was the weekly rate of increase from nadir to t (0 if no increase; irrespective of prior shrinkage), presence of NL (yes/no), and occurrence of NT-PD (yes/no); categories were not mutually exclusive. OS was analyzed by tumor type using a Cox regression model, adjusting for baseline sum, and including BR, TG, presence of NL and NT-PD as time dependent covariates. Results: Thirty-six percent of patients had NL, 26% had NT-PD, 11% achieved CR and 14% did not have shrinkage of target lesions, while 46% experienced TG (median strongest growth per patient of 0.5 mm/week). Regardless of tumor type, the presence of NL (Hazard Ratio (HR) ranging 1.4-2.5), NT-PD (HR 1.2-2.5) and TG (per 1mm/week increase; HR 1.1-1.4) were associated with worse OS, while achieving CR was associated with a longer OS (HR 0.2-0.8). Further analyses exploring the functional shape of the association between BR and TG, and OS are ongoing. This includes putting TG in contrast with the more usual % cutoff defining target PD. Conclusions: All three components of PD according to RECIST are independently strongly associated with OS. Quantification such as this will enable a better understanding of the role of each component (e.g. clinical aspect of NT-PD assessment) in PD evaluation. Work is ongoing to incorporate this information into an updated RECIST with enhanced prediction of subsequent survival.
Anti-AML activity of a novel beta-catenin antagonist BC2059.
Authors: Bhalla Kapil N. , Fiskus Warren , Sharma Sunil , Horrigan Stephen , Mudunuru Uma , Reyes Ruben , Abhyankar Sunil H. , McGuirk Joseph , Aljitawi Omar Salah , Ganguly Siddhartha 
Published: March 2020

10605 Background: The canonical WNT-β-catenin pathway is essential for self-renewal, growth and survivalof AML stem and progenitor cells. Deregulated WNT signaling inhibits degradation of β-catenin, causing increased nuclear translocation and interaction of β-catenin with the TCF/LEF transcription factor, which up regulates cyclin D1, Myc and survivin expression in AML progenitor cells. BC2059 (β-Cat Pharmaceuticals) is a potent, small molecule, anthraquinone oxime-analog, which inhibits WNT-β catenin pathway by promoting the degradation and attenuation of β-catenin levels. Methods: We determined the in vitro anti-AML activity of BC2059 (BC) (250 to 1000 nM) against cultured and primary human AML blast progenitors, as well as evaluated the in vivo anti-AML efficacy of BC in NOD-SCID and NOD-SCID-IL2γ receptor deficient (NSG) mice. Results: BC induced cell cycle G1 phase accumulation and apoptosis (40%) of the cultured OCI-AML3, HL-60 and HEL92.1.7 (HEL) AML cells. BC dose-dependently also induced apoptosis of primary AML versus normal progenitors. Treatment with BC resulted in proteasomal degradation and decline in the nuclear levels of β-catenin, which led to decreased activity of the LEF1/TCF4 transcription factor highlighted by reduced TOP-FLASH luciferase activity in the AML cells. This was associated with reduced protein levels of cyclin D1, MYC and survivin. Co-treatment with BC and the histone deacetylase inhibitor panobinostat (PS) (10 to 20 nM) synergistically induced apoptosis of cultured and primary AML blasts. Following tail vein infusion and establishment of AML by OCI-AML3 or HEL cells in NOD-SCID mice, treatment with BC (5, 10 or 15 mg/kg b.i.w, IV) for three weeks demonstrated improved survival, as compared to the control mice (p <0. 001). Survival was further improved upon co-treatment with BC and PS (5 mg/kg IP, MWF). BC treatment (5 or 10 mg/kg IV) also dramatically improved survival of NSG mice with established human AML following tail-vein injection of primary AML blasts expressing FLT3 ITD. Mice did not experience any toxicity or weight loss. Conclusions: These findings highlight the notable pre-clinical in vitro and in vivo activity and warrant further development and in vivo testing of BC against human AML.
p53 mutations in advanced cancers: Clinical characteristics and outcomes in a phase I setting.
Authors: Said Rabih , Hong David S. , Wheler Jennifer J. , Naing Aung , Falchook Gerald Steven , Fu Siqing , Janku Filip , Zinner Ralph , Piha-Paul Sarina Anne , Warneke Carla L , Tsimberidou Apostolia Maria , Kurzrock Razelle 
Published: March 2020

10607 Background: p53 mutation is one of the most common mutations in human tumors and plays an important role in apoptosis, genomic stability and inhibition of angiogenesis. Methods: We retrospectively reviewed 121 consecutive patients (pts) with solid tumors referred to the Clinical Center for Targeted Therapy (Phase I program) who were tested for p53 mutation, and compared clinical characteristics and outcomes in p53 positive vs. wild-type (wt) pts. Results: Of the 121 tested pts, 65 (53.7%) were p53 mutation-positive. The presence of p53 mutation was not associated with sex and race. Tumors with p53 mutation metastasized more often to the liver (44 pts (67.7%) with mutated p53 vs. 26 pts (46.4%) with wt p53, p=0.0264); there was no difference in metastasis to the bones, lungs, brain, soft tissues and adrenals. p53 mutation also showed a trend toward an association with PTEN-loss (13 out of 43 (30%) with p53 mutated vs. 4 out of 37 (11%) with wt p53, p=0.053). Among pts with the p53 mutation, the best median progression-free survival (PFS) prior to phase I trial entry was 10.97 months (range 0.85–29.04 months) when the treatment regimen included bevacizumab and 4.37 months (range 0.92–14.98 months) when the treatment did not include bevacizumab (P=0.0046). Among patients with wt p53, there was no significant difference in PFS between bavacizumab-containing regimens and regimens without bevacizumab. The median OS from diagnosis was 7.7 years (95% CI 6.32–9.84 years) vs. 11.8 years (95% CI 10.37 years, not attained) for p53 mutant vs. wild-type disease (p = 0.03). Univariate analysis for OS from diagnosis showed that mutated p53, Hispanic race (vs. Caucasians) and the shorter time from diagnosis to metastasis were associated with a worse prognosis. Conclusions: Tumors with p53 mutation have a more aggressive clinical behavior, metastasize more to the liver and may have a higher rate of PTEN loss compared to tumors with wt p53; In addition, anti-angiogenic agents may be of therapeutic value in p53-mutated pts.
Serum activinA and TGF-β as biomarkers of breast cancer bone metastasis behavior.
Authors: Addison Christina L. , Bouganim Nathaniel , Zhao Huijun , Vandermeer Lisa , Mazzarello Sasha , Mallick Ranjeeta , Berghout Koralee , Goss Glenwood D. , Clemons Mark 
Published: March 2020

10620 Background: Bisphosphonates (BP) are prescribed to pts with metastatic bone disease every 3-4 weeks regardless of individual risk for skeletal related events (SREs). In an era of personalized medicine this “one size fits all” approach is not appropriate and novel markers of SRE risk are required. TRIUMPH is an ongoing clinical trial evaluating 12 weekly IV BP therapy for 1 year in women with low risk bone metastases from breast cancer (BC) as defined by the bone resorption marker C-telopeptide (CTx,) levels <600 ng/L. This sub-study evaluated the utility of novel biomarkers in better predicting the risk of developing SREs. Methods: Serum obtained from pts at baseline and 6 weeks post-entry were analyzed for tumor growth factor-β (TGF-β) and activinA levels by ELISA (sensitivity ~15-30 pg/ml). Levels were correlated with pt parameters including time to development of bone metastasis, and number of previous SREs using linear regression analysis. Changes in levels of biomarkers from baseline to 6 weeks were used to calculate odds ratios using logistic regression analysis. Results: Baseline activinA correlated with baseline CTx and bone specific alkaline phosphatase (p=0.004 and p<0.0001 respectively). Baseline activinA also correlated with weight (p=0.02), BMI (p=0.007) and trended towards total number of prior SREs (p=0.07). Baseline TGF-β correlated with pt age (p=0.02), weight (0.006), BMI (p=0.0005) and duration of metastatic bone disease (p=0.004), but did not correlate with any other biomarker. Change in activinA (baseline to week 6) was the only biomarker that trended to predict coming off study early (p=0.053) as per protocol (i.e. CTx>600 ng/ml, SREs or pt/physician choice). Conclusions: Baseline levels of activinA trended to predict incidence of SREs in patients with bone metastases, and changes in levels from baseline to 6 weeks trended to predict coming off study early. These findings warrant future studies in BC pts assessing activinA as a predictor of risk associated with breast cancer bone metastases. This study was conducted with the support of the Ontario Institute for Cancer Research through funding provided by the Government of Ontario, and with funding from the Ontario Chapter of the Canadian Breast Cancer Foundation.
Diurnal proteomics and biomarker discovery in indolent versus aggressive chronic lymphocytic leukemia patients.
Authors: Bjarnason Georg A. , Spaner David , Ackloo Suzanne , Li Jieran , Zhu Pei Hong , Nuin Paulo S , Geraci Joseph , Dharsee Moyez , Martino Tami , Wang Cathy , Evans Kenneth R. 
Published: March 2020

10622 Background: In rodents, 10-20% of the genome has a 24-hour (h) rhythm in RNA expression. A molecular clock consisting of transcription / translation feedback loops of clock-genes controls this rhythmicity. In a microarray study (Affymetrix HG_U133_Plus2 chip) on RNA extracted from CLL cells sampled every 4 hours over 24 hours (6 samples) from 3 male (M) and 6 female (F) patients (pts) with chronic lymphocytic leukemia (CLL) we found 15,094 and 13,415 rhythmic transcripts (Cosinor analysis) in M and F respectively, only 6,629 of which were common to both M and F. We hypothesized that these gender differences in rhythmic RNA expression might have clinical implication for biomarker discovery with some important biomarkers only found at a certain times of day and with gender differences. Methods: Sampling was performed again at 6 time points in M and F CLL patients with indolent CLL (10pts, 5 M, 5F) and aggressive CLL (10 pts, 5M, 5F). An 8-plex iTRAQ kit was employed for mass spectrometry (MS) based relative quantification. Each iTRAQ block comprised all time-points for a single patient including a universal control. Results: At least 300 proteins were identified at a 95% confidence level in each iTRAQ experiment. Of these, 74 proteins displayed significant change between aggressive and indolent pts in 24-hour average or single time point normalized expression based on a non-parametric U-test (p<0.05). The JTK_CYCLE algorithm was used to detect 24-hour rhythmic patterns in the proteomic datasets. Significant rhythmic expression was found for 44 proteins (p<0.10) identified by iTRAQ. Data for each time point were independently analyzed using an in-house Butterfly clustering algorithm based on discrete dynamical systems. The 4 PM time point was found to be optimal for stratifying aggressive and indolent disease. Cellular pathways with significant association to differentially expressed proteins included PPAR signaling, fatty acid metabolism, and granzyme-A signaling. Confirmation by selected reaction monitoring (SRM) MS is ongoing. Conclusions: Rhythmic protein expression may have clinical implications for biomarker discovery.
Early changes in angiogenesis and hypoxia following bevacizumab therapy in primary breast cancer.
Authors: Mehta Shaveta , Hughes Nicholas Peter , Jubb Adrian M. , Turley Helen , Han Chen , Li Sonia Patricia , Taylor N Jane , Padhani Anwar R. , Adams Rosemary Frances , Makris Andreas , Harris Adrian L. 
Published: March 2020

1066 Background: Bevacizumab (BV), a monoclonal antibody directed against vascular endothelial growth factor (VEGF), is an approved anti-angiogenic agent, but despite its widespread use, little is known about how tumours develop resistance to BV. We have conducted a window-of-opportunity study in which BV is administered as a short-term first-line treatment for primary breast cancer (PBC) patients, and assessed histological markers of tumour angiogenesis and hypoxia before and after therapy. Methods: 47 patients with locally advanced breast cancer were prospectively enrolled. Informed consent was obtained from all patients. A single infusion of BV (15 mg/kg) was given 2 weeks before starting neoadjuvant chemotherapy. Dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) and core biopsies for immunohistochemistry (IHC) analysis were performed immediately prior to and 2 weeks after BV. 36 patients with invasive ductal carcinoma and good quality MRI scans and core biopsies were included in this analysis. Wilcoxon rank test and Spearman’s correlation test were used for statistical analysis. Results: IHC revealed a significant upregulation of carbonic anhydrase 9 (P = 0.04) and hypoxia inducible factor-1a (P = 0.001) following BV therapy along with a significant reduction in plasmalemma vesicle associated protein (PLVAP) (p=0.01) and Ki67 (p= 0.006). DCE-MRI analysis revealed a significant reduction in vessel permeability and blood flow following BV, as measured by a decrease in the forward transfer constant Ktrans (P < 0.0001) and the reverse rate constant kep (P < 0.0001). In addition, we found a significant negative correlation between CA9 levels and median Ktrans at baseline (Spearman’s rho = -0.46; P = 0.01). Conclusions: Using combined DCE-MRI and IHC analysis, we found that PBC patients treated with single-agent BV showed a decrease in markers of tumour angiogenesis, together with a corresponding increase in tumour hypoxia. Our results suggest that tumour hypoxia may be a key mechanism governing the early onset of resistance to BV therapy, and argue for the use of suitable combination therapies to overcome the resistance and ultimately improve patient survival.
Outcomes of 47 patients with human immunodeficiency virus infection treated for breast cancer: A 20-year experience.
Authors: Ochoa Roberto Enrique , Kyriakopoulos Christos , Hurley Judith 
Published: March 2020

1071 Background: Patients (pts) with Human Immunodeficiency Virus (HIV) are living longer and non-AIDS defining malignancies have been increasingly reported in these patients. Methods: Retrospective review identified 47 pts with breast cancer (BC) and HIV who were seen at the University of Miami Sylvester Comprehensive Cancer Center/Jackson Memorial Hospital between January 1999 and June 2011. Results: Pt characteristics: 46 female, 1 male, mean age 46 years (range 31-65). Race: African American 79%, Caucasian 21%. Ethnic: Hispanics 14%, non-Hispanics 86%. Premenopausal 68% postmenopausal 32%. Tumor characteristics: Stage: Tis 4%, Stage I: 6 % , Stage II: 38%, Stage III: 38%, Stage IV: 9%. ER positive (50%) her-2 positive (15%), Triple negative (21%). HIV characteristics: 36 pts with HIV before or concurrent with the diagnosis of BC. 6 pts diagnosed with HIV within 1 year of BC diagnosis. HIV dx date unavailable in 5 pts. 27% had AIDS. CD4 counts (in cells/µL)were: > 500 (23%); 201-500 (37%), 51 – 200 (20%) < 50 (20%). 15 pts were diagnosed with BC in preHAART era. Of those dx with BC after 1996, 60% were on HAART. BC treatment: 43 pts had localized disease. 32 underwent modified radical mastectomy, 8 breast conservation and 3 pts refused surgery. 26 pts received curative or palliative chemotherapy. Complications of BC treatment: serious side effects were reported in 11 (42%) including neutropenic fever/sepsis (10 pts), ARDS (1 pt). Zoster infection was reported in 12% of the pts. 3 patients developed rapidly progressive and fatal AIDS within 6 months of completion of chemotherapy. Survival: See Table. Conclusions: BC in patients with HIV infection spans the spectrum of BC presentations. Hormonal therapy, surgery and radiation therapy were well tolerated. Infectious complications were common in patients treated with chemotherapy and routine use of growth factors and prophylactic acyclovir should be considered. [Table: see text]
Comparing the outcome between multifocal, multicentric, and bilateral breast cancer and the impact of guideline-adherent adjuvant treatment: A retrospective multicenter cohort study of 5,308 patients.
Authors: Schwentner Lukas , Wolters Regine , Novopashenny Igor , Wischnewsky Manfred , Kreienberg Rolf , Wöckel Achim ,   BRENDA Study Group
Published: March 2020

1078 Background: Beside unifocal-unilateral (UU) breast cancer (BC) there are several subtypes including multifocal, multicentric and bilateral BC. This study tries to answer the following questions:(1) Does localization (multifocal/multicentric/bilateral) influence outcome concerning BC mortality? (2) Is there an impact of guideline-adherent adjuvant treatment in these BC subtypes? Methods: This German multi-center retrospective cohort study called BRENDA included 5277 patients obtained from 1992 until 2005. The definition of guideline adherence was based on the German national S3 breast cancer guideline (2004). Results: 4085 (77.4%) were UU, 698 (13.2%) multifocal, 282 (5.3%) multicentric and 212 (4.0%) bilateral BC. RFS in multifocal [p=0.003; HR=1.35 (95% CI: 1.11-1.65)], multicentric [p<0.001; HR=1.76 (95% CI: 1.31-2.34)] and bilateral [p<0.001; HR=2.28 (95% CI: 1.76-2.97)] BC was significantly lower compared to unilateral-unifocal BC. Concerning OAS we found only a borderline difference between UU and unilateral-multifocal [p=0.057; HR=1.22 (95% CI: 0.99-1.48)], but a significant difference between multicentric [p= 0.018; HR=1.42 (95% CI: 1.06-1.90)] resp. bilateral [p<0.001; HR=2.87 (95% CI: 2.21-3.74)] and UU-BC. There was a significant impact by guideline adherent adjuvant therapy [UU: p<0.001, HR=2.76,95%C.I.:2.25-3.38], [unilateral-multifocal: p=0.001, HR=2.04,95%C.I.:1.33-3.14], [unilateral-multicentric: p=0.020, HR=2.13,95%C.I.:1.13-4.01] and [bilateral: p=0.042, HR=2.10,95%C.I.:1.03-4.31]. After stratifying for 100% guideline adherent treatment and adjusting for age, tumor size, nodal status and grading there was no significant difference in RFS/OAS in patients with multifocal [p=0.282/p=0.610], multicentric [p=0.829/p=0.609] or bilateral BC [p=0.457/p=0.773] compared to patients with UU-BC. Conclusions: Patients with multicentric and bilateral BC have primarily a worse prognosis in terms of RFS and OAS. However if guideline adherent adjuvant treatment was applied it was no more possible to demonstrate significant differences in survival.