bluuebunny/crossref_metadata_2025_split huggingface dataset:
Performance of next-generation sequencing for detection of clinically actionable genetic variants in cancer.
Authors: Hussaini Mohammed Omar , Hagemann Ian S. , Cox Teresa Mary , Lockwood Christina , Seibert Karen , Kulkarni Shashikant , Pfeifer John , Duncavage Eric James 
Published: March 2020

11099 Background: Next-generation sequencing (NGS) allows for simultaneous detection of numerous actionable somatic variants in cancer. We have implemented a clinical NGS panel to detect genetic alterations in 25 genes with established roles in cancer and report here the frequency of clinically actionable genetic variants in a variety of cancer types. Methods: NGS testing was performed in a CAP-certified, CLIA-licensed environment on DNA extracted from FFPE tissue in 209 cases spanning 41 histologic tumor types. DNA was enriched by hybrid capture and sequenced to >1,000x average coverage on Illumina sequencers with 2x101bp or 2x150bp reads. Variants were called using clinically validated parameters using the Genome Analysis Toolkit, Pindel, and the custom-written Clinical Genomicist Workstation. Results: Non-small cell lung cancer (45%), pancreatic cancer (10%), and colorectal cancer (8%) were the most common tumors sent for NGS analysis. An average of 3 (range 1- 16) non-synonymous, non-SNP sequence variants per case (SNVs and indels) were detected in the 130kb exonic target. Variants were most commonly seen in TP53, KRAS, and EGFR. 27% of cases (56/209) had one or more variants with therapeutic implications for the tumor type tested (e.g., EGFR mutation in NSCLC). 15% of cases (32/209) showed actionable variants not generally associated with the malignancy tested (e.g., detection of an activating KITvariant in thymic carcinoma). 10% of cases (21/209) had variants that were prognostically significant but not directly targetable. Some cases (9%) had variants that were prognostic/diagnostic and targetable. In 117 cases (56% of total), no therapeutically or prognostically significant variants were identified. Overall, in 92 cases (44%), NGS testing yielded information with therapeutic (majority), prognostic, or diagnostic ramifications. Conclusions: We found that 44% of unselected cancer cases have clinically relevant sequence variants in a set of 25 commonly mutated cancer genes. Our data suggest that clinical NGS testing may serve as an integral tool in realizing the potential of precision medicine in oncology.
Application of MET pharmacodynamic assays to compare effectiveness of five MET inhibitors to engage target in tumor tissue.
Authors: Srivastava Apurva K. , Hollingshead Melinda G. , Weiner Jennifer , Covey Joseph M , Liston Dane , Peggins James O , Bottaro Donald P. , Wright John Joseph , Kinders Robert J. , Tomaszewski Joseph E. , Parchment Ralph E. , Doroshow James H. 
Published: March 2020

11103 Background: Several MET inhibitors are currently being developed that block aberrant HGF/MET signaling in different cancers. We utilized validated MET pharmacodynamic (PD) assays to compare time course, magnitude, and reversal of MET suppression by 5 MET inhibitors in preclinical models. Methods: Immunoassays (total MET, pY1234/35MET, and pY1356MET) were developed and validated to measure modulation of MET by 5 MET inhibitors (crizotinib, tivantinib, cabozantinib, foretinib, and EMD1214063). The comparison was implemented in 3 sequential stages: 1) establish time course and magnitude of MET inhibition after single drug administration of 4 different doses; 2) determine dose(s) and schedule for sustained MET inhibition and downstream signaling at optimal levels; and 3) compare efficacy of MET inhibitors at MTD and equal MET inhibition. The preclinical models include an autophosphorylation gastric tumor (SNU5) model and a paracrine MET activation model in hHGF knock-in mice. Plasma and tumor exposures were measured using LC-MS/MS to correlate with PD effects. Results: We completed phase one in the SNU5 model and determined inhibition of pY1234/35MET and total MET in tumor tissues after single administration of MET inhibitors. Time course and magnitude of pY1234/35MET inhibition varied considerably among MET inhibitors, with the most rapid (>80% suppression in 30 min) and sustained inhibition (up to 48 h) observed with EMD1214063 at a dose of 30 mg/kg. The maximal inhibition of pY1234/35MET and time taken for biomarker recovery were wide-ranging among MET inhibitors. Tumor drug exposures were concomitantly higher than plasma for all drugs and correlated inversely with pY1234/35MET, except for tivantinib which, unlike other drugs, is not ATP competitive inhibitor. Conclusions: We applied validated PD assays to directly compare similarities and differences in extent and duration of MET inhibition by 5 MET inhibitors. Our results provide important foundation for head-to-head comparison of efficacies of MET inhibitors at MTD and equal MET inhibition. Funded by NCI Contract No HHSN261200800001E.
Plasma osteopontin and the prognosis of pleural mesothelioma.
Authors: Pass Harvey I. , Donington Jessica S. , Gadgeel Shirish M. , Chachoua Abraham , Wozniak Antoinette J. , Liu Geoffrey , Tsao Ming Sound , de Perrot Marc , Goparaju Chandra 
Published: March 2020

11109 Background: Cytoreductive surgery for malignant pleural mesothelioma (MPM) should be reserved for patients with favorable tumor biology. Osteopontin (OPN) and the ratio of absolute neutrophil to absolute lymphocyte counts (NLR) have been reported as possible prognostic biomarkers. These were studied with other clinical/ laboratory variables in a mixed surgical/non-surgical MPM population to define independent predictors of survival (OS) and progression (TTP). Methods: Forty-four MPM patients (12 F, 32M; 26 cytoreduction, 18 no cytoreduction; 31 epithelial, 13 non-epithelial; 15 Stage I/II, 29 Stage III/IV) were examined with regard to pretreatment plasma OPN (ELISA, R&D, Minneapolis, MN), NLR age, gender, therapy, histology, stage, platelet count and WBC count. Cut points for age, OPN, NLR, platelets, and WBC were determined by X-tile Software (Yale, New Haven, CT) and univariate/multivariate Cox analyses performed. Results: Median OS were 11 m, 21m, and 8m for all 44 MPMs, cytoreduced and non-cytoreduced MPMs, respectively. Of platelet count, WBC, NLR, and OPN, only OPN was statistically significant between Stage I/II and Stage III/IV (80.3 ng/ml vs 148 ng/ml, p<0.018). The only independent covariate predictive of OS was plasma OPN. For TTP in cytoreduced patients, only age, stage, platelet count, and OPN were significant in univariate analysis, and multivariate modeling retained stage (p=0.04, HR=2.75, 95% CI=1.0517 to 7.1879) and OPN (p=0.0008, HR=17.471, 95% CI=3.3054 to 92.3461). Conclusions: Plasma OPN is promising for the stratification of tumors into good or bad risk categories and to help select potential candidates for cytoreduction and further postoperative therapy. [Table: see text]
The role of Pirh2 C-terminal residues and ubiquitin lysine chains in ubiquitination mechanism.
Authors: Abou Zeinab Rami Mahmoud , Leng Roger 
Published: March 2020

11110 Background: Pirh2, a p53 inducible gene, is proposed to be a main regulator of p53 family proteins fine tuning the DNA damage response by acting as an E3 ligase. A negative feedback loop between Pirh2 and p53 exists where under unstressed conditions, Pirh2 induces p53 ubiquitination followed by proteosomal degradation. In case of cellular stress when the activity of tumor suppressors is essential, Pirh2 is self-ubiquitinated releasing p53 continuous repression. Interestingly among all E3 ligases, Pirh2 is the only one to be over-expressed in a wide range of human tumors. This over-expression indicates a disruption in the self-ubiquitination mechanism or a defect in the degradation mechanism post ubiquitination. Based on that, we aimed to analyze Pirh2 ubiquitination mechanism through mapping Pirh2 domains to reveal the essential residues for this process and the ubiquitin chains utilized. Methods: Pirh2 constructs deleting major residues in the three domains were designed, and also ubiquitin mutant constructs were designed through single/multiple mutations at specific positions where lysine residues are mutated to arginine. Using these constructs and in comparison to WT proteins, we tested Pirh2 in-vitro self and p53 ubiquitination activity. Results: Regarding Pirh2, we were able to reveal that residues 240-250 of the c-terminal along with the ring domain are essential for self-ubiquitination.K63R and K48R ubiquitin did not affect Pirh2 self-ubiquitination minimizing the impact of ubiquitin mutations on Pirh2 self-ubiquitination. However, KO, which had all lysine residues mutated to arginine, showed total inhibition of Pirh2 self-ubiquitination confirming the importance of lysine residues. Interestingly, Pirh2 self-ubiquitination reaction showed no difference in the presence or absence of p53 proteins. Concerning Pirh2-p53 ubiquitination, K48 was found to be critical for E3 ubiquitin ligase activity because K48R and not K36R showed defective ubiquitination. All results were confirmed by quantifying ubiquitin. Conclusions: Our data added knowledge to the Pirh2 self-ubiquitination mechanism that can resolve the constant overexpression of Pirh2 proteins hence maximizing p53 response to DNA damage.
Hormone receptor-dependent regulation of ABAT and beta-alanine metabolism in breast cancer.
Authors: Budczies Jan , Brockmoeller Scarlet F. , Mueller Berit , Dietel Manfred , Fiehn Oliver , Denkert Carsten 
Published: March 2020

11112 Background: Recently, we identified beta-alanine as biomarker for breast cancer using GC-MS based metabolomics. Beta-alanine is increased in breast cancer compared to normal tissues and in the more aggressive ER- subtype compared to ER+ breast cancer. Beta-alanine is a substrate of 4-aminobutyrate aminotransferase (ABAT), can be catabolised to malonate semialdehyde and used for reduction of NAD and acetylation of coenzyme A. The aim of the current study is to analyze ABAT protein and RNA expression in a large cohort of breast cancers. Methods: The specificity of a polyclonal antibody against ABAT was validated using siRNA in MFC7 cells. A cohort of 164 paraffin-embedded breast cancer tissues from the METAcancer biobank was investgated by immunohistochemistry. Tumor cells were evaluated separately for staining intensity (low, moderate or high) and percentage of stained cells. A cohort of 156 METAcancer samples was investigated for gene expression using whole genome DASL. Results: ABAT protein intensity correlated strongly with estrogen receptor (ER) status (p < 0.001), but not with HER2 status. In particular, the ABAT protein was highly expressed in 41% of the ER+ tissues, but only in 2% of the ER- tissues. Further, ABAT intensity correlated strongly with tumor grade (p < 0.001). ABAT intensity did not correlate with tumor stage or nodal status. Explorative evaluation of ABAT protein in normal cells revealed weak expression in some of the ducts and negative expression in adipose cells. ABAT protein and RNA expression strongly correlated in the subcohort investigated by DASL. Analysis of a large external data set (publicly available at www.kmplot.com) showed that low ABAT expression is associated with an unfavorable prognosis of breast cancer. Both, ABAT protein and RNA expression, showed a strong negative correlation with beta-alanine abundance. Conclusions: We reported on changes in beta-alanine metabolism that occur between the molecular subtypes of breast cancer and normal breast tissue. High expression of ABAT in ER+ breast cancer is compatible with catabolic use of beta-alanine. Differently, beta-alanine might be preferable used anabolic in ER- breast cancer, possibly for the synthesis of carnosine.
Impact of lymph node ratio (LNR) on prognosis of early breast cancer.
Authors: Donnellan Eoin , O'Keefe Jo , O'Connor Derbrenn , O'Hanlon Deirdre , Murphy Conleth G. , Bird Brian 
Published: March 2020

1115 Background: Breast cancer is currently staged according to the TNM (tumors, nodes, metastases) classification of the American Joint Committee on Cancer (AJCC) Staging System. Lymph node ratio (LNR, the ratio of positive axillary lymph nodes to the total number of nodes examined) may provide additional prognostic information to that provided by TNM scores. Furthermore, LNR may potentially identify subpopulations within the traditional AJCC stages that are at increased risk of adverse outcomes. Methods: We performed a single institution retrospective study of all patients diagnosed with early breast cancer between January 2000 and January 2011. Patients were divided into low- (≤0.14), intermediate- (0.15-0.39) and high-risk (≥0.4) LNR groups. We assessed the impact of LNR and conventional AJCC staging parameters on overall survival (OS) and disease-free survival (DFS). Results: 786 patients were included in the analsyis, 238 of whom were node positive. As expected nodal status according to pathologic nodal (pN) stage was prognostic for OS and DFS with OS decreasing from 88.3% in pN1 patients to 40.8% in those with pN3 disease (p<0.001). LNR was also significantly associated with prognosis. OS decreased from 94% in the low-risk LNR group to 64% in the high-risk group, while DFS decreased from 92% in the low-risk LNR group to 50% in the high-risk (p<0.001). When Stage III patients were divided into low- and high-risk LNR groups, OS decreased from 100% in the low LNR group to 63% in the high LNR group (p<0.05). Similarly, DFS decreased from 96% in the low LNR group to 56% in the high LNR group (p<0.05). A similar trend was not observed when Stage III patients were stratified according to pN status. LNR was also found to be prognostic when pN1 patients were divided into low- and high-risk LNR groups. Although both LNR and nodal status were significantly associated with OS and DFS on univariate analysis, LNR retained its significance on multivariate analysis, while nodal status did not. Conclusions: LNR can identify subpopulations within the traditional AJCC staging that are at higher risk of adverse outcomes. These findings should be examined in larger retrospective studies and, if validated, be considered as a stratification factor in future adjuvant trials.
Sentinel lymph node biopsy (SNB) in pregnancy-associated breast cancer (PABC).
Authors: Gropper Adrienne , Zabicki Calvillo Katherina , Troyan Susan , Dominici Laura Stewart , Rhei Esther , Economy Katherine E. , Schapira Lidia , Tung Nadine M. , Meisel Jane L. , Partridge Ann H. , Mayer Erica L. 
Published: March 2020

1117 Background: SNB in PABC is not often pursued due to concerns for potential fetal harm. There are only limited data available regarding the safety and efficacy of SNB in patients (pts) with PABC. Methods: Pts with PABC who underwent SNB were identified from within an existing multi-institutional PABC cohort diagnosed 1996-2013. Factors evaluated included method and result of SNB evaluation, maternal disease outcome, and fetal outcomes. Results: Within a cohort of 78 PABC pts, 53 had breast surgery while pregnant; 23 (43%) underwent SNB, 27 (51%) underwent initial axillary node (AN) dissection, 18 of whom were clinically node negative, and 3 had no nodal evaluation. Of SNB pts, 21 (91%) had stage 1-2 disease; 14 (61%) had ER/PR+ disease and 7 (30%) HER2+. Eight (35%), 9 (39%), and 6 (26%) women had SNB in the first, second, and third trimesters, respectively. 99-Technetium-labelled sulfur colloid (99-Tc) alone was used for SNB in 14 pts; methylene blue (MB) dye alone was used in 7. SN was identified in 100% of pts; see Table. There were no SNB-associated complications. At a median of 2.4 years from diagnosis, there were no locoregional recurrences, 3 (13%) distant recurrences, and 1 (4%) death from breast cancer. Among pts who underwent SNB, there were 20 liveborn infants and 3 pregnancies ongoing. Of the 20 infants born, 18 were healthy, 1 unknown, and 1 had cleft palate (in setting of maternal risk factors including smoking and methadone). Conclusions: SNB in PABC appears to be a safe and accurate procedure using either 99-Tc or MB techniques. This is one of the largest experiences reported to date of SNB during PABC; however, numbers remain limited and rates of SNB in our cohort were lower than current rates in non-PABC patients. Additional research and monitoring for safety of this procedure is warranted in women with PABC. [Table: see text]
Nomogram for predicting breast-conservation surgery after neoadjuvant chemotherapy.
Authors: Kim Min Kyoon , Han Wonshik , Moon Hyeong-Gon , Kim Jisun , Ahn Soo Kyung , Lee Jun Woo , Noh Dong Young , Kim Taeryung , Kim Ju yeon 
Published: March 2020

1128 Background: The indications for neoadjuvant systemic treatment (NST) have broadened to early breast cancer patients and more patients can undergo breast conservation with results in better cosmetic outcomes. However, a significant number of patients with operable breast cancer still require mastectomy after NST with a small number of patients experiencing disease progression which may hinder complete surgical resection. Therefore, accurate prediction of each patient’s likelihood of achieving breast conservation after NST is important for establishing a treatment plan for patients with operable breast cancers. Methods: We identified 534 women from the Seoul National University Hospital Breast Care Center, who were stage II and III, and treated with neoadjuvant chemotherapy and surgery from Jan. 2001 to Dec. 2010. Breast conservation surgery (BCS) and tumor size reduction to less than 3cm were clinical outcome variables for nomograms, and we analyzed the various clinicopathologic factors best predicting these outcomes. To develop well-calibrated and exportable nomograms for BCS and for residual tumor size, we built each model in a training cohort and validated it in an independent validation cohort. Results: Of the 513 patients, pCR was observed in 10.5% and BCS was performed in 50.1%. The nomogram for predicting BCS and tumor size reduction to less than 3cm were constructed using logistic regressing model. Initial tumor size(p<0.001), the distance between the lesion and the nipple (p < 0.001), the presence of suspicious calcifications in the mammography (p = 0.0127) and multicentricity (p = 0.0146) were independently associated with breast conservation surgery. ER status (p = 0.001), initial tumor size (p < 0.001), histologic type (p = 0.012) were independently associated with a residual tumor size <3cm. Mastectomy rate in the larger than 3cm tumors were 72.7%, and breast conservation surgery in smaller than 3cm tumors were 63.2%. (p < 0.001). Conclusions: In conclusion, we have established a new model to predict BCS and residual tumor size after NST. The model showed the outperformed prediction accuracy compared with previous similar models with reflecting novel factors impacting on surgical decision making.
Influence of guideline-concordant adjuvant therapy on all-cause and disease-specific survival among breast cancer patients in rural Georgia.
Authors: Guy Gery P. , Gillespie Theresa Wicklin , Goodman Michael , Richardson Lisa Carolyn , Ward Kevin C. , Lipscomb Joseph 
Published: March 2020

1130 Background: This study examines whether receipt of chemo-, radiation, and hormonal therapy regimens that are jointly guideline concordant improve survival outcomes among women diagnosed with breast cancer in a rural region of the United States. Methods: All women identified by the state cancer registry residing in rural southwest Georgia diagnosed with early stage breast cancer during 2001-2003 were included. Medical chart abstraction and registry data were used to determine treatment concordance with the 2000 NIH consensus development conference guidelines on breast cancer treatment. Patients were Concordant versus Non-Concordant according to whether their receipt (or non-receipt) of each adjuvant therapy type was according to guidelines. To examine the effects of concordance on all-cause and breast cancer-specific survival, Cox models were developed that used both propensity score weighting and 2-stage residual inclusion instrumental variable techniques to adjust for patient selection effects. Results: In all-cause analyses, Concordance versus Non-Concordance was associated with significantly better survival (hazard ratios (HRs) 0.41 (95% CI: 0.24-0.72) to 0.54 (95% CI: 0.33-0.87). Similar findings emerged in breast cancer-specific survival analyses, with HRs significantly less than 1.0 in most cases. Diagnosis at older age or later disease stage strongly predicted poorer survival outcome; being not married was significant in all-cause but not breast cancer-specific models. Survival was not generally associated with surgical treatment delay, insurance status, socioeconomic status, rural/urban status, comorbidities, tumor grade, or hormonal status. HR for black women versus white was greater than 1.0 across models but never significant (p=0.05). Conclusions: Breast cancer patients in rural Georgia who received guideline-concordant adjuvant therapy had significantly better all-cause and breast cancer-specific survival, based on Cox model analyses that attempted to control for multiple clinical and demographic factors, as well as selection effects. These findings extend the evidence that guideline bundles of care improve outcomes.
Breast cancer risk prediction using the novel germ-line signatures in epigenome regulatory pathways.
Authors: Adaniel Christina , Rendleman Justin , Smith Julia Anne , Klein Robert J. , Schnabel Freya Ruth , Shao Yongzhao , Offit Kenneth , Kirchhoff Tomas 
Published: March 2020

1500 Background: Epigenetic regulatory pathways are intensely studied for their involvement in breast tumorigenesis, however little is currently known about the genetic variation in epigenome components contributing to the risk and/or prognosis of breast cancer. In this study we have tested how the novel germline genetic signatures identified in epigenetic regulatory genes (ERGs) may potentially contribute to clinical prediction of breast cancer risk. Methods: We have genotyped 711 SNPs tagging 87 ERGs in 1985 breast cancer cases and 1609 controls, using Sequenom i-Plex. The samples were of white European origin with the fraction of Ashkenazi Jewish (AJ) ancestry (n=1642). The association of SNPs with breast cancer risk was assessed using logistic regression, adjusted by age, AJ status and estrogen-receptor (ER) status. The predictive ability of SNP signatures was tested by ROC curves using logistic regression fitting the SNP/clinical covariate models, and the area under the curve (AUC) was used to assess their utility in the classification of breast cancer risk. Results: We have identified the signature of 20 SNPs tagging 13 ERGs, significantly associated with breast cancer risk. The strongest association has been observed for RUNX1 (rs7280097, OR=0.83, CI 95%: 0.71-0.94, p=0.006) and PRDM16 (rs12135987, OR=1.22, CI 95%: 1.06-1.42, p=0.007). The inclusion of predictor variables (age, AJ status, ER status) and 20 associated SNPs in logistic regression ROC curve analysis yielded in best fitting model involving 10 SNPs tagging 8 ERGs with AUC of 0.723, compared to 0.660 with predictor variables alone (p=0.003). Conclusions: We have identified a signature of 20 SNPs in epigenetic regulatory genes (20-SNP-ERG) significantly associated with breast cancer risk. In addition, the incorporation of 10 SNPs from 20-SNP-ERG into risk prediction model increases the ability to classify breast cancer risk in addition to other clinical and demographic covariates. The results suggest the promising clinical potential of 20-SNP-ERG signature in identification of high-risk individuals in the population, and point to possible biological implication of germline patterns in epigenetic enzymes in breast tumorigenesis.