bluuebunny/crossref_metadata_2025_split huggingface dataset:
Strategy for sensitive and specific somatic SNV/InDel calling: Leveraging different callers with in-house generated gold standard variant sets.
Authors: Huang Xiu , Sun Ruobai , Cingolani Pablo , Bjonnes Andrew , Lyle Stephen , Protopopov Alexei , Vuzman Dana 
Published: September 2018

e13104 Background: Somatic mutation calling is critical for cancer genotyping. Although rapid development of mutation detection is witnessed with the maturity of NGS, the need for high sensitivity often results in compromised specificity and manual inspection. Here, we propose a methodology that leverages different variant callers to account for specificity without compromising sensitivity. Methods: We designed a cohort of training samples (n = 22), each with known set of SNVs/InDels that were discovered by KEW CANCERPLEX platform. We assessed the performance of four prevailing mutation callers that utilize different statistical approaches and therefore have different calls, using the training samples. We optimized the parameters of the four variant callers to detect all expected variants. We then examined the intersections of every combination of the four callers and identified the best one that eliminated the highest rate of false calls. A customized tool was developed for the intersection of component SNVs and InDels and the report differences among different callers. We also collected another set of validation samples (n = 28), each with true mutations that were both curated and orthogonally validated. We used this set to further test the efficacy of the refined calling strategy. Results: From the training samples, we chose the combination that provides highest sensitivity and specificity. This refined mutation calling strategy removed ~20% false SNV calls and ~50% false InDel calls in average for each sample. This result was further confirmed by the validation samples. Conclusions: The curated set of mutations from the genetic test platforms can provide valuable gold standard to test and tune mutation callers. The conclusions drawn from the curated variants are in line with the experimentally validated variants and showcase the validity of this practice, which we applied to demonstrate that the strategy of intersecting variants from optimized variant callers will generate mutation calls of higher specificity without compromising sensitivity. This methodology reduces the number of variants for curation and improves curation procedures and turn-around time.
Large germline next generation (NGS) sequencing panel of uterine serous carcinoma.
Authors: Romero Ignacio , Garcia-Casado Zaida , Lopez-Reig Raquel , Fernandez-Serra Antonio , Illueca Carmen , Poveda Andres , Lopez-Guerrero Jose Antonio 
Published: September 2018

e13106 Background: Genetic predisposition to uterine serous carcinoma (USC) remains unclear and has been related to Lynch Syndrome (LS) and BRCA1/2 mutations. Wide NGS panels for this condition are starting to be implemented and data remain scarce. Methods: Consecutive USC were identified from a prospective endometrial cancer database (ECD) in a single institution. Clinical information including stage, follow-up, a three-generation pedigree, Microsatellite Instability (MSI) with 8 markers and the Mismatch Repair Protein (MMRPro) staining status, was retrieved from the ECD. Germline genetic testing was performed using a commercially available NGS panel including 80 familial cancer genes (Onco-GeneSGKit) on a MiSeq sequencer. Pathogenic or likely pathogenic variants were confirmed by Sanger sequencing. Results: Twenty-one women out of a total of 150 (14%) cases contained in the ECD were diagnosed with a USC. Median age was 65 (40-84 yo), median Body Mass Index of 26 (19-40), and histologically 18 were defined as pure and 3 as mixed USC. FIGO 2009 stages were I/II and III/IV in 42% and 58% of cases respectively. Adjuvant Chemotherapy (CT) was administered to 76%. MSI-High and MMRPro loss was described in 5%, 19% fulfilled Bethesda criteria, 23% had previous breast cancer and 5% personal Lynch related cancer history, 28% presented with pathological features of Lynch Syndrome such as dedifferentiation, Tumor Infiltrating Lymphocytes (14%), peritumoral lymphocytes or lower uterine location (14%). A median of 5 [range: 2-8] genetic alterations (pathogenic, variants of uncertain significance (VUS) and not described) per patient were observed, including 3 (14.3%) pathogenic mutations, 18 VUS and 43 not described. Among the three pathogenic mutations one was in MSH6 (p.Glu255Ter), another one in DKC1 (p.S280A) and the last one in the recessive gene MUTYH (p.Glu466del). VUS were detected in 57% of cases among 12 different genes: ATM (n = 3), AXIN2 (n = 2), BARD1 (N = 2), RAD50 (n = 2), RET (n = 2) and one case each of BMPR1A, BRIP1, CHEK2, MLH1, MSH6, SLX4 and TSC2. Conclusions: In our series 14% of USC harbored mutations in cancer predisposition genes.VUS are as high as 57% and represent a clinical challenge.
Breast cancer phenotype in patients with hereditary gene mutations other than BRCA1 and BRCA2.
Authors: Arun Banu , Elsayegh Nisreen , Lin Heather Y. , Clifton Katherine , Gutierrez-Barrera Angelica M. , Litton Jennifer Keating , Albarracin Constance T. 
Published: September 2018

e13121 Background: Use of multi-gene panel (MGP) testing for hereditary breast cancer (BC) has increased significantly. Unlike in case of TNBC diagnosed before age 60 and ordering BRCA testing; for MGP testing, healthcare providers depend on personal and/or family history of cancer as tumor phenotype and on patient characteristics for non-BRCA hereditary BC genes which are not well described. Therefore, we planned to evaluate tumor phenotype of BCs associated with hereditary gene mutations other than BRCA 1 and BRCA2. Methods: Consecutive patients with invasive BC who are in a prospective cohort study and who underwent MGP testing based on published criteria as clinically indicated were included in the study. All patients’ breast pathology slides were reviewed by breast pathologists at our institution. For statistical analysis: Patients’ demographic and clinical characteristics were summarized using descriptive statistics such as frequency distribution, mean (± s.d.) and median (range). SAS version 9.4 and S-Plus version 8.04 were used to carry out the computations for all analyses. Institutional IRB approval was obtained. Results: Between 2013 and 2017, 1607 patients underwent MGP testing and 347 were found to be positive for a pathogenic variant. For the study purposes we included only patients with invasive breast cancer (N = 146). Median age was 45.1 yrs (Range: 25-78). Genetics testing results were as follows: BRCA1: 38 (26%), BRCA2: 37 (25%), CHEK2 15 (10%), PALB2: 12 (8%) , ATM: 12 (8%), TP53: 9 (6%), CDH1 : 5 (3%), PTEN: 3 (2%), BRIP1: 3 (2%), and 12 patients (8%) positive for other genes (CDKN2A, MUTYH, PMS2, APC, BARD1, MLH1, NBN, RAD51C, and SDHD). Tumor phenotype by gene mutation in shown in table 1. Conclusions: Several hereditary BC genes are associated with ER positive BC which could have implications for chemoprevention, while others associated with ER neg/TNBC that could have therapeutic implications. These findings and implications need to be further studied in larger cohorts. [Table: see text]
The MetAction project: Biomarker-directed molecularly matched therapy for end-stage cancer implemented in clinical practice.
Authors: Ree Anne Hansen , Flatmark Kjersti , Nygaard Vigdis , Heinrich Daniel , Boye Kjetil , Dueland Svein , Nygaard Vegard , Hovig Eivind , Beiske Klaus , Lund-Iversen Marius , Flørenes Vivi A , Johansen Christin , Bergheim Inger Riise , Sathermugathevan Menaka , Nakken Sigve , Geitvik Gry A , Lingjærde Ole Christian , Børresen-Dale Anne-Lise , Russnes Hege G , Mælandsmo Gunhild M ,   The MetAction Clinical Trial Team
Published: September 2018

e14033 Background: The MetAction project consists of two clinical trial phases. The completed first phase established the required diagnostic infrastructure, implemented security-approved systems for handling of sensitive information, educated the entire project staff within the context of tumor boards, and estimated costs of the initiative within public health services. The endeavor enabled expedite and safe mutation profiling of metastatic tumors in order to offer biomarker-based treatment with molecularly matched medication to patients with end-stage cancer, as reported in Ree et al., ESMO Open 2017. The ongoing second trial phase investigates the feasibility of the established MetAction pipeline in clinical practice. Methods: An eligible patient has end-stage metastatic disease from a solid cancer. Metastatic tissue is analyzed by DNA sequencing (Ion Oncomine™ Comprehensive Panel), where called variants are filtered prior to assessment and prioritization, supplemented with fluorescence in situ hybridization to cover relevant biomarkers. The Molecular Tumor Board interprets the findings within the likelihood of signaling pathway activity, and the sequential Clinical Tumor Board (CTB) may conclude on treatment with any systemic tumor-directed medication. Results: At the time of writing, 19 patients enrolled onto the second trial phase have accomplished the diagnostic procedures from sampling of metastatic tissue to CTB conclusion. Biopsy procedures were undertaken at lung or pleural sites (five cases), liver or superficial or deep peritoneal sites (13 cases), and an inguinal lymph node (one case) and did not cause adverse events. Histologic entities were 12 adenocarcinomas and one case each of squamous cell and undifferentiated carcinoma, cholangiocarcinoma, and four different sarcoma entities. Twelve patients have been found eligible for off-label use of molecularly matched therapy (inhibitor of ALK-, BRAF-, EGFR-, FGFR-, mTOR-, PARP-, or PD-1-mediated signaling). Conclusions: We will report on patient outcome (progression-free survival, overall response rate, and tolerance) to this biomarker-directed treatment in end-stage cancer. Clinical trial information: NCT02142036.
Lipid-insertion to enable targeting functionalization of paclitaxel loaded erythrocyte membrane nanoparticle by tumor-penetrating bispecific recombinant protein.
Authors: Sha Huizi , Chen Hong , Liu Baorui 
Published: September 2018

e14047 Background: There is a great interest in targeting and penetrating of cancer cells for research or therapeutic purposes. Red blood cells (RBCs) are readily available and fully biocompatible long-circulating intravascular carriers that are amenable to chemical modifications, drug loading and reinjection. The purpose of this study was to design a tumor-targeting biocompatible drug delivery system for delivery of antitumor drugs. Methods: DSPE-PEG-MAL, phospholipid derivatives was used to insert into erythrocyte membrane nanoparticles. To make nanoparticles active targeting to the tumor site, a tumor-penetrating bispecific recombinant protein named anti-EGFR-iRGD was used. The characterization, bio-distribution, tumor targeting ability and antitumor activity of paclitaxel loaded anti-EGFR-iRGD modified erythrocyte membrane nanoparticle were evaluated. Results: In this study, anti-EGFR-iRGD-RBC-PTX nanoparticles was successfully constructed with a size of around 100 nm. A lipid-insertion method is employed to functionalize these nanoparticles without the need for direct chemical conjugation. It showed signifcantly targeted skill and increased cytotoxic effect toward both nontargeted RBC-PTX and combination of anti-EGFR-iRGD and RBC-PTX. The tissue distribution and antitumor assays in mice bearing gastric cancer xenograft confrmed the superior penetration tumor effcacy and antitumor activity of anti-EGFR-iRGD-RBC-PTX. Conclusions: We designed and successfully prepared a novel anti-EGFR-iRGD decorated, erythrocyte membrane sourced nanoparticle for targeted drug delivery, with enhanced tumor targeting and anti-tumor effect. Anti-EGFR-iRGD-RBC-PTX represents a potential effective nanomedicine against gastric cancer.
Combined treatment using the anti-p53 drug, APR-246 and eribulin: Synergistic growth inhibition in p53-mutated breast cancer cells.
Authors: Synnott Naoise C , Murray Alyson M. , O'Donovan Norma , Duffy Michael J. , Crown John 
Published: September 2018

e14098 Background: TP53 is the most frequently mutated gene in triple-negative breast cancer, being present in approximately 80% of cases. APR-246 is a novel anticancer drug that acts by reactivating the mutant p53 protein, thereby converting it to a form with wild-type properties. Previously, we showed that APR-246 had antiproliferative, anti-migratory and pro-apoptotic activities in a panel of 23 breast cancer cell lines, including triple-negative (TN) cell lines. The aim of this study was to investigate if combined treatment with APR-246 and different cytotoxic agents resulted in enhanced growth inhibition. Methods: Cell viability was determined using the MTT assay. Combination index (CI) values were calculated using Calcusyn software, based on the Chou-Talalay method. Apoptosis was detected using Annexin V-FITC Apoptosis Detection Kit followed by FACs analysis. Results: Highly synergistic cell growth inhibition was found when APR-246 was combined with eribulin (Eisai Ltd.) in 6 different p53-mutated cell lines (mean CI values range from 0.38 to 0.77). In contrast, enhanced growth inhibition was not found using this combination in the 3 p53-WT cell lines investigated (mean CI values ranged from 1.13 to 2.9). Overall, p53 mutated cell lines had a significantly lower CI values than p53 wild-type cells (p = 0.008). In all the 4 p53-mutated cell lines investigated, a significant increase in apoptosis was also seen when APR-246 was combined with eribulin. This enhanced apoptosis appeared to result from increased mRNA expression of the pro-apoptotic factors PUMA and NOXA by the drug combination compared to either compound alone. In contrast to our findings with eribulin, combined treatment with APR-246 plus docetaxel, doxorubicin, cisplatin or carboplatin was cell line-dependent. Thus, docetaxel plus APR-246 was synergistic in 1/6 cell lines, while doxorubicin, cisplatin or carboplatin plus APR-246 was synergistic in 3/6 cell lines. Conclusions: Clinical trials investigating the combination of APR-246 and eribulin should be considered in patients with a p53 mutation such as triple-negative breast cancer.
Targeting mutant p53 with PK11007: A new approach for the treatment of patients with triple-negative breast cancer?
Authors: Synnott Naoise C , Bauer Matthias R , Madden Stephen F. , Murray Alyson M. , Klinger Rut , O'Donovan Norma , O'Connor Darran , Gallagher William M. , Crown John , Fersht Alan R , Duffy Michael J. 
Published: September 2018

e14099 Background:The identification of a targeted therapy for patients with triple-negative breast cancer (TNBC) is one of the most urgent needs in breast cancer therapeutics. Since the p53 gene is mutated in approximately 80% of TNBC patients, it is a potential therapeutic target for this form of breast cancer. PK11007 is a 2-sulfonypyrimidine that stabilizes and reactivates mutant p53 (Bauer et al, PNAS 2016). The compound recently was reported to preferentially decrease viability in p53-compromised cancer cells. The aim of this investigation was to evaluate PK11007 as a potential new treatment for TNBC. Methods: Cell viability was determined using the MTT assay. Apoptosis was detected using Annexin V Apoptosis Detection Kit. Migration was determined by Transwell migration assay. Knockdowns of p53 protein were carried out using predesigned Flexitube sequences (Qiagen). Results: IC50 values for inhibition of proliferation by PK11007 in the panel of 17 breast cell lines ranged from 2.3 to 42.2 μM. There were significantly lower IC50values for TNBC than for non-TNBC cell lines (p = 0.03) and for p53-mutated cell lines compared with p53 WT cells (p = 0.003). Response to PK11007 however, was independent of ER or HER2 status of the cells. In addition, PK11007 induced apoptosis and inhibited migration in p53 mutant cell lines. Using RNAseq and gene ontogeny analysis, we found that PK11007 altered the expression of genes enriched in pathways involved in regulated cell death, regulation of apoptosis, signal transduction, protein refolding and locomotion. To establish if PK11007 acts by targeting mutant p53, we used siRNA to knockdown p53 in 3 p53-mutated TNBC cell lines. Reduction in p53 protein levels resulted in a significant decrease in the growth inhibitory effects of PK11007, in all 3 cell lines investigated, suggesting that PK11007 mediates growth inhibition via p53. The observations that PK11007 inhibited cell growth, induced apoptosis, blocked cell migration and altered genes involved in cell death, are all consistent with the ability of PK11007 to activate mutant p53. Conclusions: Based on our data, we conclude that targeting mutant p53 with PK11007 is a potential approach for treating p53-mutated TNBC.
ASN003, a highly selective BRAF and PI3K inhibitor: Preclinical and phase 1 clinical data in patients with advanced solid tumors.
Authors: Rasco Drew W. , Sullivan Ryan J. , Lakhani Nehal J. , Reddy Sanjeeva , Rao Niranjan Sathyanarayana , Denis Louis J. , Tolcher Anthony W. , Flaherty Keith 
Published: September 2018

e14102 Background: RAS-RAF-MEK and PI3K-AKT-mTOR are two major signaling pathways involved in tumorigenesis. Components of these two pathways are frequently mutated in a broad range of tumors. ASN003 is a novel and highly selective small-molecule inhibitor of the RAS-RAF-MEK and PI3K pathways. Methods: The activity of ASN003 was determined using PI3K and BRAF enzymes, and efficacy was studied in human tumor xenograft models in mice. ASN003 is currently being investigated in patients with solid tumors in a Phase 1 trial using an accelerated dose titration design. In Part A, safety and tolerability of ASN003 is being studied in patients with advanced solid tumors. In Part B, safety, tolerability and preliminary efficacy of ASN003 will be evaluated in melanoma, CRC and NSCLC patients with a BRAF, PIK3CA or PTEN mutation. Pharmacokinetic (PK) profile and the pharmacodynamic (PD) effects of ASN003 on biomarkers such as pERK and pS6 are investigated in both parts of the study. Results: ASN003 showed potent and highly selective inhibition of BRAF and PI3K-α and -δ, and low affinity for PI3K-ß. ASN003 showed strong antiproliferative activity in cell lines and caused significant tumor growth inhibition in xenograft models harboring BRAF and PIK3CA or PTEN mutations. ASN003 showed antiproliferative activity in B-RAF and MEK inhibitor resistant cell lines. ASN003 had a strong antitumor activity in a BRAFV600mutant melanoma PDX model resistant to BRAF inhibitors, vemurafenib and dabrafenib. In humans, to date, ASN003 was well tolerated at 10 and 20 mg QD. Adverse events were mild and peak plasma level of 120 nM at 10 mg QD was achieved with a half-life of > 12 h. Dose escalation is ongoing. Conclusions: ASN003 is a unique small molecule, with highly selective and potent inhibition of BRAF, PI3-α and -δ kinases. ASN003 has strong antitumor activity in various xenograft tumor models harboring both BRAF and PIK3CA/PTEN mutations, and in a BRAF inhibitor resistant melanoma PDX model. To date, ASN003 was well tolerated and achieved good systemic exposure. Updated and detailed clinical, PK and PD results will be presented. Clinical trial information: NCT02961283.
Evolution of radiomic features on serial CT scans as an imaging based biomarker for evaluating response in patients with non-small cell lung cancer treated with nivolumab.
Authors: Xie Yuanqi , Khunger Monica , Thawani Rajat , Velcheti Vamsidhar , Madabhushi Anant 
Published: September 2018

e14534 Background: Nivolumab is a PD-1 inhibitor that is FDA approved for treatment of chemotherapy refractory advanced NSCLC. The current standard clinical approach to evaluating tumor response is sub-optimal in evaluating clinical benefit from immunotherapy drugs. Our study aims to explore whether changes in radiomic features of the tumor between baseline and 2-week post-treatment CT scans can predict treatment response. Methods: 41 NSCLC patients treated with nivolumab were included in this study. 22 patients with pre- and post-nivolumab CT scans were used as a learning set and the remaining 19 for independent testing. Patients who did not receive nivolumab after 2 cycles due to lack of response or progression as per RECIST were classified as ‘non-responders’, and patients who had radiological response as per RECIST, or stable disease as per RECIST and clinical improvement were classified as ‘responders’. Lung nodules on pre-treatment CT scans were annotated with 3D SLICER software by a radiologist. 312 texture features of lung nodules were extracted and investigated in the study. The percent difference of each extracted feature was calculated based on the baseline and 2 week post-therapy CT scan. In the learning set, the six features that most significantly changed between baseline and post-treatment scans and also maximally differentially expressed between responders and non-responders were identified. Unsupervised clustering was applied on the set of 6 features for the 19 patients in the test set to predict which patients did and did not respond. Results: The top 6 features predictive of response corresponded to the Haralick, Gabor and Laws texture families. Unsupervised clustering yielded an accuracy of 78.95%. Conclusions: Our results suggest that changes in certain radiomic texture features between baseline and post-treatment CT scans following nivolumab could identify early clinical response to treatment. Additional validation of these novel quantitative imaging based approaches is warranted to accurately define clinical benefit from immunotherapy.
Tumor-penetrating peptide iRGD conjugation effectively potentiates intratumor T cell infiltration.
Authors: Ding Naiqing , Su Shu , Meng Fanyan , Sha Huizi , Chen Fangjun , Wei Jia , Chen Hong , Du Shiyao , Liu Baorui 
Published: September 2018

e14543 Background: Poor infiltration of activated lymphocytes into solid tumors can be a fundamental factor limiting their efficacy. The purpose of this study was to determine whether a cycled tumor-penetrating peptide, iRGD, with a well-defined role in delivering drugs into extravascular tumor tissues, could facilitate lymphocytes infiltration into tumors in both the iRGD combination regimen and conjugated pattern. Methods: We used polyethylene glycol-conjugated phospholipid (PEG-lipid) derivatives, a time-efficient and versatile platform, to immobilize iRGD on T cell membrane, and examined the ability of iRGD to improve lymphocytes infiltration into tumors in multicellular spheroids and two xenograft mouse models. Furthermore, the synergy effect of iRGD modification and PD-1 gene knock out in adoptive T cell transfer immunotherapy was evaluated in a xenograft model of EBV associated gastric cancer. Results: In this study, we first showed that systematic injection of iRGD could double the number of CD3+ T cells in 4T1 tumor in BALB/C mouse and the synthetic iRGD-PEG-lipid, which could spontaneously transfer from solution to cell surfaces, had no effect to cell vitality, proliferation, phenotype and function. In adoptive transfer studies, the infiltration of T cells could be promoted by the co-administration with iRGD while T cells modified with iRGD could spread more extensively throughout both the multicellular spheroids and tumor mass. Furthermore, We demonstrated that iRGD modified T cells had superior antitumor efficiency to iRGD combination regimen due to increased T cell infiltration, and exhibited robust synergy effect with PD-1 gene knock out. Conclusions: Our study offers a simple method to target immune cells into tumors and may have the potential to enhance the clinical efficacy of adoptive T cell immunotherapy.