bluuebunny/crossref_metadata_2025_split huggingface dataset:
Polymorphisms in the dopamine (DA) signaling to predict outcome in patients (pts) with metastatic colorectal cancer (mCRC): Data from TRIBE, MAVERICC, and FIRE-3 phase III trials.
Authors: Battaglin Francesca , Cao Shu , Loupakis Fotios , Stintzing Sebastian , Parikh Aparna Raj , Puccini Alberto , Tokunaga Ryuma , Naseem Madiha , Berger Martin D. , Arai Hiroyuki , Millstein Joshua , Lonardi Sara , Zhang Wu , Cremolini Chiara , Mancao Christoph , Falcone Alfredo , Heinemann Volker , Lenz Heinz-Josef 
Published: May 2019

3048 Background: Strong evidence supports the critical role of the gut-brain axis in modulating gastrointestinal function and homeostasis. Available data suggest an involvement of the dopaminergic pathway in CRC dynamics. DA could inhibit proliferation and migration of tumor endothelial cells and enhanced 5-fluorouracil efficacy in CRC preclinical models. Hence, we hypothesized that genetic variants in DA signaling may predict treatment outcomes in mCRC pts. Methods: The impact on outcome of 22 selected single nucleotide polymorphisms (SNPs) in 9 genes of the DA signaling pathway ( DRD1, DRD2, DRD3, DRD4, DRD5, TAAR1, SLC6A3, SLC18A2, PPP1R1B) was analyzed on a total of 884 pts enrolled in three independent randomized first-line trials: TRIBE (n = 324), MAVERICC (n = 324), and FIRE-3 (n = 236). Genomic DNA from blood samples of pts was genotyped through the OncoArray, a custom array manufactured by Illumina. A meta-analysis approach using the METASOFT software was used to quantify SNPs prognostic effects and heterogeneities across treatment arms. P values were adjusted for multiple testing using the false discovery rate (FDR) method. Results: Overall, DRD3 rs3732790, rs9817063 and rs2134655 showed a significant nominal p value ( P) in association with tumor response (TR) across trials ( P= 0.032, P= 0.021, P= 0.027, respectively). TAAR1 rs8192620 showed an association with both progression free survival (PFS) ( P= 0.01) and overall survival (OS) ( P= 0.033), similar to DA transporter SLC6A3 rs6347 ( P= 0.016 and P= 0.002, respectively). SLC6A3 rs6347 association with OS remained significant after FDR ( PFDR= 0.045). Subgroup analyses showed a significant association with PFS for DRD1 rs267410 and SLC6A3 rs2652510 in females ( PFDR= 0.056), and between SLC6A3 rs6347 and OS ( PFDR= 0.041) and SLC6A3 rs6876890 and TR ( PFDR= 0.05) in KRAS wild type. Conclusions: Our results suggest that SNPs in DA signaling may have a prognostic value in mCRC pts receiving first-line treatment. Upon validation, these findings may provide novel insight on the role of DA signaling in CRC and possibly contribute to open novel therapeutic perspectives.
Genome-wide cell-free DNA (cfDNA) methylation signatures and effect on tissue of origin (TOO) performance.
Authors: Liu Minetta C. , Jamshidi Arash , Venn Oliver , Fields Alexander P. , Maher M. Cyrus , Cann Gordon , Amini Hamed , Gross Samuel , Bredno Joerg , Miller Meredith , Schellenberger Jan , Kurtzman Kathryn N. , Fung Eric T. , Maddala Tara , Oxnard Geoffrey R. , Klein Eric A. , Spigel David R. , Hartman Anne-Renee , Aravanis Alex , Seiden Michael 
Published: May 2019

3049 Background: For multi-cancer detection using cfDNA, TOO determination is critical to enable safe and efficient diagnostic follow-up. Previous array-based studies captured < 2% of genomic CpGs. Here, we report genome-wide fragment-level methylation patterns across 811 cancer cell methylomes representing 21 tumor types (97% of SEER cancer incidence), and define effects of this methylation database on TOO prediction within a machine learning framework. Methods: Genomic DNA from 655 formalin-fixed paraffin-embedded (FFPE) tumor tissues and 156 isolated cells from tumors was subjected to a prototype 30x whole-genome bisulfite sequencing (WGBS) assay, as previously reported in the Circulating Cell-free Genome Atlas (CCGA) study (NCT02889978). Two independent TOO models, one with and one without the methylation database, were fitted on training samples; each was used to predict on the test set. A WGBS classifier was used to detect cancer at 98% specificity; reported TOO results reflect percent agreement between predicted and true TOO among those detected cancers (166 cases: 81 stage I-III, 69 stage IV, 16 non-informative). Results: Genome-wide methylation data generated from this database allowed fragment-level analysis and coverage of ~30 million CpGs across the genome (~60-fold greater than array-based approaches). Incorrect TOO assignments decreased by 35% (20% to 13%) after incorporating methylation database information into TOO classification. Improvement was observed across all cancer types and was consistent in early-stage cancers (stage I-III). Respective performances in breast cancer (n = 23) were 87% vs 96%; in lung cancer (n = 32) were 85% vs 88%; in hepatobiliary (n = 10) were 70% vs 90%; and in pancreatic cancer (n = 17) were 94% vs 100%. Results using an optimized approach informed by these results in a large cohort of CCGA participants will be reported. Conclusions: Incorporating data from a large methylation database improved TOO performance in multiple cancer types. This supports feasibility of this methylation-based approach as an early cancer detection test across cancer types. Clinical trial information: NCT02889978.
Training and validation study for sequential monitoring of CAMLs in circulation to predict ongoing progression in lung cancer patients undergoing definitive radiotherapy.
Authors: Adams Daniel , He Jianzhong , Qiao Yawei , Xu Ting , Gao Hui , Reuben James M. , Komaki Ritsuko , Liao Zhongxing X. , Wistuba Ignacio Ivan , Raghavakaimal Ashvathi , Tang Cha-Mei , Augustyn Alexander , Lin Steven H. 
Published: May 2019

3053 Background: Cancer Associated Macrophage-Like cells (CAMLs) are a recently described circulating stromal cell common in the peripheral blood of cancer patients that are prognostic for progressive disease. Further, it has been shown that changes in CAML size (i.e. enlargement above 50µm) can predict progression free survival (PFS) in thoracic cancers (e.g. lung). We enrolled 104 unresectable non-small cell lung cancer (NSCLC) patients, with an initial training set review of 54 patients, to determine if change in CAML size after radiation therapy was predictive PFS. Methods: A 2 year single blind prospective study was undertaken to test the relationship of ≥50µm CAMLs to PFS based on imaging in lung patients before and after induction of chemo radiation, or radiation therapy. To achieve a 2-tailed 90% power (α = 0.05) we recruited a training set of 54 patients and validation set of 50 patients all with pathologically confirmed unresectable NSCLC: Stage I (n = 14), Stage II (n = 16), Stage III (n = 61) & Stage IV (n = 13). Baseline (BL) blood samples were taken prior to start of therapy & a 2nd blood sample (T1) was taken after completion of radiotherapy (~30 days). Blood was filtered by CellSieve filtration and CAMLs quantified. Analysis by CAML size of < 49 µm or ≥50 µm was used to evaluate PFS hazard ratios (HRs) by censored univariate & multivariate analysis. Results: CAMLs were found in 95% of samples averaging 2.7 CAMLs/7.5mL sample at BL, with CAMLs ≥50 µm having reduced PFS (HR = 2.2, 95%CI1.3-3.8, p = 0.003). At T1, 18 patients had increased CAML size ≥50 µm with PFS (HR = 4.6, 95%CI2.5-8.3, p < 0.001). In total, ≥50 µm CAMLs at BL was 76% accurate at predicting progression within 24 months while ≥50 µm CAMLs at T1 was 83% accurate at predicting progression. Conclusions: In unresectable NSCLC patients, enlargement of CAMLs during treatment is an indicator active progression. We identify that a single ≥50 µm CAML after induction of radiotherapy, in our training set and confirmed in our validation set, is an indicator of poor prognosis. We suggest that changes in CAML size during therapy may indicate the efficacy of therapy and could potentially help shape subsequent therapeutic decisions.
Analytical validation of a tumor-agnostic integrated multianalyte circulating tumor DNA (ctDNA) assay in early-stage cancer.
Authors: Hartwig Anna , Artieri Carlo , Jaimovich Ariel , Van Seventer Emily E. , Parikh Aparna Raj , Corcoran Ryan Bruce , Baca Arthur , Talasaz AmirAli 
Published: May 2019

3057 Background: ctDNA sequencing has been rapidly adopted for the identification of targetable somatic alterations (alts) in patients with advanced cancers. However, early stage disease detection has been hindered by low levels of ctDNA in circulation and the presence of confounding non-tumor-related somatic alts. We developed and validated a ctDNA assay that combines somatic and epigenomic signals to detect early stage tumors without tumor tissue or white blood cells (WBC). Methods: Using a single input sample, our assay integrates the sensitive detection of genomic alts with quantification of epigenomic signals associated with cancer. Non-tumor alts (e.g., clonal hematopoiesis of indeterminate potential; CHIP) are excluded using a newly developed bioinformatic classifier. To assess analytical sensitivity, specificity, and positive and negative reproducibility, we tested 337 clinical and contrived samples. Results: Clinical specificity was determined using 80 plasma samples from 50-75 year old presumptive cancer-free donors, and resulted in a single false positive (99% specificity). Analytical sensitivity (limit of detection) was established using a dilution series of 4 different late stage CRC pts tested in triplicate at a clinically relevant DNA input (30 ng) across multiple batches. 100% sensitivity was maintained even at the lowest tested level (estimated 0.1% tumor level). Positive/negative reproducibility was assessed by testing triplicates of diluted late stage samples and age-matched healthy donors, respectively, across different cfDNA inputs, and multiple reagent lots. Both positive and negative calls were 100% concordant across all replicates. Independent estimation of tumor levels from epigenomic or genomic signals produced highly concordant results (correlation r-value: 0.82, p-value: 3e-16). Conclusions: We designed and validated a highly specific ctDNA assay that integrates both genomic and epigenomic signals to allow for accurate and quantitative tumor level detection in early stages of the disease without requiring tumor tissue or WBC.
The i3+3 design for phase I clinical trials.
Authors: Ji Yuan , Liu Meizi 
Published: May 2019

3066 Background: Other than the 3+3 design, new model-based statistical designs like the mTPI design (Ji and Wang, 2013, JCO) are alternative choices for oncology dose-finding trials, including immune oncology dose-finding trials (Atkins et al., 2018, Lancet Oncology). One major criticism of the 3+3 design is that it is based on simple rules, does not depend on statistical models for inference, and leads to unsafe and unreliable operating characteristics. However, the rule-based nature allows 3+3 to be easily understood and implemented in practice, making it practically attractive and friendly. Can friendly rule-based designs achieve great performance seen in model-based designs? For four decades, the answer has been NO. Methods: We propose a new rule-based design called i3+3, where the letter "i" represents the word "interval". The i3+3 design is based on simple but more clever rules that account for the variabilities in the observed data. In short, the i3+3 design simply asks clinicians to compare observed toxicity rates with a prespecified toxicity interval, and make dose escalation decisions according to three simple rules. No sophisticated modeling is needed and the entire design is transparent to clinicians. Results: We compare the operating characteristics for the proposed i3+3 design with other popular phase I designs by simulation. The i3+3 design is far superior than the 3+3 design in trial safety and the ability to identify the true MTD. Compared with model-based phase I designs, i3+3 also demonstrates comparable performances. In other words, the i3+3 design possesses both simplicity and transparency of the rule-based approaches, and the superior operating characteristics seen in model-based approaches. An online R Shiny tool is provided to illustrate the i3+3 design, although in practice it requires no software to design or conduct a dose-finding trial using the design. Conclusions: The i3+3 design could be a practice-altering method for the clinical community. It may increase the safety and efficiency of dose finding trials.
Radiomics features to identify distinct subtypes of triple-negative breast cancers.
Authors: Itakura Haruka , Ikeda Debra M. , Okamoto Satoko , Chen Shu-Tian , Rister Blaine , Gude Dev , Mattonen Sarah A. , Alkim Emel , Todderud Julia , Schueler Emil , Rubin Daniel , Sledge George W. , Kurian Allison W. 
Published: May 2019

3069 Background: We sought to gain new insight into triple-negative breast cancer (TNBC), an aggressive, clinically distinct subgroup of breast cancers, by applying a sequence of computational approaches to tumor segmentation, three-dimensional anatomic characterization, and tumor subtyping. We extracted algorithmically-derived quantitative imaging (radiomics) features from each TNBC lesion in breast magnetic resonance imaging (MRI) to identify underlying subtypes. Methods: We evaluated tumors on pre-treatment, post-contrast MRI from 90 patients with non-metastatic TNBC. We employed active contour segmentation and semi-automated identification of tumor regions-of-interest. We extracted 900 radiomics features from each segmented tumor using an algorithm that characterizes the size, shape, texture, and edge sharpness of tumors at the voxel level. We applied k-means consensus clustering, a statistical tool for unsupervised discovery, and performed 1000 bootstraps with resampling on the feature vectors to examine all resulting clusters from k=2 to 10. Based on two diagnostic metrics of consensus stability, we selected the optimum cluster number. We performed Significance Analysis of Microarrays to identify statistically significant radiomics features for each cluster. Results: We identified three distinct image-based clusters in 117 tumors from 90 TNBC patients (multifocal lesions in n=13). Cluster 1 (n=97) was distinguished by 330 radiomics features (False Discovery Rate [FDR] <5%) and Cluster 2 (n=13) by 85 features (FDR<5%), whereas Cluster 3 (n=7) was not significantly associated with features. Clinical characteristics did not differ across the three clusters, with mean age (49.1±11.7) and clinical stage distributions (stage I: 20.7%, II: 55.4%, III: 23.9%) for the cohort mirroring those of individual clusters. Among those who received neoadjuvant therapy, we observed pathologic complete response in 50% (23 of 46, 95% CI, 0.36-0.64) of patients in Cluster 1, 83% (5 of 6, 95% CI, 0.54-1.0) in Cluster 2, and 0% (0 of 3) in Cluster 3. Conclusions: Radiomics features providing voxel-level characteristics of tumor morphology differentiated TNBC into three distinct subtypes. These subtypes, defined by radiomics biomarkers, may be associated with clinical response to neoadjuvant therapy.
First-in-human study of AZD5153, a small molecule inhibitor of bromodomain protein 4 (BRD4), in patients (pts) with relapsed/refractory (RR) malignant solid tumor and lymphoma: Preliminary data.
Authors: Wang Judy Sing-Zan , De Vita Serena , Karlix Janet L. , Cook Carl , Littlewood Gillian M. , Hattersley Maureen M. , Moorthy Ganesh , Edlund Helena , Fabbri Giulia , Sachsenmeier Kris F. , Davison Chris , Clark Edwin , Moore Kathleen N. , Bauer Todd Michael , Ulahannan Susanna Varkey , Patel Manish R. , Hamilton Erika Paige 
Published: May 2019

3085 Background: BRD4 is a bromodomain and extraterminal (BET) protein that regulates oncogenic programs by modifying gene transcription and additional mechanisms. AZD5153 is a novel, reversible BRD4 inhibitor with bivalent mechanism of action and enhanced antitumor activity in preclinical models. This phase 1, multicenter, dose escalation study (NCT03205176) assesses AZD5153’s safety, pharmacokinetics (PK), and pharmacodynamics (PD). We report here preliminary, unvalidated data from AZD5153 monotherapy in pts with RR solid tumor, including lymphoma. Methods: Adult pts received oral AZD5153 QD/BID to determine the MTD. During dose escalation, a continual reassessment model was used to estimate toxicity and all final decisions were made by the Safety Review Committee. PK and PD were characterized using standard methods. Results: As of 1 Nov 2018, 28 pts (78.6% female, median age 66.5 y) were treated in 7 cohorts: 2 mg QD (3 pts), 5 mg QD (3 pts), 10 mg QD (3 pts), 10 mg BID (5 pts), 15 mg BID (4 pts), 20 mg BID (7 pts), and 30 mg QD (3 pts). Treatment was ongoing in 8 pts at data cut-off. Safety findings showed 50% of pts experienced treatment-related AEs. 25% of pts experienced treatment-related Grade ≥3 AEs, which were thrombocytopenia and fatigue (7.1% each), and anemia, diarrhea, and platelet count decreased (3.6% each). SAEs were observed in 25% of pts; none of the SAEs was attributable to AZD5153 alone. Dose-limiting toxicities of thrombocytopenia (1 pt) and diarrhea with herpetic rash leading to discontinuation (1 pt) occurred at 20 mg BID. 53.6% of pts discontinued due to disease progression. Total median treatment duration was 1.3 mo (range up to 8.9 mos). Dose proportional increase in Cmax and AUC were observed across the dose range tested. Tmax ranged from 0.5 to 3 h and t1/2 was 6 h. Dose-dependent changes in expression of target genes (eg, HEXIM1, HIST2H2BF, CD274, and CCR2) and platelet counts were observed in the peripheral blood. Conclusions: AZD5153 monotherapy is safe and tolerated at doses up to 30 mg QD and 15 mg BID. Linear increase in PK was observed. Additional safety and efficacy updates will be reported at the annual meeting. Clinical trial information: NCT03205176.
PIPA: A phase Ib study of selective ß-isoform sparing phosphatidylinositol 3-kinase (PI3K) inhibitor taselisib (T) plus palbociclib (P) in patients (pts) with advanced solid cancers—Safety, tolerability, pharmacokinetic (PK), and pharmacodynamic (PD) analysis of the doublet combination.
Authors: Lopez Juanita Suzanne , SelviMiralles Manuel , Ameratunga Malaka , Minchom Anna , Pascual Javier , Banerji Udai , Bye Hannah , Raynaud Florence I. , Swales Karen E , Malia Jason , Hubank Michael , Garcia-Murillas Isaac , Parmar Mona , Ward Sarah Emily , Finneran Laura , Hall Emma , Turner Alison Joanne , De Bono Johann S. , Yap Timothy A , Turner Nicholas C. 
Published: May 2019

3087 Background: Oncogenic hyperactivation of the PI3K pathway is common in multiple cancers, with preclinical data showing that CDK4/6 inhibitors sensitise PIK3CA mutant cancers to PI3K inhibitors. We report the activity of the P+T in solid tumors with PI3K pathway activation, along with the PD biomarker analysis. Methods: We previously reported the dose escalation phase identifying 125mg P given 3-weeks-on, 1-week-off in combination with T 2mg as the recommended phase 2 dose (R2PD, Lim, ASCO 2017). We report the results in solid tumors with confirmed activating mutations (mts) in the PI3K pathway, from dose escalation and expansion, with no prior exposure to CDK4/6 or PI3K pathway inhibitors. PD studies include analyses of platelet-rich plasma (PRP) and paired tumour biopsies. Results: 20 pts (median age 61, range 34-72) were treated at the doublet RP2D, M/F 7/13, with a median 4 prior treatments (range 2-11). Tumour types included colorectal, breast, lung, endometrial,oligodendroglioma and head and neck cancers. Durable disease control occurred in 3 patients with ER+ advanced breast cancer with responses lasting >6 months including 1 pt with a H1047R PIK3CAmt with an ongoing RECIST PR>36 cycles, 2 pts with PIK3CAmt colorectal cancer had RECIST SD for >5 months, and 1 patient with a PIK3CGmt anaplastic oligodendroglioma had clinical and radiological benefit lasting 5.5 months. Treatment was well tolerated with predictable G1-2 adverse events (AEs). G3 toxicities of neutropenia (n=6), thrombocytopenia (2), rash (2), mucositis (1) and raised transaminases (1 each) were all transient with no G4/5 AEs. Significant decreases in tumour pRb, and pAKT and pGSK3ß in PRP, confirmed modulation of both CDK4/6 and PI3K pathways at R2PD. Conclusions: Doublet P+T is well tolerated at the combination RP2D, with PD evidence of PI3K and CDK4/6 modulation in both plasma and tumor. Promising preliminary anti-tumor activity is seen in a mixed histology cohort selected for activating PIK3 mutations. Clinical trial information: NCT02389842.
A phase I/II first-in-human trial of oral SRA737 (a Chk1 inhibitor) given in combination with low-dose gemcitabine in subjects with advanced cancer.
Authors: Banerji Udai , Plummer Elizabeth Ruth , Moreno Victor , Ang Joo Ern , Quinton Amy , Drew Yvette , Hernández Tatiana , Roda Desamparados , Carter Louise , Navarro Alejandro , Kristeleit Rebecca Sophie , Arkenau Hendrik-Tobias , Sarker Debashis , Castellano Daniel E. , Walter Harriet , Roxburgh Patricia , Blagden Sarah Patricia , Anthoney Alan , Verdon Ines , Jones Robert Hugh 
Published: May 2019

3095 Background: SRA737 is a potent, highly selective and orally-bioavailable inhibitor of checkpoint kinase 1 (Chk1). SRA737-02 was designed to investigate the safety, tolerability and preliminary activity of SRA737 in a novel combination with sub-therapeutic doses of gemcitabine (low dose gemcitabine; LDG) utilized to potentiate SRA737’s activity by induction of replication stress in subjects with advanced solid tumors. Methods: Phase 1 dose escalation investigated cohorts of 3 to 6 subjects receiving escalating doses of SRA737 for 2 days after LDG administration on days 1, 8, 15 of 28-day cycles. Phase 2 expansion cohorts explored the hypothesis that LDG strongly synergizes with SRA737 in subjects with genetically-defined tumors hypothesized to be sensitive to Chk1 inhibition: urothelial, high grade serous ovarian, small cell lung, soft tissue sarcoma, and cervical or anogenital cancers. Results: A total of 55 subjects received SRA737 in 13 dose escalation cohorts at doses of 40 to 600 mg SRA737 combined with LDG doses of 50 to 300 mg/m2. No protocol-defined dose limiting toxicities (DLTs) have been observed. The pharmacokinetic profile of SRA737 revealed an AUC0-24 and Cmax of 3550 ng∙h/mL and 548 ng/mL at 150 mg SRA737. At this dose, the Cmin (52 ng/mL) exceeded that determined in preclinical models to be effective. Enrollment into expansion cohorts was initiated at 500 mg SRA737 plus 100 mg/m2 LDG with intra-patient dose escalation permitted to 250 mg/m2 LDG. Approximately 80 subjects were planned and 82 have been treated. Median treatment duration was 51 days (range 1 to 358). The most common treatment-emergent adverse events were nausea (53%), vomiting (45%), fatigue (40%), diarrhea (38%), and anemia (28%); the majority were of mild to moderate severity. Proof-of-concept clinical activity has been seen in tumor types such as anal, cervical, and rectal. Conclusions: The combination of LDG and SRA737 has been well tolerated. This first-in-human clinical study provides proof-of-concept that sub-therapeutic LDG effectively potentiates SRA737. This novel replication stress-targeted therapy warrants further evaluation in genetically pre-defined solid tumors. Clinical trial information: NCT02797977.