bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pharmacokinetics of ciclopirox prodrug, a novel agent for the treatment of bladder cancer, in animals and humans.
Authors: Weir Scott James , Wood Robyn , Baltezor Michael Jay , Reed Greg , Brinker Amanda E , Ham Tammy , Schorno Karl , Toren Paul , Ramamoorthy Prabhu , Zhukova-Harrill Valentina , Dalton Michael , McCulloch William , Patel Manish R. , Ulahannan Susanna Varkey , Burris Howard A. , Falchook Gerald Steven , Jensen Roy A. , Anant Shrikant , Taylor John Arthur 
Published: May 2019

e14705 Background: Ciclopirox Prodrug (CPX-POM) is a novel anticancer agent currently being evaluated in patients with advanced solid tumors participating in a First-in-Human, Phase 1 safety, dose tolerance, pharmacokinetics (PK) and pharmacodynamics trial at four US sites. In vitro and in vivo preclinical proof of principle was established in high grade human urothelial cancer cell lines as well as a mouse model of bladder cancer.Methods: A series of in vivo PK studies were conducted in mice, rats and dogs to characterize the absolute bioavailability of CPX following intravenous (IV), subcutaneous (SC) and oral administration of CPX-POM. The single dose and steady-state plasma and urine pharmacokinetics of CPX-POM are also currently being characterized in patients participating in the ongoing Phase 1 trial. Plasma and urine concentrations of the prodrug and metabolites were determined by LC-MS/MS validated in each specie and matrix. Non-parametric pharmacokinetic parameters were generated from resultant plasma and urine drug and metabolite concentration-time data. Results: CPX-POM is rapidly and completely metabolized to CPX in blood via circulating phosphatases in animals and humans. CPX is completely bioavailable following IV CPX-POM administration in mice, rats and dogs. CPX and its major inactive glucuronide metabolite (CPX-G) are extensively eliminated in urine in all animal species. SC administration of CPX-POM demonstrated excellent bioavailability in rats and dogs. Following IV administration of 30-900 mg/m2CPX-POM to patients, the apparent elimination half-life of CPX ranged from 2 to 8 hours, CPX systemic exposure was dose-proportional and time-independent in cancer patients, and a major portion of the dose was eliminated as CPX-G. Conclusions: IV CPX-POM achieves plasma and urine CPX exposures that exceed in vitro IC50 values several-fold at well tolerated doses in animals and humans. CPX pharmacokinetics observed in animals were predictive of human systemic clearance based on allometric scaling. Clinical trial information: NCT03348514.
Effect of MALAT1 in the crosstalk between nucleus and mitochondria on mitochondrial reprogramming in hepatocellular carcinoma cells.
Authors: Zhao Yijing , Cui Jiuwei , Hu Jifan , Hoffman Andrew R 
Published: May 2019

e14711 Background: Mitochondria-nuclear crosstalk is a bidirectional pathway of communication between mitochondria and nucleus that influences many cellular and organismal activities. This crosstalk can regulate several oncogenic pathways involved in tumorigenesis. MALAT1 (metastasis-associated lung adenocarcinoma transcript 1), a nucleus-encoded lncRNA, dysregulated in multiple human malignancies is recently found to drive mitochondria dysfunction in Mitochondria-nuclear crosstalk. Methods: RNA sequencing, “RNA reverse transcription-associated trap sequencing” (RAT-seq), RNA immunoprecipitation(RIP), fluorescence in situ hybridization (FISH), were performed to detect the position of the MALAT1, and its interaction protein and DNAs in HepG2 cell line. After silencing MALAT1 by shRNAs, Seahorse, ATP production, lysotracker staining, Western blot, and electronic microscope were used to measure metabolism, ROS amount, mitophagy, apoptosis and mitochondrial morphology of the silencing cell lines. Results: By combining mitochondrial RNA-Seq with FISH, it is surprised to discover that MALAT1 was enriched in the mitochondria of HepG2 cells. Using RAT-seq approach, MALAT1 was found to utilized it 3’-fragment to interact with multiple loci of mitochondrial DNA( D-loop, COX2, ND3, and CYTB ). The RIP and affinity RNA pulldown assays suggested that the RNA-binding protein HuR mediated the transportation of MALAT1 to the mitochondria. Also, mitochondria transmembrane protein mitochondrial carrier 2(MTCH2) is found to interacted MALAT1, suggesting that MALAT1 may through the MTCH2 to get into the inside of the mitochondria. Knockdown of MALAT1 induced multiple abnormalities in mitochondrial functions, including low OXPHOS, low ATP production, reduced mitophagy, declined mtDNA copy number, and activation of the mitochondrial apoptosis pathway. Conclusions: Together, this study greatly expands our knowledge of the nucleus-encoded lncRNA MALAT1 driving the mitochondria dysfunction. Our study establishes MALAT1 as a regulator through interacting with MT-DNA, HuR, MTCH2 protein, revealing a new regulatory mechanism of mitochondria. Many novel nucleus-encoded RNAs existing in mitochondria were identified at the first time, suggesting novel biological functions of lncRNAs, laying the foundation for further clarifying their roles.
Effect of tivantinib on VEGF signaling pathways and apoptosis of gastric cancer cells with c-MET or VEGFA amplification.
Authors: Kim Hyeong Su , Zang Dae Young , Sohn Sung-Hwa , Kim Bohyun , Sul Hee Jung 
Published: May 2019

e14719 Background: VEGFA is the key mediator of angiogenesis in cancer and previous studies reported that VEGFA expression was significantly up-regulated in gastric cancer tissues compared with matched normal tissues. We showed that increased levels of VEGFA are significantly associated with expression of hepatocyte growth factor receptor (MET) (r = 0.6255, P < 0.0001). In addition, it is well known that c-MET is potentially a highly plausible target for cancer therapy in gastric cancer. In this study, cytotoxic activity of tivantinib were evaluated in gastric cancer cells with high c-MET expression or VEGFA amplification. Methods: In this study, Western blot and quantitative real-time PCR analysis were used to detect the expression of protein and genes after treatment of tivantinib. In addition, MTS, flow cytometry, and migration assay were used. Results: Tivantinib inhibited growths of a high c-MET-expressed or VEGFA-amplified cell lines. Furthermore, in migration and apoptosis analysis, tivantinib induced apoptosis of SNU620, MKN45 (carried VEGFB mutation), AGS, and MKN28 cells but not in KATO III (carried VEGFB and VEGFC mutation) cells. We also found that tivantinib inhibited the VEGF signaling pathway and MYC expression in VEGFA-amplified gastric cancer cell lines. Conclusions: The data indicate that tivantinib could be a potential therapeutic agent for the treatment of gastric cancer with high c-MET expression or VEGFA amplification.
FBXO4 as a novel ubiquitin ligase that targets Cyclin D in the pathogenesis of breast cancer.
Authors: Dhar Ruby , Rath Goura Kishor , Karmakar Subhradip 
Published: May 2019

e14722 Background: Members of ubiquitin ligase family are reported to be associated with cancer. Genome wide RNAi screen using Dharmacon on target Plus RNAi library identified FBXO4 as one of the potential hit . We therefore aimed to study its detailed role on proliferation of MCF7 breast cancer cells with special focus on cell cycle genes. We want to expand it further and study its involvement in context to E2 signaling in breast cancer. We hypothesized that increase in CCND1 expression, could mimic some of the E2 transcriptional regulation and that CCND1 overexpression could lead to E2 independent ER alpha binding to estrogen response element (ERE). Methods: Cell lines: MCF7 grown in MEM alpha supplemented with 10% FBS . For stimulation studies, cells were maintained in phenol free MEM alpha supplemented with 10% FBS and 10 nM estradiol. RNAi knockdown studies: On-target plus siRNA were used to knockdown FBXO4 in MCF7 cells. Western Blot: Western Blot was performed following standard protocols. IHC/Tissue Array: Paraffin embedded malignant breast cancer (ER/PR/EGFR +ve) tissue samples that are scored by pathologist were used for the study. Gene Expression Studies: Microarray and NGS based approach. Results: FBXO4 has been identified as a potential hit in our RNAi screen showing a hyper-proliferative phenotype in MCF7 cellsupon its knockdown. Western blot and ubiquitination assay identified cyclin D (CCND1) as a dedicated FBXO4 target as revealed by confocal microscopy where FBXO4 knockdown showed an enrichment of CCND1 in cytoplasm. Ingenuity pathway analysis and ChIP assay revealed an exploitation of E2 signaling and enhanced recruitment of ER alpha to estrogen response element (ERE) in FBXO4 depleted cells. CCND1 further seems to co-occupy ESR binding motifs thereby representing ER functions. These effects were observed even in absence of any E2 stimulation. Further we observed a significant overlap of differentially expressed genes in E2 stimulated and FBXO4 knockdown cells that were nullified by CCND1 siRNA. Conclusions: Our study elucidated that CCND1 is spared from degradation following loss of FBXO4 which in turn leads to a hyper-proliferative state. Our findings co-related with TCGA and METABRIC databases indicating a poor patient survival and relapse in FBXO4 low and CCND1 high cohorts of ER +ve breast cancer thereby implying a diagnostic value. Along with traditional hormonal therapy, an effective targeted therapy in breast cancer should be aimed to restore FBXO4 levels.
Utility of the Breast Cancer Index (BCI) in the clinical practice.
Authors: Kodali Saranya , Tipirneni Eswar , Dittus Kim 
Published: May 2019

e14723 Background: Extended endocrine therapy (EET) greater than 5 years in early stage hormone receptor positive (HR+) breast cancer (BC) patients has shown benefit. However, EET is associated with side effects and there is no validated assay to determine which group of patients would derive benefit. Breast Cancer Index (BCI) is a validated bio-marker test that incorporates 2 distinct genomic assays and is prognostic/predictive. The objective of this study is to assess patient characteristics, pathologic features and patient preferences with regards to extending endocrine therapy after reviewing the BCI results. Methods: We performed a retrospective chart review on early stage HR+ BC patients from Jan, 2016 to Jan, 2017 at the University of Vermont Medical Center. We identified 25 cases on whom BCI was submitted. Results: Median age was 68 years. Majority of the patients were stage IA (64%). 56% of the tumors were moderately differentiated. All patients were ER +ve and 12% were HER2+. Median tumor size was 1.4 cm (0.3-4). 76% had poor tolerance to the ET and preferred the test to be sent. In LN-patients, BCI identified 42% as high risk and 52% as low risk for late recurrence and 32% who derive high benefit from EET. In LN+ patients, BCI identified 75% as high risk for late recurrence and 25% as low risk for late recurrence. 40% of the entire group were identified to highly benefit from EET (70% agreed to continue ET and 30% denied due to side effects). Conclusions: BCI is a reasonable test to consider in early stage HR+ BC, especially in patients with poor tolerance to ET. This test might aid in decision making with tolerability/compliance challenges to EET. [Table: see text]
HER2 targeted therapy and outcome in HER2-equivocal cases after 2018 ASCO/CAP HER2 guideline modification.
Authors: Crespo James , Sun Hongxia , Wu Jimin , Ding Qingqing , Tang Guilin , Robinson Melissa , Chen Hui , Sahin Aysegul A. , Lim Bora 
Published: May 2019

e14729 Background: The best targeted therapeutic approach for HER2-equivocal cases remains unclear. New ASCO/CAP HER2 guidelines are intended to decrease this ambiguity by combining immunohistochemistry and in situ hybridization to resolve equivocal cases as positive or negative. However, the benefit of anti-HER2 therapy in HER2-equivocal cases is unknown. Methods: We retrospectively reviewed patients who visited MD Anderson from April 2017 to March 2018 with equivocal HER2 results based on the 2013 ASCO/CAP guidelines. The population was divided into 2 cohorts according to biopsy origin (primary cohort: biopsy from breast or axilla; recurrent/metastatic cohort: biopsy from recurrent or metastatic site). HER2 status was redefined using the 2018 ASCO/CAP guidelines. OS and PFS were calculated (Kaplan-Meier method) based on redefined HER2 status and use of HER2 targeted therapy. Results: A total of 139 equivocal results were found. Primary cohort had 90 patients (33 received neoadjuvant and 57 adjuvant therapy). HER2 IHC results were 0 (6.6%), 1+ (37.7%), 2+ (50%), 3+ (1.1%), and no IHC (4.4%). 94% of HER2-equivocal results became HER2 negative. Only 5 patients received anti-HER2 therapy, all of them in the HER2-negative group. After median follow-up of 1.91 yrs, 3 deaths and 8 progressions had occurred. There was no statistically significant association between anti-HER2 therapy and OS (p = 0.67) or PFS (p = 0.49). The recurrence/metastatic cohort had 49 cases with equivocal results. HER2 IHC results were 0 (6.1%), 1+ (22.4%), 2+ (26.5%), and no IHC (44.9%). 55% of HER2-equivocal results became HER2 negative, and only 1 patient received anti-HER2 therapy. After median follow-up of 2.96 yrs, 15 deaths and 35 progressions had occurred. There was no statistically significant association between anti-HER2 therapy and OS (p = 0.61) or PFS (p = 0.78). Conclusions: Most HER2-equivocal results were redefined as HER2 negative using the new ASCO/CAP guidelines. Association between anti-HER2 therapy and OS or PFS according to the new HER2 status was not observed. Although this is a small sample with short follow-up, patients with HER2-equivocal breast cancers seem to have clinical behavior similar to HER2-negative breast cancer.
ALK actionable mutations (muts) within cancer types and their responses to crizotinib (CZ).
Authors: Li Lin , Liu Caixia , Zhao Jun , Gen Lin , Dong Xiaorong , Yu Fenglei , Ai Xinghao , Huang Dongning , Chen Likun , Cheng Xiangyang , Kong Jinliang , Guo Renhua , Miao Liyun , Lin Li , Liu Li , Huang Gui , Wang Qiaoli , Chen Rongrong , Xia Xuefeng 
Published: May 2019

e14739 Background: CZ was recommended by NCCN for ALK-rearranged metastasis NSCLC as first-line therapy. Knowledge on the occurrence of ALK actionable muts within cancer types and the responses of ALK fusion types to CZ could better guide the treatment of ALK-rearranged pts. Methods: 772 ALK-mutated pts (with any ALK muts) detected by tissue/ctDNA NGS in our institution from Oct. 2016 to Oct. 2018 were included. ALK+ (with any ALK actionable muts) and EGFR- (with no EGFR actionable muts) pts treated with CZ at any line were included for survival analysis. Progress-free survival (PFS) was estimated using Kaplan-Meier method and compared using log-rank test. Results: 339 ALK+ pts were analyzed, including 331 lung cancer (LC: 265 NSCLC; 1 SCLC; 65 Unknown histology), 3 brain cancer (BC), 1 colon cancer (CC), 3 cancer of unknown primary (CUP), and 1 with no clinical information. The most common ALK mut was fusion (331/339), including 315 EML4-ALK, 5 KIF5B-ALK, 4 STRN-ALK, 1 ACSL3-ALK, 1 CLIP4-ALK, 1 DCTN1-ALK, 1 HIP1-ALK, 1 SRBD1-ALK, 1 TFG-ALK, and 1 ZFP161-ALK. Fusion position was known for 308 EML4-ALK, including 132 V1, 108 V3, 32 V2, 19 V5’, and 17 other variants (Vx). Except for 2 V1 with CUP, 1 KIF5B-ALK with CUP, 1 Vx with CC, and 1 EML4-ALK (no variant information) with BC, all the other fusions occurred in LC. ALK F1174L was detected only in 2 pts, both of whom had BC, specifically neuroblastoma. CZ was given to 76 ALK+ EGFR- pts (mPFS: 9 mo, 95% CI: 8 – 13), including 70 EML4-ALK and 6 non- EML4-ALK (mPFS: 10 vs. 9 mo, p = 0.7). Though non-significant, V1 (n = 32) on average had a longer mPFS than V3 (n = 28) (12 vs. 8 mo, p = 0.3), which may partially be explained by the younger age at diagnosis of V1 than V3 (48 vs. 53, p = 0.005). 1 TFG-ALK, 1 CLIP4-ALK, 1 DCTN1-ALK, 1 HIPI-ALK, 1 ZFP161-ALK, and 1 KIF5B-ALK achieved a PFS of 3, 4, 8, 9, 13, and 19 mo on CZ, respectively. 1 SCLC (V3) received CZ at first-line progressed after 6 mo. Conclusions: Though majority of the ALK actionable muts were commonly found in LC, some alterations may occur more often in other cancer types, such as F1174L in neuroblastoma. Some fusion types (e.g. TFG-ALK) may benefit less from CZ than others (e.g. KIF5B-ALK). Limited by relative small sample size, these results merit further validation and investigation.
Tumor mutational burden reference materials for assay standardization.
Authors: Butler Matt , Konigshofer Yves , Clement Omoshile , Liu Li , Zhao Chen , Arcila Maria E. , Zehir Ahmet , Kohle Ravindra , Magliocco Anthony Martin , Gligorich Keith , Gloeckner Christian , Lovejoy Alexander F. , Hantash Feras , Sougnez Carrie , Lennon Niall , Anekella Bharathi , Garlick Russell 
Published: May 2019

e14746 Background: Next Generation Sequencing based assays are designed to detect genomic aberrations in a limited number of target regions. However, there is a need for accurate measurement of tumor mutational burden (TMB) as low as 4 to as high as 50. As TMB assessment is added to various targeted panels, consistent results between panels are required to advance the broad use of this biomarker. Properly designed reference materials aid measurement standardization and are required to demonstrate assay concordance. We developed reference materials that vary in TMB score, tumor content 5-50% and are prepared in FFPE format. Methods: Seven lung and two breast tumor cell lines as well as matched “normal” lymphoblastoid cell lines were expanded in cell culture. Genomic DNA (gDNA) from each cell line was extracted. Tumor/normal mixes were made by mixing DNA and by embedding cells in FFPE blocks. Whole exome sequencing (WES) results were obtained using Agilent SureSelectXT for library construction and an Illumina Novaseq for sequencing. The Friends of Cancer Research TMB consensus method for analyzing WES data was used to filter variants and calculate TMB scores. Results: The cell lines were grown at large scale to produce extractable gDNA. 100% gDNA tumor, 30% gDNA tumor mixes and 30% FFPE cell line mixes were prepared. Preliminary results show that a clinically-relevant range of TMB values ranging from 4 to 35 mutations per million bases. The several thousand mutations that were observed across the lines were found in a variety of genes, which may explain why TMB in targeted panels is influenced by the specific target regions. Also, the initial results show that 30% cell line mixes showed similar TMB results to 100% gDNA. Conclusions: Our approach with wide ranging TMB values as tumor normal mixes is flexible and can be used to test different tumors and assays. For this study we established WES as the ground truth measurement for comparison to other assay formats and obtained comparison data from other panels. This approach also allows laboratories to test additional variables including formalin fixation, sample extraction, gene panel size, target regions, sequencing depth, filtering and limits of detection.
An aggressive RhoC phenotype is associated with relapse after external beam radiation therapy of a prostate cancer xenograft model.
Authors: Vilhelmsson Timmermand Oskar , Strand Sven-Erik , Ceberg Crister , Ceder Jens Adam 
Published: May 2019

e14748 Background: Relapsed treatment resistant prostate cancer remains the second most common cause of male mortality in the western world. New therapies for therapy resistant prostate cancer depend on defining tumor cell sub-populations capable of surviving, reinitiating, and sustaining net growth of the cancer. In this study we focused on RhoC expression in a prostate cancer model after external beam radiation therapy (EBRT). RhoC has earlier been implicated in metastatic processes in most solid tumors. Methods: In mice, established s.c. LNCaP xenografts (n = 12) were irradiated, the beam collimated with lead to restrict it to the xenograft, with X-rays (200 kV, 1 Gymin-1, Gulmay Medical) for an absorbed dose of 15 Gy. Tumor tissue was collected after seven days or after 3-4 weeks when recurrent growth was seen. RhoC, AR, CD166 and Ki67 immunohistochemistry in tumor sections was visualized by using DAB or Peroxidase Green and nuclear red or haematoxylin blue as counter stain. Sections stained for RhoC and Ki67 were quantified with the Halo software (v2.3.2089.34) using the Indica Labs – cytonuclear v1.6 algorithm. The intensity of the RhoC staining was also quantified in a separate set of sections only stained for RhoC. Results: The RhoC staining intensity was significantly higher in relapsed xenografts (P = 0.003). Also, a significant difference in percentage of RhoC expressing cells in the two populations (P = 0.045) with 40.6 ± 5.8% (mean ± SEM) in relapsed tumors as compared to 15.0 ± 8.1% after 7d. The percentage of cells expressing Ki67 was not significantly different (P = 0.477). However, the percentage of double positive cells (Ki67, RhoC) was significantly higher in treated relapsed xenografts (P = 0.042). Further, a subpopulation of RhoC-positive cells were positive for AR and the stem cell marker CD166. Conclusions: Here we show that a subpopulation of proliferating RhoC-positive cells are more prevalent in relapsing PCa xenografts after EBRT, suggesting an aggressive phenotype that is associated with both proliferation and invasiveness. Another subpopulation of RhoC cells was found to express the prostate stem cell marker CD166, suggesting that pathways and properties involved in cellular self-renewal and invasiveness may be responsible for survival and recurrent growth in relapsed prostate tumors.
Association of Ras-Raf-MEK-Erk/JNK pathway mutations with overall survival for lung squamous cell carcinoma patients.
Authors: Xu Long , Liu Ming , Huang Tanxiao , Peisu Suo , Song Lele , Liu Yuanyuan , Fu Mimi , Zhang Chunmei , Edwards Jeremy , Chen Shifu 
Published: May 2019

e14754 Background: Genomic alterations often lead to aberrant signaling pathways which play an important role in tumorigenesis and development. Here we report the mutational status of genes associated with the Ras-Raf-MEK-Erk/JNK signaling pathway as a biomarker for predicting overall survival (OS) for Lung squamous cell carcinoma (SQCC) patients. Methods: We used the cBioPortal platform to analyze a cohort of 494 SQCC samples from TCGA data. The general Ras-Raf-MEK-Erk/JNK signaling pathway includes 26 genes (KRAS, HRAS, BRAF, RAF1, MAP3K1, MAP3K2, MAP3K3, MAP3K4, MAP3K5, MAP2K1, MAP2K2, MAP2K3, MAP2K4, MAP2K5, MAPK1, MAPK3, MAPK4, MAPK6, MAPK7, MAPK8, MAPK9, MAPK12, MAPK14, DAB2, RASSF1, RAB25). We analyzed the number of samples with/without mutations in the Ras-Raf-MEK-Erk/JNK pathway and found is 214 and 284 that had, or didn’t have, mutations in this pathway, respectively. The overall survival of these two groups was analyzed using the Kaplan-Meier Estimate, and the statistical difference between these groups was calculated using the log-rank test afterwards. Results: The log-rank test p-value is 2.086e-3, which indicates a significant difference in the overall survival between the two groups. It shows that the group with alterations in the Ras-Raf-MEK-Erk/JNK signaling pathway had a longer overall survival than the group without those alterations. The details are as follows: Conclusions: Ras-Raf-MEK-Erk/JNK pathway mutations are significantly associated with longer OS for lung SQCC patients. Mutations in this pathway can be a potential indicator for SQCC patients, but the biological reasons behind this relationship remain to be explored.[Table: see text]