bluuebunny/crossref_metadata_2025_split huggingface dataset:
The use of plasma microRNAs to predict toxicty following liver stereotactic body radiation therapy.
Authors: Cuneo Kyle Clifford , Sun Yilun , Schipper Matthew J , Tewari Muneesh , Lawrence Theodore Steven , Feng Mary Uan-Sian 
Published: February 2017

245 Background: Stereotactic body radiation therapy (SBRT) is an effective treatment for patients with hepatocellular carcinoma or liver metastases. Predictive biomarkers for liver toxicity would allow for careful patient selection and the adaptation of therapy. Prior studies have shown specific miRNAs are elevated prior to clinical signs of toxin induced liver injury. We hypothesized that miRNAs can be used to predict radiation induced liver toxicity prior to clinical manifestations. Methods: As part of an IRB approved clinical trial (NCT01522937) patients with liver tumors underwent a split course of SBRT. All patients underwent liver function testing using indocyanine green clearance (ICG) followed by three SBRT fractions. One month later ICG was reassessed and two more fractions were given if the patient did not have a decline in liver function. Plasma samples were obtained at baseline and 1 month after finishing three of five SBRT fractions for 89 patients. For this exploratory analysis, we selected the 10 patients that had a 2+ point increase in Child-Turcotte-Pugh score within 6 months of completing therapy and 19 additional patients without toxicity. The levels of 752 miRNAs were quantified for each sample using qPCR. We then used a univariate tree based classifier and the elastic net with 10-fold cross validation to calculate the AUC for predicting liver toxicity in individual and small groups of miRNAs, respectively. Results: Several miRNAs were found to be potentially predictive of toxicity on univariate tree based classifier analysis including the liver specific microRNA miR.122.3p, the epithelial specific miR.141.3p and miR.200b.3p, the neuroendocrine related miR.375 and miR.217, and miR.125a.5p which plays a role in hepatitis and regulates ERBB2 and ERBB3 signaling. The elastic net model achieved a conservative AUC estimate of 0.74 +/- 0.04 using 69 baseline miRNAs and 0.76 +/- 0.06 using 11 mid-treatment miRNAs to predict toxicity. Conclusions: Our preliminary analysis of the miRNAome from 29 patients receiving liver SBRT shows promising results for the ability of these markers to select patients at risk for radiation induced liver toxicity. Further validation in a larger patient cohort is needed. Clinical trial information: NCT01522937.
Assessment of hyaluronic acid in tumor microenvironment (TME) of intrahepatic cholangiocarcinoma (CCA).
Authors: Padrnos Leslie Jane , Marella Mathieu , Kosiorek Heidi , Thind Komal , Barrett Brandon , Garrovillo Sheryl , Jiang Ping , Mounajjed Taofic , Ramanathan Ramesh K. , Borad Mitesh J. 
Published: February 2017

248 Background: Improved understanding of TME in CCA may allow for development of novel therapeutics targeting stromal components. Hyaluronic acid (HA) is a polysaccharide that has been found in the TME of a number of solid tumors characterized by desmoplastic stroma, such as pancreatic cancer. Elevated HA levels were prognostic in these malignancies. HA prevalence and association with clinic-pathological features in CCA is unknown. Methods: A retrospective study was conducted using clinically annotated formalin-fixed paraffin embedded tissue from resected intrahepatic CCA samples. Specimens were analyzed for HA, scored using a positive pixel count algorithm (Aperio Imagescope) and positivity was calculated as % of total pixel count. Clinical variables were examined by chi-square or ANOVA F-test. Overall survival (OS) and progression-free survival (PFS) were estimated using Kaplan-Meier method and compared via log-rank test. Multivariate analysis was conducted using Cox proportional hazards regression models. Results: 142 patient samples were stained for HA. HA was identified in all samples (100%), with a range of HA positivity of 32.8 – 91.8%. Median HA value was 67.1% and 95% of patients had HA positivity ≥ 45%. Factors associated with higher than median HA ( > 67%) included perineural invasion (PNI) (40% vs. 21%, p = 0.011), necrosis (67% vs. 41%, p = 0.003), lymph node positivity (32% vs. 14%, p = 0.027), and small tumor size ( < 6.8 cm vs. > 8.4cm, p = 0.014). Stratification of HA staining by median positivity value was not an independent predictor of survival based on multivariate analysis. OS for patients with HA > 67% was 40.1 months (mo) vs 48.5 mo with HA ≤ 67%, p = 0.537. PFS for patients with HA > 67% was 14.4 mo vs. 25.7 mo with HA ≤ 67%, p = 0.177. Conclusions: Prevalence of HA staining in resected CCA is higher than seen in many solid tumors and is ubiquitous in our study. Absence of statistically significant association with OS and PFS might be attributable to ubiquitous prevalence, narrow signal range, and association with known negative prognostic factors. Further pre-clinical and clinical evaluation would be warranted.
Molecular pathways associated with micro-vascular invasion HCC.
Authors: Chia Caroline Yun Ling , Tan Wilson Lek Wen , Shannon Nicholas Brian , Foo Roger Sik Yin , Chow Pierce Kah Hoe 
Published: February 2017

249 Background: Microvascular invasion (MVI) in hepatocellular carcinoma (HCC) has a reported incidence of 15-57%. It is associated with decreased overall and recurrence free survival in post-surgical resection and transplant patients. Currently, the biology of MVI+ HCC remains unknown and the absence of effective adjuvant therapy limits management options to prevent recurrence. Aim: To correlate gene signatures observed at the transcriptomic level with the presence of MVI in HCC, analyze molecular pathways with gene expression tools and validate with TCGA database. Methods: Whole genome expression was studied in two groups of Asian resected HCC tumour specimens: (i) MVI present (MVI+) (n = 14) and (ii) MVI absent (MVI-) (n = 33) both without macrovascular invasion on radiological imaging. 2 distinct pathway analysis tools – gene set enrichment analysis (GSEA) and ingenuity pathway analysis (IPA) were performed to identify significantly enriched pathways potentially explaining the observed MVI+ HCC phenotype. Selected gene sets from the identified pathways were subjected to in-silico validation with TCGA data to confirm their enrichment within MVI+ HCC. Results: Within 14 MVI+ and 33 MVI- HCC studied, we have found a total of 1401 significantly differentially expressed genes between them; 766 genes were up-regulated and 635 genes were down-regulated in MVI+ HCC. At p < 0.05 and FDR < 0.25, GSEA and IPA analyses identified enrichment of PI3K/AKT/mTOR, HIF1α, AMPK signaling and actin-mediated cell kinetics pathways: actiny, Cdc42 signaling and actin pathways regulated by Rho. A 90 gene signature derived from these enriched pathways, created on the basis of biological function was used to compare between average expression within the MVI+ vs MVI- HCCs in the TCGA Asian cohort. Genes found differentially expressed at p < 0.05 corresponded with the enriched pathways: actiny, AMPK signaling and PI3K/AKT/mTOR. Conclusions: These pathways underscore functions in regulation of cell metabolism, growth, proliferation, survival, protein synthesis and cytoskeleton organization in MVI+ HCC. Further studies in these pathways may assist in development of molecular targeted therapies for MVI+ HCC. We propose to carry out a prospective study to validate this.
Whole-exome tumor sequencing study in patients with biliary cancer with a response to MEK inhibitors.
Authors: Ahn Daniel H. , Gulcin Ozer Hatice , Hancioglu Baris , Lesinski Gregory B. , Timmers Cynthia Dawn , Bekaii-Saab Tanios S. 
Published: February 2017

253 Background: We conducted a phase-II study with selumetinib (AZD6244), a small molecule inhibitor of MEK1/2, in advanced biliary tract cancers (BTC). The observed preliminary activity was confirmed with another MEK inhibitor (MEK162) that was tested in a similar patient population. To assess for tumor-specific genetic variants that mediate sensitivity to MEK inhibition in BTC, we performed whole-exome sequencing in patients with an objective response including a complete response to selumetinib. Methods: Normal and tumor DNA from available formalin-fixed paraffin-embedded tissue from biopsies of primary or metastatic tumor from two patients who experienced an objective response underwent whole-exome sequencing. Raw sequence reads were processed with GATK workflow and tumor-specific variants were identified using MuTect and VarScan 2. Following, we assessed the functional consequences of the variants. Copy number changes and potential gene fusion events were also screened. We compared the findings to assess for any commonality between the two samples. Ingenuity Pathway Analysis was used to assess whether the identified somatic variants were intrinsic to the MAPK pathway. Results: 1169 and 628 tumor-specific variants were identified in the two tumor samples. Further analysis demonstrated a similar number of functional and novel variants between the two samples, which were 60 and 53, respectively. No common variants or detectable fusion events were observed between the two samples. Copy number changes were found in chromosomes 1, 5, 6, 9, 10, 12, 17, 20, 21 and 22 in sample one, and in chromosome 11 and 12 on sample two with no common findings. Several variants in genes associated with ERK signaling were present in each tumor sample. Conclusions: Although no common tumor-specific somatic changes of significance several genes associated with ERK signaling were identified in the patients with an objective response. Confirmatory studies investigating the role of the identified genes need to be further investigated.
Correlation of high density of CD8+and FoxP3+ lymphocytes with overall survival in intestinal-type periampullary adenocarcinoma.
Authors: Warfvinge Carl Fredrik , Elebro Jacob , Heby Margareta , Nodin Bjorn , Eberhard Jakob , Jirstrom Karin 
Published: February 2017

266 Background: Periampullary cancers can be divided into different morphological subtypes where those having an intestinal-type (I-type) morphology have a better prognosis than those with a pancreatobiliary-type (PB-type) morphology. In recent years much focus of antineoplastic research has been directed towards the central role played by various subsets of T-lymphocytes. Yet, very little is known of their role in different subtypes of periampullary cancer. Therefore, the aim of this study was to analyze the density of CD8+ (cytotoxic) and FoxP3+ (regulatory) T-cells in periampullary cancer, with particular reference to their relationship with survival by morphological subtype. Methods: Immunohistochemical expression of CD8 and FoxP3-positive tumor-infiltrating lymphocytes (TILs) was analyzed in tissue microarrays with tumors from 175 consecutive cases of periampullary adenocarcinoma, 110 of PB-type and 65 of I-type morphology, treated with pancreaticoduodenectomy. Kaplan-Meier and univariable and multivariable Cox regression analysis, adjusted for age, T-stage, N-stage, grade, sex, invasion of blood vessels, lymphatic vessels, adjuvant chemotherapy and resection margins were applied to determine the impact of CD8 and FoxP3 expression on 5-year overall survival (OS). Results: In I-type tumors, a high density of CD8+ as well as FoxP3+ TILs was significantly associated with a prolonged overall survival (HR = 0.39, 95% CI 0.19-0.80 and HR = 0.32, 95% CI 0.15 –0.67). The association between high density of FoxP3+ TILs and survival remained significant in multivariable analysis (HR = 0.37, 95% CI 0.17-0.84) while the association between CD8+ TILs and survival did not. The density of CD8+ and FoxP3+ TILs was not prognostic in PB-type tumors. Conclusions: High density of CD8+ and FoxP3+ TILs correlates with a prolonged overall survival in I-type but not in PB-type periampullary adenocarcinomas. Thus, morphological subtype appears to be an important determinant of the prognostic and predictive impact of the inflammatory microenvironment in periampullary carcinoma, and should be considered in future studies.
Tremelimumab, a monoclonal antibody against CTLA-4, in combination with subtotal ablation (trans-catheter arterial chemoembolization [TACE], radiofrequency ablation [RFA] or cryoablation) in patients with hepatocellular carcinoma (HCC) and biliary tract carcinoma (BTC).
Authors: Duffy Austin G. , Makarova-Rusher Oxana V. , Pratt Drew , Kleiner David E , Fioravanti Suzanne , Walker Melissa , Carey Stephanie , Figg William Douglas , Steinberg Seth M. , Anderson Victoria , Levy Elliot , Krishnasamy Venkatesh , Wood Bradford J. , Greten Tim F. 
Published: February 2017

270 Background: Tremelimumab is a fully human monoclonal antibody that binds to CTLA-4 expressed on the surface of activated T lymphocytes and results in inhibition of B7-CTLA-4-mediated downregulation of T-cell activation. Transcatheter arterial chemoembolization (TACE), radiofrequency ablation (RFA) and cryoablation (CA) have been shown to induce a peripheral immune response which may enhance the effect of anti-CTLA4 treatment in patients with advanced HCC. Methods: Patients with HCC [Childs Pugh A/B7; BCLC B/C; ECOG 0/1; post-sorafenib (BCLC stage C only)] or refractory BTC were enrolled in a study of Tremelimumab combined with subtotal TACE, RFA or CA performed on week 6. All BTC patients received RFA as the immune-stimulant in combination with tremelimumab. Tumor biopsies were performed at baseline and at time of RF/TACE. Results: 34 pts enrolled (28 HCC, 6 BTC). Characteristics: M:F 26:8; Median age 54(range 42-76); In HCC pts cirrhosis present in 17pts, BCLC Stage B/C: 9/19; Hepatitis B/C/neg: 4/15/9. 13 pts received TACE, 16 underwent RFA (inc 6 BTC pts), 3 CA during week 6 of tremelimumab therapy. 2 pts did not receive an ablative procedure. No DLT encountered. Most common toxicity was pruritus. One patient developed pulmonitis and was taken off study but remained disease-free at 16m. Of N = 17 pts evaluable for response outside of TACE/RFA-treated lesion 4 (23.5%) achieved confirmed partial responses. 8 of 9 pts with quantifiable HCV experienced a marked reduction in viral load. 6-week tumor biopsies showed immune cell infiltration on all evaluable patients. Median PFS for the evaluable HCC population (N = 25) was 5.7m. Conclusions: Tremelimumab in combination with subtotal TACE, RFA or CA in patients with advanced HCC and BTC is safe and feasible. Obtaining tumor biopsies at baseline and at the time of RFA/TACE is safe. Evidence of immune cell infiltration was seen on evaluable patients. Encouraging clinical activity seen with objective confirmed responses, PFS 5.7m and possibly surrogate reductions in HCV viral load. Clinical trial information: NCT01853618.
High frequency irreversible electroporation (H-FIRE) as a novel method of targeted cell death.
Authors: Siddiqui Imran A , Kirks Russell C. , Baker Erin H , Latouche Eduardo , Dewitt Matt , Swet Jacob , Vrochides Dionisios , Iannitti David A , Davalos Rafael , Mckillop Iain 
Published: February 2017

277 Background: Irreversible electroporation unlike ablation is excellent in inducing cell death via apoptosis. It, however, has disadvantages of electrical conduction via cardiac and nervous tissue. This results in requiring cardiac monitoring and general anesthesia and paralytics while performing electroporation. We hypothesized a novel high-frequency IRE (H-FIRE) system employing ultra-short bipolar pulses would obviate the need for cardiac synchronization and paralytics while maintaining measurable effect on cell death. Methods: Female swine (55-65Kg) were used. Two H-FIRE electrodes were inserted into the liver (1.5-cm spacing). In the absence of paralytics H-FIRE pulses were delivered (2250V, 2-5-2 pulse configuration) at different on times (100 vs. 200μs) or number of pulses (100 vs. 300). Next electrodes were placed across major hepatic vascular structures and H-FIRE performed. At conclusion tissue was resected and analyzed histologically. Results: 24 H-FIREs were performed (mean ablation time 275 secs). No EKG abnormalities or changes in vital signs were measured during H-FIRE procedures. In 1/24 H-FIREs minor twitching of the rectus abdominis was recorded coinciding with pulse delivery. Histologically, tissues had effective electroporation as evidenced by cell death and caspase activity. Blinded scoring was performed for necrosis and apoptosis. Areas of cell death were predictable. No significant vascular damage or coagulated/thermally-desiccated blood was detected within major vessels following H-FIRE. Conclusions: H-FIRE is a novel way of liver electroporation. It produces predictable cell apoptosis without the requirement of paralytics and alteration of electrocardiographic signals as compared to traditional electroporation, while preserving underlying vascular integrity. Its application in cancer cell death needs to be further studied, but it has a potential for clinical use in targeting tumors with minimal morbidity and associated cardiac and neurologic side effects.
Adding targeted inhibition of PI3K and MAPK signaling pathways to standard chemotherapy in experimental pancreatic cancer.
Authors: Awasthi Niranjan , Schwarz Margaret A. , Schwarz Roderich 
Published: February 2017

278 Background: Treatment of pancreatic ductal adenocarcinoma (PDAC) remains a formidable challenge as gemcitabine (Gem) plus nab-paclitaxel (NPT) represent the current standard for systemic therapy of advanced PDAC. More than 90% of PDAC tumors harbor an activating mutation in the KRAS oncogene. Currently no therapeutics exist that can effectively target this oncogene product, but alternative strategies focus on inhibition of downstream effectors of KRAS signaling pathways. The RAF-MEK-ERK (MAPK) and the AKT-PI3K signaling pathways are well-described mediators of KRAS induced transformation and tumorigenesis and can be explored as targets for combination therapy. Methods: We evaluated combination treatment benefits of NPT+Gem with the MEK inhibitor trametinib (Tra) and the AKT inhibitor MK-2206 (MK) in experimental xenografts to test their therapeutic potential against PDAC. Results: Median animal survival in human intraperitoneal PDAC xenografts in mice revealed that the median survival was 21 days in controls; this was significantly improved by the NPT+Gem combination (35 days, a 67% increase over controls, p = 0.0007). Median survival was further increased by addition of MK-2206 or trametinib to NPT+Gem chemotherapy group: NPT+Gem+MK (39 days, a 86% increase over controls, p = 0.0003), NPT+Gem+Tra (43 days, a 105% increase over controls, p = 0.0003) and NPT+Gem+MK+Tra (48 days, a 129% increase over controls, p = 0.002). In human subcutaneous PDAC xenografts, MK-2206 or trametinib were able to enhance NPT+Gem effects. Compared to controls (100±34.8), the percent net local tumor growth in different therapy groups was: NPT+Gem 21.8±5.9 (p = 0.003), NPT+Gem+MK 17.2±4.8 (p = 0.002), NPT+Gem+Tra 7.1±11.2 (p = 0.002) and NPT+Gem+MK+Tra 5.7±9.1 (p = 0.001). In vivo effects of Tra and MK correlated with reduced expression of phospho-ERK and phospho-AKT in Western blots of tumor samples. Conclusions: These findings suggest that the effects of NPT+Gem can be enhanced through combined inhibition of MAPK and PI3K signaling pathways, which clinically could yield in improved antitumor results.
Molecular profiling of advanced biliary cancer: Lost in translation from bench to bedside.
Authors: Doherty Mark , Chiu Joanne Wing-Yan , McNamara Mairead Geraldine , Horgan Anne M. , Serra Stefano , Kamel-Reid Suzanne , Zhang Tong , Bedard Philippe L. , Hedley David W. , Dhani Neesha C. , Jang Raymond Woo-Jun , Knox Jennifer J. 
Published: February 2017

283 Background: Advanced Biliary Cancer (ABC) is a collection of diseases which carry poor prognosis, and many patients derive limited benefit from chemotherapy. Identification of molecular drivers of ABC may help to predict treatment response and direct development of targeted therapy. Methods: Formalin fixed paraffin embedded (FFPE) tissue form patients with ABC treated at Princess Margaret Cancer Centre was analysed by MassARRAY Sequenom panel (23 genes, 279 mutations), or by next general sequencing (NGS) using Proton or Illumina MiSeq TruSeq Amplicon Cancer Panel (48 genes, 212 amplicons, ≥500x coverage). Clinicopathologic and treatment data were collected from electronic health records. Results: Of 112 tested patients, 16 had insufficient DNA, and 96 had data for analysis: 13 with ampullary cancer (AC), 19 with hilar/distal bile duct (DBD), 43 with gallbladder (GBC), and 21 with intrahepatic (IHC). 13 patients had Sequenom testing, 85 had NGS with Miseq or Proton. 127 mutations were identified in 60 patients, 36 had no mutations detected: 23 in AC, 54 in GBC, 24 in IHC, 26 in DBD. The most frequent mutations were in TP53 (34%) and KRAS (20%). TP53 and SMAD4 mutations appeared most common in GBC, BRAF and KRAS mutations were most common in AC, and IDH1 and FGFR2mutations were seen only in IHC. 14 patients (15%) had a mutation for which targeted treatment could be applied. Conclusions: Profiling of patients with ABC is feasible and can identify some molecular drivers, with different tumour sites demonstrating distinct biological patterns. Only a limited number of patients are shown to have clinically relevant mutations with current NGS techniques, suggesting additional techniques (whole genome/RNA sequencing) may be required to fully characterise these diseases and identify new therapeutic targets. [Table: see text]
Comprehensive genomic analysis in metastatic pancreatic ductal adenocarcinoma (PDAC).
Authors: Wong Hui-Li , Jones Martin , Eirew Peter , Karasinska Joanna , Schrader Kasmintan A , Lim Howard John , Shen Yaoqing , Jones Steven , Yip Stephen , Laskin Janessa J. , Marra Marco , Schaeffer David F. , Renouf Daniel John 
Published: February 2017

285 Background: In the absence of defined tumor molecular subtypes and validated predictive markers, PDAC has been largely treated as a single disease. Recent studies of molecular subtyping in PDAC reveal a complex mutational landscape with data suggesting the presence of genomic and gene expression signatures that may have prognostic and therapeutic significance. These studies predominantly focused on resected PDAC and lack data on metastatic tumors. We aim to explore the clinical utility of whole genome sequencing (WGS) and transcriptome analysis from metastatic biopsy samples in patients (pts) with advanced PDAC. Methods: Pts with incurable advanced cancers undergo tumor biopsy for in-depth WGS and RNA sequencing (RNASeq) as part of an ongoing prospective study (NCT02155621). Comprehensive bioinformatics analysis is performed to identify somatic cancer aberrations, gene expression changes and cellular pathway abnormalities. Here we describe clinical and molecular data on the subset of pts with advanced PDAC. Results: Sixteen PDAC pts have been enrolled; median age 59 years, 8 males (50%), 10 with de novo metastases (63%). Full WGS and RNASeq were completed in 11 pts (1 failed biopsy, 4 had insufficient tumor). KRAS codon 12 and TP53 mutations were present in all but one pt. CDKN2A and SMAD4 were also frequently altered (7 and 4 pts respectively). Gene expression analysis for classical and basal subtypes similar to those recently described (PMID 26343385) identified 3 and 6 pts with classical and basal expression patterns respectively, and 2 pts with mixed expression. Overall survival (OS) was significantly worse for the basal subtype vs all others (median OS 7 vs. 13.9 months (ms), p = 0.017). When separated into 3 subtypes a significant difference was still noted (median OS 7 ms in basal, 19.2 ms in classical and 11.8 ms in mixed subtype, p = 0.032). Conclusions: WGS analysis demonstrated a similar mutation pattern to that described in resectable PDAC, with no novel actionable mutations identified. Gene expression analysis demonstrated the presence of distinct gene expression signatures significantly associated with outcome, despite small pt numbers. These results need to be validated prospectively in larger cohorts. Clinical trial information: NCT02155621.