bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mice with targeted KrasG12D and loss of p53 in the liver: A robust model for studying immunologic interventions for treating cholangiocarcinoma
Authors: Han Booyeon Julia , Figueroa Nathania , Belt Brian , O'Dell Michael , Hezel Aram F. , Linehan David 
Published: January 2019

281 Background: Inflammation in the tumor microenvironment—chronically elevated cytokines, chemokines, and inflammatory cells—promotes tumorigenesis. Cholangiocarcinoma (CC) is the most common liver malignancy within the biliary tree with few treatment options and a poor 5-year survival. CC tumors are characterized with a dense tumor stroma and abundant inflammatory immune cell infiltrate, yet little is known about the immune dynamics underlying the disease. Here, we characterize immune signaling pathways in human CC and a spontaneous mouse model of the disease to identify potential targets susceptible to immune based therapies. Methods: Histology and immunohistochemistry (IHC) were performed on archived human specimens and tissue microarrays of 52 CC specimens constructed under an IRB approved protocol to identify the prognostic significance of cytokine and immune markers. Peripheral blood, bone marrow, and tissue from mice with targeted activation of KrasG12D and loss of p53 (Kras-p53-/-) in the liver that spontaneously developed CC tumors versus normal controls were collected and analyzed by histology, IHC, quantitative gene expression, and flow cytometry based studies. Results: High levels of inflammatory leukocytes in human CC were predominantly of monocytic and granulocytic origin including macrophages (TAM) and granulocytic-myeloid derived suppressor cells (G-MDSC) respectively. Malignant cells expressed high levels of CCL2 and TAM stained positive for its cognate receptor CCR2. In addition, CD8+ and CD4+ T cells expressing PD-1 were associated with PD-L1+ tumor cells. Kras-p53-/- mice developed CC tumors histologically similar to human disease: tumors had high levels of cytokines and induced myelopoiesis leading to significantly more monocytes and granulocytes in the bone marrow, blood, and spleen compared to normal liver controls. Tumors also expressed higher levels of CCL2 and PD-L1 with more CCR2+ TAMs and PD-1+ T cells compared to controls. Conclusions: Human CC utilizes immune signaling pathways and Kras-p53-/- mice recapitulate the immune dynamics of the disease representing a model to study immune based therapies for treating CC.
Relationship between mismatch repair status and long-term survival in patients with resected periampullary adenocarcinoma.
Authors: Heby Margareta , Lundgren Sebastian , Elebro Jacob , Nodin Bjorn , Eberhard Jakob , Jirstrom Karin 
Published: January 2019

289 Background: Periampullary adenocarcinomas, including pancreatic cancer, are a heterogenous group of tumors with poor prognosis. Emerging evidence indicates that tumor morphology, i.e. intestinal type (I-type) or pancreatobiliary type (PB-type), is a more relevant prognostic factor than anatomical tumor origin. The extent and clinical significance of deficient mismatch repair (dMMR) in periampullary adenocarcinoma is relatively unexplored. In this study, we examined the associations of MMR status with survival in patients with resected periampullary adenocarcinoma, with particular reference to tumor morphology and adjuvant treatment response. Methods: MMR status was assessed by immunohistochemistry on tissue microarrays with primary tumors from a retrospective consecutive cohort of 172 patients with periampullary adenocarcinoma treated with pancreaticoduodenectomy during 2001-2011 in Malmö and Lund University Hospitals, Sweden. Cox proportional hazards models were applied to calculate hazard ratios (HR) and 95% confidence intervals (CI) for death. Results: After a mean follow-up of 46.5 months (range 1.9-185.1), 35 patients (20.3%) were alive, 24 with I-type and 11 with PB-type tumors. Adjuvant chemotherapy was given in 77 (44.8%) cases, 18/63 (28.6%) I-type tumors and 59/109 (54.1%) PB-type tumors. MMR status could be evaluated in 170 cases, in which dMMR was denoted in 22 (12.9%) cases, 13/61(21.3%) in I-type and 9/109 (8.3%) in PB-type tumors. dMMR was associated with a significantly prolonged overall survival in the entire cohort (HR = 0.32, 95% CI 0.17-0.61), and in I-type tumors (HR = 0.27, 95% CI 0.09-0.79), however not independent of conventional prognostic factors. In PB-type tumors, dMMR was only prognostic in non-adjuvant treated cases (HR = 0.26, 95% CI 0.08-0.85), and there was a significant negative interaction between dMMR and adjuvant treatment (pinteraction= 0.008). Conclusions: dMMR signifies a prolonged survival in patients with periampullary adenocarcinoma, but may be a negative predictor of response to adjuvant chemotherapy in PB-type tumors. This finding may be highly relevant for clinical decision making and warrants further study.
Detection of copy number aberrations in cholangiocarcinoma using shallow whole genome sequencing of plasma DNA.
Authors: Farooq Maria , Egan Jan B. , McDonald Bradon , Markus Havell , Contente-Cuomo Tania , Fernandez-Zapico Martin , Vasmatzis George , Braggio Esteban , Borad Mitesh J. , Murtaza Muhammed 
Published: January 2019

293 Background: Cholangiocarcinoma (CCA) is a deadly cancer with ~20% five year survival. Obtaining tissue to confirm diagnosis of CCA is often challenging. This also limits the use of tumor genotyping that could guide potential molecularly targeted treatment (such as FGFR inhibitors for a subset of cases). We investigated whether circulating tumor DNA (ctDNA) analysis in plasma is feasible for noninvasive tumor genotyping in patients with advanced CCA. Methods: We collected and processed plasma samples for ctDNA analysis from 17 patients with CCA at presentation and from 11 healthy volunteers. Following cell-free DNA extraction and quality assessment using digital PCR, we performed low-pass, shallow whole genome sequencing (sWGS). We analyzed sequencing data to identify copy number aberrations and quantify tumor fraction in plasma using recently published computational approaches. Results: Median total cfDNA concentration in patients with CCA was 7,003 genome equivalents (GEs)/mL plasma (range: 1,512- 107,707 GEs/mL) and significantly higher than healthy volunteers (two tailed t-test p < 0.04, median: 1,658 GEs/mL, range: 661-4,938 GEs/mL). We successfully sequenced all tumor libraries, generating a median of 173 million paired-end reads. ctDNA was detectable in 10/17 samples using sWGS. In these 10 samples, median tumor fraction in plasma DNA was 7.1% (range: 3.9%-44.6%). We found recurrent copy number aberrations expected in CCA including 1q gain in 80%, 7p gain in 50%, 1p loss in 70% and 3p loss in 50% of cases. Conclusions: ctDNA analysis for noninvasive tumor genotyping is feasible in patients with advanced cholangiocarcinoma. On-going work is focused on expanding these results using targeted and whole-exome sequencing.
Utility of next-generation sequencing in clinical decision making in hepatocellular carcinoma (HCC).
Authors: Thota Ramya , Lewis Mark Andrew , Raghunath Sharanya , Haslem Derrick S. , Nadauld Lincoln , Rhodes Terence Duane , Moulton Bryce , Abraham Tyler , Romero Robin , Fulde Gail , Christensen Bryce , Barker Tyler ,   Intermountain Precision Genomics Group
Published: January 2019

295 Background: HCC is a heterogeneous disease with diverse genomic alterations. The prior genomic studies have identified common alterations in TERT, P53, WNT pathways. However, most of these alterations are not targetable with current FDA approved targeted agents. In this study, we determine the clinical impact of targeted next generation sequencing in patients with advanced HCC. Methods: We retrospectively assessed all patients with gastrointestinal (GI) malignancies who have undergone next generation sequencing (NGS) between January 2013 and August 2017. The primary endpoint is to determine the frequency of clinically actionable mutations in HCC. Secondary endpoint is to identify number of patients eligible for current FDA approved targeted agents. Results: Of the 299 consecutive GI tumors sequenced, 29 cases were identified as HCC. Clinically actionable mutations were noted in 22 of 29 patients (pts) (76%). Most pts (52%) were found to harbor more than one potentially actionable genetic alterations (n = 15). The common pathways involved: P53 in 9 pts (22%), cell-cycle regulation in 7 pts (17.1%) and mitogen-activated protein kinase in 6 pts (14.6%). Other pathways involved were DNA repair in 4 pts (9.8%), WNT in 3 pts (7.3%), MYC in 3 pts (7.3%), NOTCH in 2 pts (4.9%), HNPCC in 2 pts (4.9%), APC in 2 pts (4.9%), phosphatidylinositol 3-kinase-AKT-mTOR in 1 patient (pt) (2.4%), BRINP in 1 pt (2.4%) and angiogenesis in 1 pt (2.4%). We noted 10 pts (34.5%) harbor alterations that could potentially be targeted with FDA approved treatments such as palbociclib (for CCND1/2 amplification), PARP inhibitors (for DNA repair defects), and immunotherapy (for MMR defects) on precision medicine clinical trials such as TAPUR or MATCH. Conclusions: Mutational profiling using a targeted NGS panel identified clinically actionable alterations in nearly 75% of advanced HCC patients. Almost one third of these patients were potential candidates for current FDA approved treatments. NGS and enrollment in clinical trials should be considered in all fit patients with HCC who had progression on current standard of care treatments.
Comprehensive genomic profiling of appendiceal adenocarcinoma.
Authors: Raghav Kanwal Pratap Singh , Loree Jonathan M. , Fournier Keith F. , Shaw Kenna Rael , Taggart Melissa W. , Foo Wai Chin , Matamoros Aurelio , Mehdizadeh Amir , Ahmed Shahab U. , Guerra Jennifer L. , Mansfield Paul F. , Royal Richard Eldon , Overman Michael J. , Eng Cathy 
Published: January 2019

298 Background: Appendiceal adenocarcinomas (AAs) are orphan tumors. Little is known about their molecular profile limiting understanding of their biology and development of novel targeted therapies. The purpose of this study was to delineate the molecular landscape of AAs. Methods: We performed a retrospective review of AAs patients (pts) who were evaluated at MD Anderson Cancer Center between October 2012 and April 2017 and underwent next-generation sequencing (NGS) with internal or external assays (at least 45 genes) using either tumor tissue specimens or peripheral blood for circulating cell-free DNA (cfDNA). The primary outcome was to assess the prevalence of genomic alterations (GAs) in AAs. We then performed comparative exploratory analyses of GAs using TCGA colorectal cancer (CRC) sequencing. Results: A total of 78 patients were identified of which 57 (73%) and 18 (23%) underwent tissue based and ctDNA based sequencing, respectively (3 cases had both). At least 1 GA was found in 61 (78%) of AA specimens, with a mean (SD) of 2.8 (1.6) GAs per case. Of these 44 (72%) had ≥ 2 GAs and 31 (51%) had ≥ 3 GAs. The most frequent GAs were KRAS (38 [62%]), TP53 (22 [36%]), GNAS (17 [28%]), SMAD4 (11 [18%]), PIK3CA (10 [16%]), APC (9 [15%]), ATM (8 [13%]), BRAF (5 [8%]), KIT (5 [8%]), NRAS (3 [5%]) and MET (3 [5%]). GNAS mutations frequently co-occurred with KRAS mutations (42% v 5%, OR 14.3, P < 0.001). No GA was associated with grade, mucinous histology or overall survival (OS). Besides these mutations, we also found unusual cases with targetable mutations such as ALK, EGFR, MET, IDH1 and ERBB2. In our comparative analyses, mutations in KRAS (p = 0.009), TP53 (p = 0.020), GNAS (p < 0.001) and APC (p < 0.001) genes were significantly different from CRC whereas there was no difference in prevalence of PIK3CA, SMAD4 and ATM genes. Conclusions: To date, our analysis of one of the largest cohorts of AAs, demonstrate a majority of AAs harbor at least 1 GAs. Although treatment paradigms in AAs are extrapolated from CRC, the molecular profile of these tumors differs significantly. Molecular characterization of these rare tumors is a necessary first step towards discovery of opportunities for use of targeted therapies in these patients.
Kinetics and dosimetric predictors of acute radiation-induced lymphopenia in pancreatic cancer.
Authors: Ellsworth Susannah G. , Mereniuk Todd , Hobbs Robert F , Zhang Hong , Herman Joseph M. , Grossman Stuart A. , O'Neil Bert H. , Shahda Safi , Mohan Radhe , Kong Feng-Ming (Spring) , Jin Jianyue 
Published: January 2019

300 Background: Radiation (RT) induced lymphopenia (RIL) is an adverse prognostic factor in pancreatic cancer (PC) and is likely due to the irradiation of lymphocytes in the RT field. The goal of this study was to identify dosimetric predictors for high rates of absolute lymphocyte count (ALC) loss during RT for PC. Methods: This was a retrospective study of 34 PC patients in an institutional database who had received concurrent 5-FU or gemcitabine-based chemoradiation (50-54 Gy) and had ≥ 3 ALCs measured during RT. Baseline ALC was normal (>1000 cells/uL) in 28/34 (82%) and grade 3-4 RIL occurred in 24/34 (71%). ALC was plotted against fraction # and a best-fit line for each patient was created to determine per-fraction loss in ALC (PFLAC). Linear regression was used to correlate PFLAC with dosimetric parameters including mean dose to gut, liver, kidney, spleen, and cisterna chyli, as well as estimated dose to immune cells (EDIC), which calculates dose to immune cells according to the % of body lymphocytes contained in each organ. Results: All patients exhibited exponential loss in ALC during RT. Mean PFLAC was 6.8% (range 1.7-13.4); fraction # was strongly correlated with ALC (mean R2 = 0.89). Patients with >/= grade 3 lymphopenia had a significantly higher PFLAC than those with grade 0 - 2 lymphopenia (mean daily loss 7.8% in Gr 3-4 vs. 4.8% in Gr 0-2, p = 0.001; independent sample T test). Field size was not correlated with PFLAC for high (> 1 Gy) or low (< 0.5 Gy) isodose volumes. Mean whole body (r = 0.59, p < 0.001), bowel (r = 0.39, p = 0.012), liver (r = 0.42, p = 0.007), and cisterna chyli (r = 0.583, p = 0.004) doses were moderately correlated with PFLAC; mean kidney (r = 0.22, p = 0.11) and spleen (r = 0.26, p = 0.06) doses were weakly correlated with PFLAC. EDIC was more strongly correlated with PFLAC than any individual organ mean dose (r = 0.69, p < 0.001). Conclusions: Patients undergoing RT for PC experience a predictable RIL characterized by an exponential loss of lymphocytes per day. PFLAC is a useful method of characterizing RIL and facilitates evaluation of dosimetric predictors of RIL. We identified dose to cisterna chyli as a significant contributor to RIL in PC; however, EDIC has a stronger correlation with RIL severity than any single organ dose.
Relationship between desmoplastic pattern and lymphocytes infiltration in pancreatic cancer.
Authors: Einama Takahiro , Ao Tadakazu , Kajiwara Yoshiki , Sueyama Takahiro , Shinto Eiji , Nishikawa Makoto , Noro Takuji , Hoshikawa Mayumi , Aosasa Suefumi , Hase Kazuo , Yaguchi Yoshihisa , Hiraki Shuichi , Tsujimoto Hironori , Ueno Hideki , Yamamoto Junji 
Published: January 2019

317 Background: The proposed histologic desmoplastic reaction (DR) categorization and lymphocyte infiltration (LI) directly reflects tumor behavior in a modulating stromal environment and could provide valuable prognostic information for colorectal cancer patients, but the prognostic role of DR and LI has not been investigated in pancreatic cancer patients. Methods: A total of 87 pancreatic cancer patients who underwent potentially curative surgery for their tumors in our hospital (2008 to 2013) were included. DR was classified as mature, intermediate, or immature on the basis of the existence of keloid-like collagen and myxoid stroma-distinctive histologic products of extracellular matrix remodeling. LI was classified as Pattern I; circumferential lymphocytes zone without disruptions around tumor, Pattern II; lymphocytes zone with partial disruptions and thinning around tumor, Pattern III; focal lymphocytes foci around tumor at most invasive border without lymphocyte zone, and Pattern IV; no lymphocyte foci around tumor. Results: With regard to DR, 0, 23, and 64 patients were classified as mature, intermediate, and immature, respectively. Five-year overall survival rates (#%) were higher in immature group (p=0.0040) than those of intermediate group (#%). Multivariate analysis revealed that DR was an independent prognostic factor along with residual tumor (p=0.0300). With regard to LI, 0, 6, 70, and 11 patients were classified as Pattern I, Pattern II, Pattern III, and Pattern IV, respectively. There was no relationship between DR and LI. Conclusions: The DR categorization seemed to reflect tumor behavior and could provide valuable prognostic information for pancreatic cancer patients. We did not show any relationship between DR and LI in pancreatic cancer.
Effect of macrophages on pancreatic cancer.
Authors: Glazer Evan Scott , Reed Leighton F. , Freeburg Charlie J. , Husain S. Mazher , Deneve Jeremiah Lee , Dickson Paxton Vandiver , Shibata David 
Published: January 2019

324 Background: Pancreatic Ductal Adenocarcinoma (PDAC) is expected to be the second leading cause of cancer related deaths by 2030. TGF-β is a well-studied PDAC mediator with a context dependent role as initially a tumor suppressor with potential to convert to a tumor promoter in later stages. Tumor associated macrophages and interleukins, such as the pro-inflammatory interleukin, IL23, are not well studied regarding PDAC. We hypothesized PDAC treated with TGF-β and macrophages would induce a more aggressive phenotype. Methods: We investigated aggressive behavior with a primary PDAC cell line in vivo and a metastatic PDAC cell line in vitro. A primary pancreatic cell line, Panc-1 cells, were pre-treated with PBS, IL23, macrophages (10:1 ratio of Panc-1 cells to macrophages), IL23 + macrophages, TGF-ß, TGF-ß + macrophages, or TGF-ß + macrophages + IL23. After treatment, cells were orthotopically implanted into the pancreas of NOD SCID gamma mice with 5 mice per group. Mice weights were recorded twice weekly for 4-weeks. Primary lesions and metastasis were investigated with ANOVA. AsPC-1 cells, a metastatic pancreatic cell line, were pre-treated with the same seven treatments. We investigated pSTAT3 expression and the streak closure in vitro. Results: Panc-1 cells treated with macrophages had the largest pancreatic tumor weight and diameter compared to PBS control, IL23 alone, and TGF-β alone (P < 0.001). When macrophages treatment included TGF-β, pancreatic tumor weights and diameters decreased as compared to macrophages alone and macrophages + IL23 (P < 0.001). Macrophage treatment induced higher liver weights and higher number of surface liver metastatic lesions suggesting higher metastatic disease burden (P < 0.03). AsPC-1 cells treated with combinations of macrophages and TGF-β increased pSTAT3 expression compared to PBS control. AsPC-1 cells treated with macrophages closed the gap in the scratch assay faster than PBS control 24 hours after treatment (P < 0.001). Conclusions: We demonstrated macrophages have a key role in converting primary pancreatic cancer into a more aggressive phenotype in vivo whereas they have less effect on metastatic pancreatic cancer in vitro.
Correlation of neutrophil lymphocyte ratio, platelet lymphocyte ratio and rate of change of CA 19.9 in predicting outcome for metastatic pancreatic cancer.
Authors: Dean Andrew Peter , Higgs Dom , Das Adarsh , Rogers-Seeley Madeline , Fennessy Sean , McGarvey Caoimhe 
Published: January 2019

326 Background: CA19.9, NLR and PLR have all been proposed as prognostic in pancreatic cancer. We analysed correlation between NLR, PLR and rate of change of CA19.9. Methods: A total of 63 metastatic pancreatic cancer patients were identified from our database and evaluated retrospectively for blood count, NLR, PLR and serial CA19.9 levels during treatment. Daily Rate of Change of CA19.9 levels were calculated for the first 90 days (DRC90) of the patient’s treatment. Kaplan-Meir curves, univariate and multivariate Cox-regression analyses were calculated to assess the effects of these 3 markers on overall survival. Results: In a univariate analysis, PLR > 240, NLR > 5 and DRC90 > 0.4% were all significantly associated with deceased overall survival. The Cox proportional hazards model showed that NLR < 5 (HR 0.475, 95% CI 0.259 to 0.873, P = 0.017), PLR < 240 (HR 0.444, 95% CI 0.229 to 0.861, P = 0.016), and a DRC90 < 0.4% (HR 0.294, 95% CI 0.102 to 0.851, P = 0.024) were independent predictors of good prognosis (22.6 months vs. 9.6 months, 22.3 months vs 12.4 months and 23.9 months vs. 9.3 months respectively). In multivariate analysis, only a DRC90 < 0.4% was independently associated with a longer survival (HR 0.239, 95% CI 0.076 to 0.752, P = 0.014). The formula (F) {PLR + (NLRxNLR) + (DRC90 x 100)} was predictive for survival, as patients with F > 190 (HR 3.295, 95% CI 1.232 to 8.807, P = 0.017), having a significantly lower survival rate than patients with F < 190 (25.1 months vs. 10.6 months, log-rank P = 0.009). Conclusions: These findings indicate the prognostic utility of the rate of CA 19.9 decline - measured as a standardised daily percentage change in value over 90 days. Our data validates daily rate of change of CA 19.9 over 90 days as an independent variable that correlates with prognosis, independent of PLR and NLR. We also identified a novel formula - PLR + (NLRxNLR) + (DRC90 x 100) - as being predictive for survival. We would like to increase the sample size to further validate our initial findings and investigate possible relationships in combining these variables for better prognostication in metastatic pancreatic cancer.
Amplitude-modulated radiofrequency electromagnetic fields target hepatocellular carcinoma stem cells through activation of Cav 3.2 T-type calcium channels.
Authors: Jimenez Hugo , Wang Minghui , Zimmerman Jacquelyn W. , Pennison Michael J. , Sharma Sambad , Brezovich Ivan , Absher Devin , Myers Richard M , DeYoung Barry R. , Caudell David , Godwin Dwayne , Ghanekar Anand , Miller Lance D , Capstick Myles , Kuster Niels , D'Agostino Ralph , Barbault Alexandre , Watabe Kounosuke , Blackman Carl F , Pasche Boris 
Published: January 2019

332 Background: Amplitude-modulated 27.12 MHz radiofrequency electromagnetic fields (AM RF EMF) delivered via a spoon-shaped antenna placed on the patient’s tongue result in shrinkage of the primary and metastatic tumors in patients with advanced hepatocellular carcinoma (HCC). (Costa FP, et al. Br J Cancer. 2011;105:640-648.) The mechanism by which AM RF EMF have direct antiproliferative effect and disruption of the mitotic spindle on cancer cells is largely unknown. (Zimmerman JW, et al. Br J Cancer. 2012;106:307-313.) Methods: We assessed the Specific Absorption Rate (SAR) level and distribution inside the human body. In vitro experiments with HCC cells were performed as previously described (Zimmerman). Immunodeficient mice were subcutaneously implanted with Huh-7 HCC cells or patient-derived xenografts (PDX). Mice were exposed to HCC-specific AM RF EMF using systems replicating human exposure levels and treatment duration. Tumor samples were examined for EMT and cell cycle markers. Results: Intrabuccal delivery results in whole-body absorption of AM RF EMF. Proliferation of hepatitis B positive and negative cell lines as well as HCC cancer stem cells (CSCs) are blocked by AM RF EMF through Cav 3.2 T-type voltage gated calcium channels (VGCC). Proliferation of HCC is inhibited in vivo and tumor shrinkage occurs by dedifferentiation of HCC cells into quiescent myofibroblasts while the growth of intestinal and blood marrow cells is unaltered. Conclusions: Whole-body SAR ranges from 0.2 to 1 mW/kg and is significantly below the international safety limits for human exposure. Intrabucally-administered AM RF EMF is a novel targeted therapy for systemic treatment of advanced HCC with minimal off target effects. Inhibition of HCC CSCs may explain the extremely long term survival (>5 years) of several patients with advanced HCC.