tbuckley/cabot-search huggingface dataset:
High on drugs: lessons from opiates in pancreatitis
Authors: Vijay P Singh
Journal: Gut (2017)

The current opiate epidemic, the widespread clinical utilisation of opiates, along with the controversies that revolve around their use, mandate that we take a fresh look at the risks and benefits of this invaluable yet potentially hazardous class of drugs. Pancreatitis is a common illness in which opiates are used extensively for pain control. With the well-known overlap between the complications of acute pancreatitis and opiate use, that is, ileus and bacterial translocation, and the difficulty in identifying the underlying causality in a clinical scenario, it is appropriate that this dilemma be approached using animal models. Additionally, the recent paradigm1 that chronic pancreatitis (for which opioids may be used for long periods) evolves from recurrent acute attacks reinforces the need to weigh the risks this usage may create apart from opiate abuse.

In the study entitled ‘Morphine worsens the severity and prevents pancreatic regeneration in mouse models of acute pancreatitis’, Balrass et al 2 present a clinically relevant argument of the multiple ways in which opiates may be worsening the outcomes of acute pancreatitis (AP). They postulate three mechanisms: (1) increased bacterial translocation, (2) a temporal delay in the reparative inflammatory response and (3) a delay in the regenerative response. Additionally, they note that morphine worsens pancreatic necrosis and acute inflammation in mechanistically distinct models. These effects of morphine are prevented in μ-opioid receptor knockout mice.

The influence …
TNF is required for TLR ligand–mediated but not protease-mediated allergic airway inflammation
Authors: Gregory S. Whitehead, Seddon Y. Thomas, Karim H. Shalaby, Keiko Nakano, Timothy P. Moran, James M. Ward, Gordon P. Flake, Hideki Nakano, Donald N. Cook
Journal: Journal of Clinical Investigation (2017)

Asthma is associated with exposure to a wide variety of allergens and adjuvants. The extent to which overlap exists between the cellular and molecular mechanisms triggered by these various agents is poorly understood, but it might explain the differential responsiveness of patients to specific therapies. In particular, it is unclear why some, but not all, patients benefit from blockade of TNF. Here, we characterized signaling pathways triggered by distinct types of adjuvants during allergic sensitization. Mice sensitized to an innocuous protein using TLR ligands or house dust extracts as adjuvants developed mixed eosinophilic and neutrophilic airway inflammation and airway hyperresponsiveness (AHR) following allergen challenge, whereas mice sensitized using proteases as adjuvants developed predominantly eosinophilic inflammation and AHR. TLR ligands, but not proteases, induced TNF during allergic sensitization. TNF signaled through airway epithelial cells to reprogram them and promote Th2, but not Th17, development in lymph nodes. TNF was also required during the allergen challenge phase for neutrophilic and eosinophilic inflammation. In contrast, TNF was dispensable for allergic airway disease in a protease-mediated model of asthma. These findings might help to explain why TNF blockade improves lung function in only some patients with asthma.
Abstract 992: Patient-derived tumor organoids of neuroendocrine prostate cancer
Authors: Loredana Puca, Rohan Bareja, Reid Shaw, Wouter Karthaus, Dong Gao, Chantal Pauli, Juan Miguel Mosquera, Joanna Cyrta, Rachele Rosati, Rema Rao, Andrea Sboner, Carla Grandori, Giorgio Inghirami, Yu Chen, Mark A. Rubin, Himisha Beltran
Journal: Cancer Research (2017)

Abstract Background: The development of neuroendocrine prostate cancer (NEPC) is one mechanism of treatment resistance to androgen receptor (AR)-targeted therapies for a subset of patients with advanced prostate cancer. This is associated with transition from a prostate adenocarcinoma to small cell/NEPC histology, low AR signaling signaling, and expression of neuroendocrine markers as Chromogranin A (CGHA), Synaphophysin (SYP) and CD56). Patient derived preclinical models recapitulating the NEPC phenotype may be used to address NEPC pathogenesis and test emerging therapeutic targets. Methods: Tumor organoids were developed according to protocols previously described (Gao et al, Cell 2015). Briefly the tissue biopsies (liver and bone biopsy) were washed, enzymatically digested and then seeded in Matrigel (BD) droplets. Organoids were characterized at genomic (WES), RNA and protein level (IHC) to confirm the expression of specific markers. Lentiviral infections were performed using shRNAs against EZH2 to knock down EZH2 in organoids. Organoids were also subcutaneously injected in NSG mice to generate patient derived xenografts (PDXs) for drug treatment in vivo. Results: We developed and characterized two NEPC tumor organoids from tumor biopsies (liver and bone) of two patients both in vitro and in vivo (as PDXs). NEPC tumor organoid models retained the molecular and histological characteristic of their matched patient samples. We successfully manipulated the activity of the histone methyltransferase EZH2 by using a catalytic inhibitor and its expression by infecting organoids with shEZH2. We showed that the absence of EZH2 affects the expression of neuroendocrine-associated programs as stem cell and neuronal pathway. Moreover treatment with EZH2 inhibitor decreased tumor organoids viability and PDXs tumor volume. Drug screening approaches on NEPC organoids were used to discovery novel drug targets and combinations that could potentially benefit NEPC patients. Top single agent hits included previously identified targets such as EZH2, AURKA, as well as novel synergies. Conclusions NEPC patient tumor organoids are clinically relevant tumor models to study the NEPC phenotype in advanced prostate cancer and may be used to elucidate novel drug targets. Citation Format: Loredana Puca, Rohan Bareja, Reid Shaw, Wouter Karthaus, Dong Gao, Chantal Pauli, Juan Miguel Mosquera, Joanna Cyrta, Rachele Rosati, Rema Rao, Andrea Sboner, Carla Grandori, Giorgio Inghirami, Yu Chen, Mark A. Rubin, Himisha Beltran. Patient-derived tumor organoids of neuroendocrine prostate cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 992. doi:10.1158/1538-7445.AM2017-992
Abstract B12: The importance of the RASA1/R-Ras/Ral-A signaling axis in melanoma tumorigenesis
Authors: Kristen S. Hill, Xue Wang, Evan R. Roberts, Youngchul Kim, Jane Messina, Minjung Kim
Journal: Cancer Research (2018)

Abstract The Ras family of small GTP-binding proteins is frequently activated by mutations, including NRAS (20%), KRAS (2%), and HRAS (1%), in melanoma. In addition to mutations, Ras isoforms can also be activated by the inactivation of Ras GTPase activating proteins (RasGAPs), such as NF1, RASA1, and RASA2. In our recent study, we observed that the inactivation of RASA1 (RAS p21 protein activator 1, also called p120RasGAP) suppressed melanoma via its RasGAP activity toward the R-Ras (related RAS viral (r-ras) oncogene homolog) isoform. We hypothesized that, although not mutated, R-Ras is activated in melanoma through the inactivation of RasGAPs and that RasGAP/R-Ras pathway activation cooperates with BRAF activation in melanoma tumorigenesis. In this study, we addressed the importance of R-Ras, a previously less-appreciated member of the Ras family, in melanoma tumorigenesis and investigated the molecular mechanisms underlying R-Ras signaling in BRAF mutant melanoma. We observed frequent activation of R-Ras in BRAF mutant human melanoma cell lines. In addition, RNAi-mediated reduced expression of R-Ras suppressed anchorage-independent colony growth and tumor growth. Moreover, among the three major RAS effector pathways, reduced R-Ras expression suppressed Ral-A activation, which may explain the mechanism of Ral-A activation in BRAF mutant melanoma. Interestingly, anchorage-independent growth driven by RASA1 inactivation and subsequent R-Ras activation was suppressed by both genetic (siRNA targeting Ral-A) and pharmacologic (Ral inhibitor BQU57) inhibition of Ral-A. To further investigate the impact of RASA1 loss, and thus R-Ras activation, on BRAF mutant melanoma development in vivo, we generated a RASA1 L/L; BRAF CA/CA; Tyr-CreERT2 mouse model in which treatment with 4OHT results in the expression of constitutively activated mutant BRAF and the deletion of RASA1 in melanocytic lineage cells. Preliminary analysis shows hyperpigmentation of the ear, tail, and foot pad in RASA1 L/L BRAF CA/CA mice compared to RASA1 +/+ BRAF CA/CA littermates and the development of melanoma in RASA1 mutant mice. This study demonstrates the importance of the RASA1/R-Ras/Ral-A signaling pathway in BRAF mutant melanoma and supports the possible combinatorial treatment strategy targeting both the BRAF/MAPK and Ral signaling pathways. Citation Format: Kristen S. Hill, Xue Wang, Evan R. Roberts, Youngchul Kim, Jane Messina, Minjung Kim. The importance of the RASA1/R-Ras/Ral-A signaling axis in melanoma tumorigenesis [abstract]. In: Proceedings of the AACR Special Conference: Advances in Modeling Cancer in Mice: Technology, Biology, and Beyond; 2017 Sep 24-27; Orlando, Florida. Philadelphia (PA): AACR; Cancer Res 2018;78(10 Suppl):Abstract nr B12.
Abstract 2707: Targeted RNA sequencing reveals thus far unknown diagnostically relevant fusion partners confirming its diagnostic potential
Authors: Niroshan Nadarajah, Manja Meggendorfer, Torsten Haferlach, Wolfgang Kern, Claudia Haferlach
Journal: Cancer Research (2017)

Abstract Introduction: The genomic landscape of hematological malignancies has been resolved mainly based on whole exome and whole genome sequencing, primarily targeting gene mutations. In addition to mutations, gene fusions have also been identified as therapeutic targets, impressively shown e.g. for BCR-ABL1 and ETV6-PDGFRB. Even though fluorescence in situ hybridization (FISH) is the current gold standard in fusion detection, it is by concept limited to the selected genes it is applied to. In contrast, targeted RNA sequencing is a valuable hypothesis-free approach to discover all possible fusion junctions in a single reaction. Aim: Explore the value of targeted RNA sequencing in a routine diagnostic work up. Patients and Methods: We sequenced 134 cases in parallel to our routine diagnostics workflow using chromosome banding analysis (CBA), FISH and real-time quantitative (RQ-PCR). Targeted RNA sequencing was performed on the NextSeq 500 using the TruSight RNA Fusion panel (Illumina, San Diego, CA) consisting of 7690 probes covering 507 genes known to be involved in gene fusions. Analysis was performed with the RNA-Seq Alignment App v1.2.0 (BaseSpace Sequence Hub) using Star for Alignment and Manta for gene fusion calling with default parameters (Illumina, San Diego, CA). Results: In 127 of 134 (95%) cases the results of FISH, subsequently confirmed with RT-PCR were also picked up by RNA Seq. This included diagnostically highly relevant fusions like BCR-ABL1 (n=8), KMT2A rearrangements (n=7), PML-RARA (n=4), and ETV6 and NPM1 rearrangements. In addition to the confirmation of orthogonal results, we were able to identify novel rare gene fusions, which we subsequently confirmed by RQ-PCR. This included immediately targetable fusions like TNIP1-PDGFRB and ETV6-EFL1, ETV6-FOXO1, IRF2PB1-RARA, RARA-SAE1). Conclusion: 1) In the vast majority of instances targeted RNA sequencing confirmed results obtained by FISH/RT-PCR and in addition discovered new rare gene fusions 2) Targetable genetic aberrations were identified, which were not identifiable by chromosome banding analysis but would now lead to more individualized treatment. 3) Thus, targeted RNA sequencing may be a valuable tool in routine diagnostics and for patients with rearrangements unresolved by standard techniques, also paving the way to precision medicine in a considerable number of patients. Citation Format: Niroshan Nadarajah, Manja Meggendorfer, Torsten Haferlach, Wolfgang Kern, Claudia Haferlach. Targeted RNA sequencing reveals thus far unknown diagnostically relevant fusion partners confirming its diagnostic potential [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 2707. doi:10.1158/1538-7445.AM2017-2707
T2–FLAIR Mismatch, an Imaging Biomarker for IDH and 1p/19q Status in Lower-grade Gliomas: A TCGA/TCIA Project
Authors: Sohil H. Patel, Laila M. Poisson, Daniel J. Brat, Yueren Zhou, Lee Cooper, Matija Snuderl, Cheddhi Thomas, Ana M. Franceschi, Brent Griffith, Adam E. Flanders, John G. Golfinos, Andrew S. Chi, Rajan Jain
Journal: Clinical Cancer Research (2017)

Abstract Purpose: Lower-grade gliomas (WHO grade II/III) have been classified into clinically relevant molecular subtypes based on IDH and 1p/19q mutation status. The purpose was to investigate whether T2/FLAIR MRI features could distinguish between lower-grade glioma molecular subtypes. Experimental Design: MRI scans from the TCGA/TCIA lower grade glioma database (n = 125) were evaluated by two independent neuroradiologists to assess (i) presence/absence of homogenous signal on T2WI; (ii) presence/absence of “T2–FLAIR mismatch” sign; (iii) sharp or indistinct lesion margins; and (iv) presence/absence of peritumoral edema. Metrics with moderate–substantial agreement underwent consensus review and were correlated with glioma molecular subtypes. Somatic mutation, DNA copy number, DNA methylation, gene expression, and protein array data from the TCGA lower-grade glioma database were analyzed for molecular–radiographic associations. A separate institutional cohort (n = 82) was analyzed to validate the T2–FLAIR mismatch sign. Results: Among TCGA/TCIA cases, interreader agreement was calculated for lesion homogeneity [κ = 0.234 (0.111–0.358)], T2–FLAIR mismatch sign [κ = 0.728 (0.538–0.918)], lesion margins [κ = 0.292 (0.135–0.449)], and peritumoral edema [κ = 0.173 (0.096–0.250)]. All 15 cases that were positive for the T2–FLAIR mismatch sign were IDH-mutant, 1p/19q non-codeleted tumors (P &amp;lt; 0.0001; PPV = 100%, NPV = 54%). Analysis of the validation cohort demonstrated substantial interreader agreement for the T2–FLAIR mismatch sign [κ = 0.747 (0.536–0.958)]; all 10 cases positive for the T2–FLAIR mismatch sign were IDH-mutant, 1p/19q non-codeleted tumors (P &amp;lt; 0.00001; PPV = 100%, NPV = 76%). Conclusions: Among lower-grade gliomas, T2–FLAIR mismatch sign represents a highly specific imaging biomarker for the IDH-mutant, 1p/19q non-codeleted molecular subtype. Clin Cancer Res; 23(20); 6078–85. ©2017 AACR.
Abstract 4488: Tumor suppressor phosphatase PHLPP1 regulates transcription factor activity and gene expression in inflammation
Authors: Ksenya Cohen Katsenelson, Joshua D. Stender, Christopher K. Glass, Alexandra C. Newton
Journal: Cancer Research (2017)

Abstract Epigenetic mechanisms play a key role in cancer and are a major contributor in driving the aberrantly high levels of oncogenic receptor tyrosine kinases (RTK) in cancer. Understanding mechanisms leading to altered transcription of oncogenes and tumor suppressors has the potential to provide new therapeutic targets. Here we show that the PH domain leucine-rich repeat protein phosphatase 1 (PHLPP1), a tumor suppressor that directly dephosphorylates and inactivates Akt, has an additional function of regulating approximately 10% of the transcriptome. Specifically, we used non-biased high-throughput RNA-sequencing and chromatin immunoprecipitation-sequencing techniques to analyze genome-wide mRNA levels and acetylation patterns of genes in cells from wild-type and PHLPP1 knockout mice. De novo motif analysis of the promoter for the genes regulated by PHLPP1 identified enrichment in the recognition motifs for a number of transcription factors, including ones involved in inflammatory signaling. Biochemical analysis revealed that PHLPP1 regulates the phosphorylation and activation of these transcription factors, such that loss of PHLPP1 leads to enhanced inflammatory signaling. Our data support a model in which PHLPP1 dephosphorylates specific transcription factors to act as the brakes to inflammatory signaling, a hallmark of cancer. Citation Format: Ksenya Cohen Katsenelson, Joshua D. Stender, Christopher K. Glass, Alexandra C. Newton. Tumor suppressor phosphatase PHLPP1 regulates transcription factor activity and gene expression in inflammation [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4488. doi:10.1158/1538-7445.AM2017-4488
Abstract 2747: Plasma DNA methylation marker and hepatocellular carcinoma risk prediction model for the general population
Authors: Hui-Chen Wu, Hwai-I Yang, Qiao Wang, Chien-Jen Chen, Regina M. Santella
Journal: Cancer Research (2017)

Abstract Metastases in the later stages of hepatocellular carcinoma (HCC) cause the majority of deaths associated with the disease, making early detection crucial to patient survival. Risk models that assess HCC risk in the general population can be used for risk stratification for further HCC surveillance, however, none have been validated externally. Methylation of circulating DNA shows potential for noninvasive and early diagnosis of HCC. Most evidence, however, comes from cross-sectional studies raising concerns about temporality. We conducted a prospective case-control study nested within a community-based cohort. We measured methylation levels in of 6 genes (CDKN2A, RASSF1A, STEAP4, TBX2, VIM, and ZNF154) using pre-diagnostic plasma DNA from 237 HCC cases and 257 matched controls. We found TBX2 hypermethylation was associated with increased HCC risk, with ORs (95%CI) of 3.7 (1.9-7.2). The associations were mainly among high-risk subjects; among subjects infected with HBV/HCV, the OR (95%CI) of TBX2 methylation was 5.3 (2.2-12.7). Among subjects with high risk, the ORs (95%CIs) were 8.9 (1.0-73.9) for Wen-HCC score ≥16, 5.6 (2.1-14.6) for Hung-HCC score ≥15, and 7.2 (2.1-24.4) for Michikawa-HCC ≥8. Adding information on TBX2 methylation improved the accuracy of risk models for a high risk population, with the area under the curve (AUC) of 74% for TBX2 methylation and Wen-HCC score compared with 64% with Wen-HCC score alone. The AUCs were 63% for Hung-HCC score and TBX2 methylation, 53% for Hung-HCC score alone, 65% for Michikawa-HCC score and TBX2 methylation and 59% for Michikawa-HCC risk alone. Our findings suggest the potential increase in risk assessment discrimination and accuracy from incorporation of DNA methylation. Citation Format: Hui-Chen Wu, Hwai-I Yang, Qiao Wang, Chien-Jen Chen, Regina M. Santella. Plasma DNA methylation marker and hepatocellular carcinoma risk prediction model for the general population [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 2747. doi:10.1158/1538-7445.AM2017-2747
Abstract 522: Expression and functional analysis of signal peptidase complex 18 in bladder cancer
Authors: Yoshinori Shigematsu, Yohei Sekino, Naoya Sakamoto, Kazuhiro Sentani, Naohide Oue, Tetsutaro Hayashi, Jun Teishima, Akio Matsubara, Wataru Yasui
Journal: Cancer Research (2017)

Abstract Urothelial carcinoma of the bladder is a common malignancy that causes approximately 150,000 deaths per year worldwide. So far, no molecularly targeted agents have been approved for treatment of the disease. In the present study, we built an in-house oligonucleotide array, on which 394 genes were selected based on our SAGE data and previously reported array data, in order to identify the genes of most relevance to gastric carcinogenesis. Among these genes, we focused on SEC11A, because it is frequently overexpressed in gastric cancer (GC). SEC11A encodes the SPC18 protein, which is one of the subunits of the signal peptidase complex (SPC). Most secretory proteins contain amino terminal- or internal signal peptides that direct their sorting to the endoplasmic reticulum (ER). From the ER, proteins are transported to either the extracellular space or the plasma membrane through the ER-Golgi secretory pathway. The ER signal peptides are then cleaved by the SPC. In GC, SPC18 contributes to progression via EGFR pathway associated with TGF-a secretion. However, the expression and function of SPC18 have not been investigated in bladder cancer (BC). In this study, we analyzed the expression and distribution of SPC18 in human BC. Expression of SPC18 was observed in 44 (54.3%) out of 81 BC cases that was associated with T category (p=0.0002), Grade (p=0.0425), vascular invasion (p=0.0112) and CK5/6 positive/ CK20 negative basal type BC (p=0.0004). The univariate analysis indicated that expression of SPC18 (HR, 3.14; 95% CI, 1.47-7.47; P=0.0027) was associated with overall survival. In the multivariate model, SPC18 expression was an independent prognostic indicator (HR, 3.46; 95% CI, 1.35-10.00; P=0.0087). BC cells KMBC2 transfected with SPC18 expression vector significantly induced the cell growth (p&amp;lt;0.01) and invasion (p&amp;lt;0.01) activity. Western blot showed the overexpression of SPC18 induced the phosphorylation of EGFR, Akt and Erk. Real-time reverse transcription PCR analysis revealed the SPC18 forced expression cells induced mesenchymal character. These results suggest that SPC18 might contribute to the progression of BC. Citation Format: Yoshinori Shigematsu, Yohei Sekino, Naoya Sakamoto, Kazuhiro Sentani, Naohide Oue, Tetsutaro Hayashi, Jun Teishima, Akio Matsubara, Wataru Yasui. Expression and functional analysis of signal peptidase complex 18 in bladder cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 522. doi:10.1158/1538-7445.AM2017-522