tbuckley/cabot-search huggingface dataset:
Abstract 5821: Loss of <i>Pin1</i> suppresses Hedgehog-driven medulloblastoma tumorigenesis
Authors: Jean-Francois M. Rual
Journal: Cancer Research (2017)

Abstract Medulloblastoma is the most common malignant brain tumor in children. Therapeutic approaches to medulloblastoma (combination of surgery, radiotherapy and chemotherapy) have led to significant improvements, but are achieved at a high cost to quality of life. Alternative therapeutic approaches are needed. Genetic mutations leading to the activation of the Hedgehog pathway drive tumorigenesis in ~30% of medulloblastoma. In a yeast two-hybrid proteomic screen, we discovered a novel interaction between GLI1, a key transcription factor for the mediation of Hedgehog signals, and PIN1, a peptidylprolyl cis/trans isomerase that regulates the post-phosphorylation fate of its targets. The GLI1/PIN1 interaction was validated by reciprocal pulldowns using epitope-tagged proteins in HEK293T cells as well as by co-immunoprecipiations of the endogenous proteins in a medulloblastoma cell line. Our results support a molecular model in which PIN1 promotes GLI1 protein abundance, thus contributing to the positive regulation of Hedgehog signals. Most importantly, in vivo functional analyses of Pin1 in the GFAP-tTA;TRE-SmoA1 mouse model of Hedgehog-driven medulloblastoma demonstrate that the loss of Pin1 impairs tumor development and dramatically increases survival. In summary, the discovery of the GLI1/PIN1 interaction uncovers PIN1 as a novel therapeutic target in Hedgehog-driven medulloblastoma tumorigenesis. Citation Format: Jean-Francois M. Rual. Loss of Pin1 suppresses Hedgehog-driven medulloblastoma tumorigenesis [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 5821. doi:10.1158/1538-7445.AM2017-5821
Abstract 196: Adult-onset Cardiac Hypertrophy In LEOPARD Syndrome Is Caused By Both Cell Autonomous And Non-autonomous Effects That Occur During Development
Authors: Jessica Lauriol, Kimberly Keith, Boding Zhang, Roderick Bronson, Kyu-Ho Lee, Maria I Kontaridis
Journal: Circulation Research (2013)

Loss of function mutations in PTPN11 , the gene encoding the protein tyrosine phosphatase SHP2, cause LEOPARD Syndrome (LS), an autosomal dominant disorder with multiple cardiac defects, including hypertrophy. However, the mechanisms by which the LS mutants cause cardiac disease and regulate development remain unclear. Here, we utilized our inducible LS mouse model to determine whether LS mutations affect onset of cardiac hypertrophy via aberrant regulation of developmental processes. We examined hearts from wildtype (WT) or ubiquitously-expressing heterozygous LS (LS/+) and homozygous LS (LS/LS) embryos. As compared to WT, both LS/+ and LS/LS developing hearts showed diminished trabeculation, valvular hyperplasia and ventricular septal defects. In addition, LS/LS embryos had dextraposition of the aorta, leading to embryonic lethality. Gene expression analysis revealed that LS mutant hearts had decreased Foxp1/Fgf and Notch1/EphB2 signaling, suggesting perturbation of the reciprocal cross-talk between the developing endocardium and myocardium To assess this directly and to determine the in-vivo effects of lineage-specific LS expression during development, we generated, endothelial (Tie2)-, myocardial (Nkx2.5)- and neural crest (Wnt1)- specific LS/+ expressing mice. Surprisingly, the majority of LS cardiac defects, including the adult-onset cardiac hypertrophy, were recapitulated by expression of endocardial-specific LS alone, suggesting a functional necessity for the endocardium in hypertrophy of the heart. Moreover, though myocardial-specific expression of LS showed only minor developmental effects, these mice still recapitulated the adult-onset cardiac hypertrophy. Interestingly, no cardiac abnormalities were observed in the neural crest-specific expressing LS mice. Taken together, our data indicate that the LS mutations affect both cell autonomous and non-autonomous pathways necessary for the reciprocal cross-talk between endocardium and myocardium, and, importantly, that the adult-onset hypertrophy in LS is caused by aberrant signaling effects that occur during cardiac development.
Abstract 2074: Targeting SHP-1 mediated VEGF signaling to block the migration of human triple negative breast cancer
Authors: Jung-Chen Su, Ai-Chung Mar, Chun-Yu Liu, Kuen-Feng Chen, Chung-Wai Shiau
Journal: Cancer Research (2017)

Abstract Patients with triple-negative breast cancer (TNBC) had an increased likelihood of distant recurrence and death, as compared with those with non-TNBC subtype. Regorafenib is a multi-receptor tyrosine kinase (RTK) inhibitor targeting oncogenesis and has been approved for metastatic colorectal cancer and advanced gastrointestinal stromal tumor. Recently, scientists have suggested that regorafenib also acts as a SHP-1 phosphatase agonist. In this study, we aimed to investigate the role of regorafenib in suppressing metastasis of TNBC cells through targeting the SHP-1/p-STAT3/VEGF-A axis. We first observed a significant correlation between migration ability and SHP-1/p-STAT3/VEGF-A expression in several human TNBC cell lines. Importantly, we also demonstrated that VEGF-A expression is correlated with worse disease-free and distant metastasis-free survival in clinical TNBC patients. Furthermore, we showed that regorafenib could inhibit the migration of human TNBC cells, which was related to downregulation of p-STAT3 and VEGF-A. To exclude the role of RTK inhibition in regorafenib-induced anti-metastasis, we synthesized a regorafenib derivative, SC-78, that had minimal effect on VEGFR2 and PDGFR kinase inhibition, while having more potent effects on SHP-1 activation. SC-78 demonstrated superior in vitro and in vivo anti-migration to regorafenib. This study indicated that the SHP-1/p-STAT3/VEGF-A axis is a potential therapeutic target for metastatic TNBC, and SC-78 may be a promising lead compound for suppressing metastasis of TNBC. (Grant supported by MOST 104-2628-B-075-001-MY3, MOST 105-2325-B-010-007, 105F026 ) Citation Format: Jung-Chen Su, Ai-Chung Mar, Chun-Yu Liu, Kuen-Feng Chen, Chung-Wai Shiau. Targeting SHP-1 mediated VEGF signaling to block the migration of human triple negative breast 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 2074. doi:10.1158/1538-7445.AM2017-2074
Abstract 510: Topoisomerase IIβ silencing increases R loops at specific genomic loci associated with an increase of γH2AX and cell cycle progression delay in human cancer cells
Authors: Maria Delcuratolo, Jessica Marinello, Giovanni Capranico
Journal: Cancer Research (2017)

Abstract DNA topoisomerases (Top) are important players in maintaining the genome stability of cells by removing negative and positive DNA supercoils during transcription, replication and other DNA transactions. Recent evidence demonstrated that Top 1 silencing and poisoning by camptothecin affect the formation of R-loops, which are RNA/DNA hybrid structures involved in genome instability and are favored by negative supercoils of the DNA. The findings overall demonstrate that Top 1 reduces R loop levels during transcription whereas it favors R loop formation at early origins of DNA replication. Here, we address the question of whether DNA topoisomerase IIβ can also contribute to steady-state levels of R loop structures in the genome of U2OS cancer cells. We have then investigated the effects of Top2β silencing and Top2 poisons, doxorubicin and etoposide, on R loops and DNA damage in human U2OS cancer cells. Similarly to published data with camptothecin (Marinello et al., Nucleic Acids Research, 2013), Top2 poisons increase cellular R loops by IF after short treatment times and reduce them after 1 hour of treatment. The bi-phasic effect of poisons is mainly dependent on transcription. Moreover, we have determined the changes of R-loop levels by IF after Top2β silencing and the findings demonstrate that the enzyme can strongly modulate the formation of R loops as a full Top2β depletion increases nuclear R-loop levels. In addition, Top2β depletion leads to a slight increase of phosphorylation of H2AX histone along with cell cycle delay and eventually cell death. Thus, Top2β depletion can trigger genomic DNA breakage through alterations of R-loops. In order to establish which are the genomic regions of altered R loop levels, we have mapped Top2β-dependent R loop alterations by the DRIP method showing that specific genomic sites are affected by Top2β. Bioinformatic analyses of R loop maps in U2OS cells will be presented and discussed at the meeting. Altogether the findings demonstrate a critical role of Top2β in governing R loop structures in human cancer cells indicating that DNA torsional tension is a main driving factor of R loop formation and hence genome instability in cancer cells. Citation Format: Maria Delcuratolo, Jessica Marinello, Giovanni Capranico. Topoisomerase IIβ silencing increases R loops at specific genomic loci associated with an increase of γH2AX and cell cycle progression delay in human cancer cells [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 510. doi:10.1158/1538-7445.AM2017-510
Abstract 4068: HH-002, a derivative of Homoharringtonine, show promsing in diverse cancer models in preclinical characterization
Authors: Hank Rui
Journal: Cancer Research (2017)

Abstract Homoharringtonine (HHT) is an anti-cancer drug used to treat imatinib resistant CML, and a reversible inhibitor of translation acting upon the early steps in polypeptide chain elongation. BS-HH-002.SA is a derivative of HHT. BS-HH-002.SA was shown to decrease the phosphorylation of Janus protein tyrosine kinase 2 (JAK2) as well as downstream targets, such as signal transducers and activators of transcription 3 and 5 (STAT3 and STAT 5), it also reduced Myeloid cell leukemia-1 (Mcl-1) protein level significantly and resulted in apoptosis. Evaluation of BS-HH-002.SA efficacy. was test in HEL, an erthroleukemia cell line carrying a JAK2V617F mutation which is seen in 90% of patients with polycythemia vera (PCV) and half of those with essential thrombocythemia or primary myelofibrosis. HH-002.SA showed was highly potent (at low nM concentration) to HEL. Efficacy of BS-HH-002 was tested in a recombinant human erythropoietin injection (rhEpo)-induced murine model of polycythemia Vera, Treatment with BS-HH-002.SA BID for 4 days showed a significant inhibitory effect on rhEpo induced increase in reticulocytes, hematocrit and splenomegaly, as well as in red blood cell, white blood cell and platelet counts. Furthermore, histology evaluations revealed that BS-HH-002.SA exerted an inhibitory effect on rhEpo induced extramedullary hematopoiesis in spleen, and decreased cellularity in bone marrow with more predominant effect on erythroid cells than on myeloid cells. Also, BS-HH-002.SA also show potent in vitro and in vivo efficacy in pancreatic cancer cell line KP-4 and non-small cell lung cancer (NSCLC) NCI-H1975, BS-HH-002.S inhibited STAT3 Tyrosine 705 phosphorylation and reduced anti-apoptotic proteins expression Mcl-1 protein levels in both two cancer cell lines. Note: This abstract was not presented at the meeting. Citation Format: Hank Rui. HH-002, a derivative of Homoharringtonine, show promsing in diverse cancer models in preclinical characterization [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 4068. doi:10.1158/1538-7445.AM2017-4068
Abstract 2591: A guide to filtering TARGET Complete Genomics germline variants
Authors: James P. Evans, Rajesh Patidar, Zalman Vaksman, Sivasish Sindiri, Douglas R. Stewart, Javed Khan, Jun S. Wei, Sharon J. Diskin
Journal: Cancer Research (2017)

Abstract With the public release of TARGET’s pediatric cancer data, researchers are eager to investigate and integrate variants from both tumor and germline sequencing data, but caution should be used when interpreting TARGET variant calls from Complete Genomics data, as they unlike the Illumina based calls for which most of our databases and tools are customized. Here, we use germline samples from 55 neuroblastoma cases with both whole genome Complete Genomics variants and whole exome Illumina variants from GATK, Pindel, Platypus, and bam2mpg to investigate differences between germline variant calls from Complete Genomics and Illumina platforms. Our study of ~160,000 single nucleotide polymorphisms (SNPS) and ~19,000 insertions or deletions (indels) reveals that while SNP sets largely agree between Complete Genomics and Illumina, Complete Genomics data have many indels not present in Illumina calls, making it difficult to screen Complete Genomics indels against popular Illumina based variant databases like those provided by the Exome Aggregation Consortium and the National Heart, Lung, and Blood Institute Exome Sequencing Project. Further probing of Complete Genomics indels uncovered inconsistent indel formatting resulting a loss of recurrent variants, and miscalculated read depths in earlier versions of the Complete Genomics platform. To solve these issues and make Complete Genomics variant calls comparable to Illumina calls, we introduce a Snakemake pipeline that reformats Complete Genomics variant files and creates variant features for use in decision tree or random forest classifiers trained to recognize Complete Genomics variants that will be present in Illumina variant call sets. We determine that the most important features for locating Complete Genomics variants likely to be found in Illumina germline variant call sets are the presence of reads from both directions, average variant allele fraction across the cohort, a variant call in the matched tumor, the variant fraction of reads, and read depth. Using ten fold cross validation with our decision tree, we obtain &amp;gt;95% recall and &amp;gt;98% precision for SNPs, and &amp;gt;90% recall and &amp;gt;85% precision for indels. We advocate the use of our pipeline and filtering scheme for making Complete Genomics variant calls comparable to Illumina based calls. Citation Format: James P. Evans, Rajesh Patidar, Zalman Vaksman, Sivasish Sindiri, Douglas R. Stewart, Javed Khan, Jun S. Wei, Sharon J. Diskin. A guide to filtering TARGET Complete Genomics germline variants [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 2591. doi:10.1158/1538-7445.AM2017-2591
Abstract 733: Detection of HCC-derived major HBV integration junctions in urine and their implications for driver identification
Authors: Selena Y. Lin, Jamin D. Steffen, Yih-Ping Su, Surbhi Jain, Ting-Tsung Chang, Wei Song, Ying-Hsiu Su
Journal: Cancer Research (2017)

Abstract Chronic Hepatitis B Virus (HBV) infection is a major etiology of hepatocellular carcinoma (HCC), a leading cause of cancer mortality worldwide. Integration of HBV DNA into the host genome occurs during the course of chronic infection. Integrated HBV DNA is observed in most of HBV-associated HCC. The integration junctions derived from the original tumor cell become abundant (referred to as major integration junctions) in the infected liver because of clonal expansion during tumor development. Detection of circulating DNA containing these tumor-derived integration junctions may therefore be useful for cancer detection. We have adapted a method known as Primer Extension Capture (PEC) to enrich integrated HBV DNA for next-generation sequencing (NGS). Our initial studies using this approach to enrich the HBV DR1-2 region (a common site for HBV integrated breakpoints) identified major integration junctions from HBV-HCC tissue samples and matched urine. Further analysis revealed that most recurrently targeted integrations from these HCC tumors have previously reported involvement in cancer. This suggested that identification of recurrently targeted genes is applicable for driver identification. Interestingly, we show how HBV targets the TERT promoter in a localized region even though no two TERT junctions examined are identical. We have further developed this PEC to enrich for the entire HBV genome and applied it to (i) liver tissue DNA from 20 matched HCC and adjacent non-HCC samples, and (ii) DNA from urine of 20 hepatitis, 20 cirrhosis and 20 HCC patients. The HBV enriched libraries were sequenced by NGS and the integration events were analyzed using the in-house developed software. The complexity of HBV junction sites in HCC and non-HCC tissue and urine derived circulating DNA is reported. Our approach has potential to be used for liquid biopsies to study the complexities of HBV integrations in chronic HBV infection and carcinogenesis, and to identify HCC-related DNA modifications for early detection and disease management. Citation Format: Selena Y. Lin, Jamin D. Steffen, Yih-Ping Su, Surbhi Jain, Ting-Tsung Chang, Wei Song, Ying-Hsiu Su. Detection of HCC-derived major HBV integration junctions in urine and their implications for driver identification [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 733. doi:10.1158/1538-7445.AM2017-733
Utility of Fluorodeoxyglucose Positron Emission Tomography(FDG-PET) and Biomarkers, Serum Vitamin B12 and HDL for Assessing Lymphoproliferation in Children and Adults with Autoimmune Lymphoproliferative Syndrome Due to FAS Mutations (ALPS-FAS)
Authors: V. Koneti Rao, Susan Price, Lori Dodd, Remaley Alan, Millie Whatley, Jorge Carrasquillo, Clara C. Chen
Journal: Blood (2016)
Xp11.2 translocations in adult renal cell carcinomas with clear cell and papillary features.
Authors: Susanne M. Chan, Christopher G. Sherman, Manal Y. Gabril, Ingrid J. Zbieranowski, Linda M. Sugar, George M. Yousef, Georg A. Bjarnason
Journal: Journal of Clinical Oncology (2012)

4613 Background: Xp11.2 translocation renal cell carcinoma (RCC) is a rare tumor with unpredictable clinical course and prognosis in adults. Recognition of these tumors depends on the identification of a RCC with unique histology, particularly clear cell and papillary (CCP) features. Our objectives were to determine the incidence of Xp11.2 translocations in adult RCCs with clear cell and papillary features, and to characterize the clinicopathological features and prognosis of adult Xp11.2 RCCs. Methods: Slides for 1047 RCCs in adults (1999-2009) were retrieved from multiple institutions. Cases were reviewed histologically in order to detect any degree of clear cell and papillary change. Tissue microarrays were constructed from the clear cell and papillary RCCs as well as 40 non-papillary clear cell, 5 papillary, 3 chromophobe and 2 unclassified RCCs. Immunohistochemistry using TFE3, a marker highly sensitive (97.5%) and specific (99.6%) for Xp11.2 translocations was performed. Four pathologists independently reviewed the TFE3 results. Clinical and pathologic data were also retrieved. Results: Out of 1047 RCCs, 140 (13%) exhibited clear cell and papillary features. Four out of these 140 (3%) were positive for TFE3. All of the non-papillary clear cell, papillary, chromophobe and unclassified RCCs were negative for TFE3. Mean follow up for TFE3+ RCCs was 55 months. Conclusions: Xp11.2 translocation RCCs diagnosed by TFE3 immunohistochemistry were identified in 3% of adult RCCs that had clear cell and papillary changes. These tumors appear to present with smaller tumour size, lower stage and better prognosis in comparison to non-Xp11.2 CCPRCC and clear cell RCCs. In addition to Xp11.2 translocation carcinoma, coexistence of clear cell and papillary features may be present in other subsets of tumors that have yet to be characterized. [Table: see text]
Rare Genome-Wide Copy Number Variation and Expression of Schizophrenia in 22q11.2 Deletion Syndrome
Authors: Anne S. Bassett, Chelsea Lowther, Daniele Merico, Gregory Costain, Eva W. C. Chow, Therese van Amelsvoort, Donna McDonald-McGinn, Raquel E. Gur, Ann Swillen, Marianne Van den Bree, Kieran Murphy, Doron Gothelf, Carrie E. Bearden, Stephan Eliez, Wendy Kates, Nicole Philip, Vandana Sashi, Linda Campbell, Jacob Vorstman, Joseph Cubells, Gabriela M. Repetto, Tony Simon, Erik Boot, Tracy Heung, Rens Evers, Claudia Vingerhoets, Esther van Duin, Elaine Zackai, Elfi Vergaelen, Koen Devriendt, Joris R. Vermeesch, Michael Owen, Clodagh Murphy, Elena Michaelovosky, Leila Kushan, Maude Schneider, Wanda Fremont, Tiffany Busa, Stephen Hooper, Kathryn McCabe, Sasja Duijff, Karin Isaev, Giovanna Pellecchia, John Wei, Matthew J. Gazzellone, Stephen W. Scherer, Beverly S. Emanuel, Tingwei Guo, Bernice E. Morrow, Christian R. Marshall
Journal: American Journal of Psychiatry (2017)

Chromosome 22q11.2 deletion syndrome (22q11.2DS) is associated with a more than 20-fold increased risk for developing schizophrenia. The aim of this study was to identify additional genetic factors (i.e., "second hits") that may contribute to schizophrenia expression.