tbuckley/cabot-search huggingface dataset:
Abstract 1815: Massively parallel identification of conserved drug resistant mutations in kinases
Authors: Nicole S. Persky, Desiree Hernandez, Jonathon Cordova, Amanda Walker, Lisa Brenan, Federica Piccioni, Sasha Pantel, Yenarae Lee, Amy Goodale, Xiaoping Yang, Yoichiro Mitsuishi, Mariana Do Carmo, Cong Zhu, Aleksandr Andreev, David E. Root, Cory M. Johannessen
Journal: Cancer Research (2018)

Abstract Drug resistant mutations that arise in therapeutic targets often limit clinical responses. However, the discovery of such mutations has historically been performed one gene or mutation at a time, often over decades of experimental and clinical testing, limiting our understanding of conserved mechanisms of drug resistance. We hypothesized that deep mutational scanning of canonical kinases may expedite this process and identify novel conserved elements that cause drug resistance when mutated (similar to the well-studied “Gatekeeper” residue). To test this, we generated cDNA-expression libraries containing all possible amino acid substitutions in CDK6, CDK4, ERK2, and EGFR. We screened each library against clinically utilized, ATP-competitive small molecule inhibitors. We then mapped the phenotypic data for over 40,000 missense mutations onto the aligned crystal structures of each protein and searched for shared structural attributes associated with drug resistance. This analysis revealed 4 equivalent amino acid sites whose mutation conferred drug resistance to ATP-competitive inhibitors in all of our screens: the Gatekeeper residue, as well as three uncharacterized residues. One of these sites, which we have termed the “Keymaster”, was additionally found to cause resistance in published data sets of sub-saturation BRAF, HER2, BCR-ABL, and MEK1 mutagenesis screens against their respective inhibitors. We confirmed that drug resistant phenotypes are caused by these alterations utilizing growth assays and protein target phosphorylation detection assays. Mechanistically, we show preliminary evidence that Keymaster-mutant proteins are competent for drug binding, but may display elevated basal activity. Consistent with our findings, we additionally identified mutations at Keymaster residues in reported patient tumors in a number of oncogene kinases, suggesting that Keymaster mutations could be drivers of tumorigenesis, as well as drug resistance. These efforts may prove useful for characterizing somatic kinase mutations of unknown function, designing next-generation therapeutics and deepening our understanding of kinase regulation. Citation Format: Nicole S. Persky, Desiree Hernandez, Jonathon Cordova, Amanda Walker, Lisa Brenan, Federica Piccioni, Sasha Pantel, Yenarae Lee, Amy Goodale, Xiaoping Yang, Yoichiro Mitsuishi, Mariana Do Carmo, Cong Zhu, Aleksandr Andreev, David E. Root, Cory M. Johannessen. Massively parallel identification of conserved drug resistant mutations in kinases [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 1815.
Abstract 5701: Verification of the methodology for evaluating tumor-infiltrating lymphocytes in colorectal cancer
Authors: Shinji Matsutani, Masatsune Shibutani, Kiyoshi Maeda, Hisashi Nagahara, Tatsunari Fukuoka, Tatsuro Tamura, Go Ohira, Sadaaki Yamazoe, Kenjiro Kimura, Takahiro Toyokawa, Ryosuke Amano, Hiroaki Tanaka, Kazuya Muguruma, Kosei Hirakawa, Masaichi Ohira
Journal: Cancer Research (2018)

Abstract Background: The density of tumor-infiltrating lymphocytes (TILs) have been reported to reflect antitumor immune response and correlate with prognosis in malignancy. However, the methodology for evaluating the density of TILs by an immunohistochemical analysis differs among reports. The aim of this study was to verify the methodology for evaluating the density of TILs by immunohistochemical analysis and thereby identify the optimum methodology in clinical setting. Methods: Three-hundred-thirteen patients who underwent curative operation for stage II/III colorectal cancer were enrolled. We retrospectively examined the density of TILs using immunohistochemical staining according to each method as follows: 1) subset of lymphocytes (i.e. CD4+/CD8+), 2) selected fields (i.e. at random or focusing on hot spots), 3) location in low-power field (i.e. the invasive margin [TILsIM] or the center of the tumor [TILsCT] or the surface of the tumor [TILsST]), and 4) location in high-power field (i.e. in tumor stroma [sTILs] or intra-tumor cells [iTILs] or total TILs [tTILs: sTILs+iTILs]). We then assessed the prognostic value of the density of TILsIM evaluated as described above. We also evaluated the correlation between the density of TILsIM and that of TILsCT/TILsST. Results: In randomly selected fields, the densities of CD8+sTILsIM and CD8+tTILsIM were significantly associated with the survival. However, the densities of TILs evaluated via other methods were not associated with the survival. Furthermore, the density of CD8+TILsIM was significantly associated with that of CD8+TILsCT and CD8+TILsST. Conclusions: We concluded that best and easiest way to evaluate the density of TILs in the clinical setting may be to assess the density of total CD8+TILs at the invasive margin in randomly selected fields. Citation Format: Shinji Matsutani, Masatsune Shibutani, Kiyoshi Maeda, Hisashi Nagahara, Tatsunari Fukuoka, Tatsuro Tamura, Go Ohira, Sadaaki Yamazoe, Kenjiro Kimura, Takahiro Toyokawa, Ryosuke Amano, Hiroaki Tanaka, Kazuya Muguruma, Kosei Hirakawa, Masaichi Ohira. Verification of the methodology for evaluating tumor-infiltrating lymphocytes in colorectal cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 5701.
Clinical Validity of Genes for Heritable Thoracic Aortic Aneurysm and Dissection
Authors: Marjolijn Renard, Catherine Francis, Rajarshi Ghosh, Alan F. Scott, P. Dane Witmer, Lesley C. Adès, Gregor U. Andelfinger, Pauline Arnaud, Catherine Boileau, Bert L. Callewaert, Dongchuan Guo, Nadine Hanna, Mark E. Lindsay, Hiroko Morisaki, Takayuki Morisaki, Nicholas Pachter, Leema Robert, Lut Van Laer, Harry C. Dietz, Bart L. Loeys, Dianna M. Milewicz, Julie De Backer
Journal: Journal of the American College of Cardiology (2018)
The Actin-Binding Protein Girdin and Its Akt-Mediated Phosphorylation Regulate Neointima Formation After Vascular Injury
Authors: HiroshiMiyake, KengoMaeda, NaoyaAsai, ReiShibata, HitoshiIchimiya, MayuIsotani-Sakakibara, YumikoYamamura, KatsuhiroKato, AtsushiEnomoto, MasahideTakahashi, ToyoakiMurohara
Journal: Circulation Research (2011)

Rationale:It is well established that the migration and proliferation of vascular smooth muscle cells (VSMCs) have major roles in the vascular remodeling process. Our previous study showed that the Akt substrate Girdin, which is expressed in VSMCs and endothelial cells, is essential for postnatal angiogenesis. However, the function of Girdin and its Akt-mediated phosphorylation in VSMCs and their in vivo roles in vascular remodeling remain to be elucidated. Objective:We investigated the function of Girdin and its Akt-mediated phosphorylation using cultured VSMCs and animal models of vascular remodeling. Methods and Results:The depletion of Girdin by RNA interference disrupted the rearrangement of the actin cytoskeleton in VSMCs, resulting in impaired cell migration. The depletion of Girdin also inhibited VSMC proliferation. Girdin expression was highly upregulated and its serine at position 1416 was phosphorylated in the neointima of carotid arteries after balloon injury in a rat model. The introduction o...
Abstract 2362: Comprehensive portrait of canonical and non-canonical splicing in cancer
Authors: Reyka G. Jayasinghe, Song Cao, Qingsong Gao, Matthew A. Wyczalkowski, Sohini Sengupta, Matthew J. Walter, Christopher Maher, Michael C. Wendl, Feng Chen, Eduardo Eyras, Alexander J. Lazar, Ken Chen, Ilya Shmulevich, Li Ding, The Splicing Analysis Working Group
Journal: Cancer Research (2018)

Abstract Current annotation methods typically classify mutations as disruptors of splicing if they fall on either the consensus intronic dinucleotide splice donor, GT, or the splice acceptor, AG. As a group, splice site mutations have been presumed to be invariably deleterious because of their disruption of the conserved sequences that are used to identify exon-intron boundaries. While this classification method has been useful, increasing evidence suggests that mutations outside of the canonical splice site can lead to transcriptional changes beyond disruption of the nearest junction. In this study, we have developed the MiSplice pipeline to determine the local and global effects of genomic mutations on splicing across 33 cancer types. To evaluate the local effects of mutations on splicing, we applied MiSplice to identify splice-disrupting mutations (SDMs) and splice-creating mutations (SCMs), genome-wide. We identified 1,964 novel SCMs, of which 26% and 11% were mis-annotated as missense and silent mutations and validated 10 of 11 genes in a mini-gene splicing assay. SDM identification predicted complex splicing patterns associated with canonical splice site mutations and identified a handful of mutations in proximity to the canonical junction that disrupt splicing factor binding sites. Interestingly, further investigation of the novel neoantigens produced by SCMs and SDMs are likely several folds more immunogenic than missense mutations. To explore the global impact of mutations on splicing we focused on recurrent and adjacent mutations disrupting the spliceosomal complex and related splicing factor genes from over 400 curated splice related genes. In addition, we applied HotSpot3D to identify splice-factor mutations (SFMs) that are significantly proximal to one another. Our analysis has identified novel SFMs that disrupt the spliceosomal complex and globally impact downstream splicing targets creating novel peptide sequences and alter key cancer genes. The current study has greatly extended the insight into the transcriptional ramifications of genomic alterations by integrating DNA and RNA sequencing data and painting the portrait of alternative splicing across cancer genomes. Citation Format: Reyka G. Jayasinghe, Song Cao, Qingsong Gao, Matthew A. Wyczalkowski, Sohini Sengupta, Matthew J. Walter, Christopher Maher, Michael C. Wendl, Feng Chen, Eduardo Eyras, Alexander J. Lazar, Ken Chen, Ilya Shmulevich, Li Ding, The Splicing Analysis Working Group. Comprehensive portrait of canonical and non-canonical splicing in cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2362.
Abstract 3802: Human NKG2D ligand regulation of Natural Killer cell function and its implications in cancer and inflammation
Authors: Payal Dhar, Jennifer Wu
Journal: Cancer Research (2018)

Abstract The significance of ligand-induced activation of Natural Killer cell activating receptor NKG2D in controlling tumor growth has been well established in various experimental animal models. Amongst different types of NKG2D ligands, MHC I chain related molecule MICA/B is expressed most prevalently in various human malignancies, but has not been found in rodent family. Proteolytic-mediated shed-form of soluble MICA/B (sMIC) has been shown to suppress the immune system and correlate with advanced disease stages in cancer patients. Previous studies in our lab using two humanized bi-transgenic mice, one expressing native ligand (TRAMP/MICB) and alternatively expressing the shedding-resistant mutant (TRAMP/MICB.A2) revealed opposite roles of membrane-bound and soluble form of MIC in regulating tumor immunity. Mice with high levels of sMIC exhibited increased tumor progression, whereas mice expressing membrane-bound MICB.A2 in tumors enjoyed tumor-free survival. These findings raised the intriguing question of why do these structurally similar forms of MIC have vastly different effects on tumor immunity. To address this question, we investigated the signaling events and functional outcomes in NK cells upon stimulation by the two forms of ligands. In vitro co-culture studies of NK cells with tumor cell lines expressing sMICB and MICB.A2 revealed elevated pro-inflammatory cytokine production by NK cells upon stimulation with sMICB. In contrast, NK cells stimulated with MICB.A2 displayed enhanced expression of cytotoxicity mediators and signaling molecules of cytotoxicity pathway. This suggests that signaling through sMICB may polarize the NKG2D signaling pathways with preferential activation of inflammatory cytokine pathways. Our data has uncovered a new potential mechanism whereby sMIC promotes tumor progression and supports the notion that sMIC is a viable target for cancer immunotherapy. Citation Format: Payal Dhar, Jennifer Wu. Human NKG2D ligand regulation of Natural Killer cell function and its implications in cancer and inflammation [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 3802.
Abstract 482: Epstein-Barr virus-encoded miRNAs target ATM-mediated response in nasopharyngeal carcinoma
Authors: Raymond W. Lung, Po-Man Hau, Joanna H. Tong, Ka-Hei Lam, Anthony W. Chan, Kevin Y. Yip, George S. Tsao, Kwok-Wai Lo, Ka-Fai To
Journal: Cancer Research (2018)

Abstract Nasopharyngeal carcinoma (NPC) is a highly invasive epithelial malignancy that is prevalence in southern China and Southeast Asia. It is well-known to be associated with latent Epstein-Barr virus (EBV) infection. By using small RNA sequencing, we previously established a comprehensive miRNA profile in a panel of NPC samples and revealed that the EBV-encoded miRNAs derived from BamHI-A rightward transcripts (miR-BARTs) are abundantly expressed. The important roles of miR-BARTs in cancer development have been reported extensively. In the present study, we identified multiple putative binding sites of miR-BART5-5p, BART7-3p, BART9-3p and BART14-3p on the 3'-UTR of a critical DNA double-strand break (DSB) repair gene, Ataxia-Telangiectasia-Mutant (ATM). Notably, the expression of these 4 miR-BARTs represented more than 10% of all EBV-encoded miRNAs in NPC cells while downregulation of ATM expression was observed in our local primary NPC samples in both qRT-PCR and immunohistochemical (IHC) staining analysis. In addition, the abilities of miR-BARTs to downregulate ATM expression were demonstrated in the transient transfection experiments. By manipulating the miR-BARTs expression in epithelial cell lines, we further revealed that these four viral miRNAs could inhibit both ionizing radiation (IR)-induced ATM kinase activity and BZLF1-induced viral lytic reactivation. In conclusion, our findings suggest that miR-BART5-5p, BART7-3p, BART9-3p and BART14-3p work co-operatively to modulate DNA damage response and to maintain viral latency, contributing to the NPC tumorigenesis. Acknowledgement: Theme-based Research Scheme (T12-401/13-R) and GRF (14104415 and 14138016), Research Grant Council, Hong Kong. Citation Format: Raymond W. Lung, Po-Man Hau, Joanna H. Tong, Ka-Hei Lam, Anthony W. Chan, Kevin Y. Yip, George S. Tsao, Kwok-Wai Lo, Ka-Fai To. Epstein-Barr virus-encoded miRNAs target ATM-mediated response in nasopharyngeal carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 482.
Abstract 18063: Nasopharyngeal And/or Rectal Temperatures: Can They Be Used as Reliable Indirect Measures of Brain Temperature in Ischemic Stroke Patients Undergoing Mild Hypothermia?
Authors: Jie Zhao, Peng Yue, Mao Li, Sai Lu, Ying Wu
Journal: Circulation (2014)

Introduction: Hypothermia therapy has been proven to have neuroprotective effects for patients with ischemic stroke. To ensure efficacy of the therapy, it is imperative to develop reliable non-invasive measurements of brain temperature (BT). As the accuracy and the sensitivity of various indirect brain temperature measurements have yet to be established, this study was designed to determine the validity of two non-invasive measures (the nasopharyngeal temperature, NPT and rectal temperature, RT) to predict BT in ischemic stroke patients undergoing therapeutic hypothermia. Method: Fifty-four ischemic stroke patients who underwent hypothermia in the Neurological ICU of a teaching hospital were recruited. With direct BT measure as the gold standard, BT, NPT and RT were monitored simultaneously and recorded 60 minutes pre-hypothermia and every 60 minutes for the duration of the therapy. A total of 5850 temperature sets were obtained. Receiver operating characteristic (ROC) curves were employed to determine th...
Abstract 4453: Osteopontin-c mediated drug resistance in breast and ovarian carcinoma cells
Authors: Mariana C. Brum, Isabella S. Guimaräes, Luciana Bueno Ferreira, Letícia B. Rangel, Raquel C. Maia, Gabriela N. de Moraes, Etel R. Gimba
Journal: Cancer Research (2018)

Abstract Osteopontin (OPN) has been described as an important gene product mediating resistance to chemotherapeutic drugs. However, the specific roles of each OPN splice variant in mediating chemoresistance should be further investigated. This work aimed to evaluate OPNc expression patterns and its correlations with resistance to doxorubicin (DOX) and cisplatin (CIS) in breast and ovarian tumor cell lines, respectively. We used one breast cancer cell line resistant to DOX (MCF-7 DoxR), and one ovarian cancer cell line resistant to CIS (ACRP) and their corresponding parental cell lines (MCF-7 and A2780). Knockdown of OPNc expression levels has been achieved by transfecting cell lines with specific anti-OPNc phosphothiotate modified DNA oligomers. Cytotoxicity assays have been carried out using 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT), crystal violet and clonogenic assays. Gene expression has been assessed by quantitative real time PCR. Our results showed that drug-resistant cells overexpress OPNc and P-glycoprotein (P-gp), when compared to their age matched parental cell lines. After transfecting both MCF-7 DoxR and ACRP resistant cell lines with the anti-OPNc oligomers, we found a significant knockdown of OPNc isoform expression, as well as the expression of P-gp. Moreover, these cells exhibited a significantly increased sensitivity to DOX and CIS, and inhibited cell growth and colony formation (p&amp;lt;0,05). Additionally, the epithelial-plasticity phenotype of both MCF-7 DoxR and ACRP resistant cell lines has been reversed, as well the expression of epithelial-mesenchymal transition (EMT)-related interleukins. Altogether, these data evidence that OPNc overexpression can mediate resistance to these chemotherapeutic drugs, possibly by modulating the expression of P-gp and the EMT phenotype. In summary, our data provide early insights on the role of OPNc isoform as a potential molecular target in cancer. Therapeutic strategies aiming to interfere with this isoform expression are likely to overcome resistance to chemotherapeutic agents. Citation Format: Mariana C. Brum, Isabella S. Guimaräes, Luciana Bueno Ferreira, Letícia B. Rangel, Raquel C. Maia, Gabriela N. de Moraes, Etel R. Gimba. Osteopontin-c mediated drug resistance in breast and ovarian carcinoma cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4453.
Diminished Basal Phosphorylation Level of Phospholamban in the Postinfarction Remodeled Rat Ventricle
Authors: BoyuHuang, SuWang, DayiQin, MohamedBoutjdir, NabilEl-Sherif
Journal: Circulation Research (1999)

Abstract—Three weeks after myocardial infarction (MI) in the rat, remodeled hypertrophy of noninfarcted myocardium is at its maximum and the heart is in a compensated stage with no evidence of heart failure. Our hemodynamic measurements at this stage showed a slight but insignificant decrease of +dP/dt but a significantly higher left ventricular end-diastolic pressure. To investigate the basis of the diastolic dysfunction, we explored possible defects in the β-adrenergic receptor–Gs/i protein–adenylyl cyclase–cAMP–protein kinase A–phosphatase pathway, as well as molecular or functional alterations of sarcoplasmic reticulum Ca2+-ATPase and phospholamban (PLB). We found no significant difference in both mRNA and protein levels of sarcoplasmic reticulum Ca2+-ATPase and PLB in post-MI left ventricle compared with control. However, the basal levels of both the protein kinase A–phosphorylated site (Ser16) of PLB (p16-PLB) and the calcium/calmodulin–dependent protein kinase-phosphorylated site (Thr17) of PLB (p1...
Abstract 12803: Galectin-3 is a Prognostic Biomarker for Patients After Transcatheter Aortic Valve Implantation
Authors: GerdBaldenhofer, SebastianSpethmann, MichaelLaule, BjoernEilers, WasiemSanad, HenrykDreger, GertBaumann, KarlStangl, VerenaStangl, FabianKnebel
Journal: Circulation (2014)

Introduction: Until now, a reliable biomarker to predict the short- or long-term outcome for patients undergoing TAVI is still missing. Galectin-3, a novel marker indicative for myocardial fibrosis, has prognostic value in heart failure. Our goal was to investigate whether galectin-3 is suited for risk assessment in TAVI patients. Methods: We included 101 patients undergoing TAVI in this prospective, single-center, observational study. Baseline galectin-3 levels were correlated to the VARC 30-day safety and one-year efficacy endpoint as well as to total mortality and cardiovascular events at one year. Results: The VARC 30-day safety endpoint was reached by 24 patients. At one year, 43 patients met the VARC efficacy endpoint, 16 patients died, and 23 cardiovascular events were recorded. At baseline, mean galectin-3 level for the entire group was 18.1 (± 11.1) ng/ml. Of the 101 patients, 36 had a galectin-3 value above the cut-off value of 17.8 ng/ml. These patients had significantly higher systolic pulmona...