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Expression levels of therapeutic targets as indicators of sensitivity to targeted therapeutics

Riti Roy, Louise N Winteringham, Timo Lassmann, Alistair R. R. Forrest
2019 Molecular Cancer Therapeutics  
Winteringham, T. Lassmann, A.R.R. Forrest Writing, review, and/or revision of the manuscript: R. Roy, L.N. Winteringham, A.R.R. Forrest Study supervision: L.N. Winteringham, T. Lassmann, A.R.R.  ... 
doi:10.1158/1535-7163.mct-19-0273 pmid:31467181 fatcat:jge2eis365g4biyhnkwaul6pey

Myeloid Leukemia Factor 1 Associates with a Novel Heterogeneous Nuclear Ribonucleoprotein U-like Molecule

Louise N. Winteringham, Raelene Endersby, Simon Kobelke, Ross K. McCulloch, James H. Williams, Justin Stillitano, Scott M. Cornwall, Evan Ingley, S. Peter Klinken
2006 Journal of Biological Chemistry  
The nuclear content of Mlf1 was also regulated by 14-3-3 binding to a canonical 14-3-3 binding motif within the N terminus of Mlf1.  ...  Sample size was 20 ϫ 30 pixels (n Ͼ 300).  ...  (n ϭ 3) with * representing p Ͻ 0.01.  ... 
doi:10.1074/jbc.m605401200 pmid:17008314 fatcat:nfhtgblxvfaephrm74el2aycom

MADM, a Novel Adaptor Protein That Mediates Phosphorylation of the 14-3-3 Binding Site of Myeloid Leukemia Factor 1

Raelene Lim, Louise N. Winteringham, James H. Williams, Ross K. McCulloch, Evan Ingley, Jim Y-H. Tiao, Jean-Philippe Lalonde, Schickwann Tsai, Peta A. Tilbrook, Yi Sun, Xiaohua Wu, Stephan W. Morris (+1 others)
2002 Journal of Biological Chemistry  
However, a mutant consisting of amino acids 122-267 did not bind Madm, indicating that regions in the N terminus of Mlf1 were also required for interaction.  ...  In addition, the N-terminal region of Madm is rich in glutamic acid and serine residues, which could potentially bind SH2 modules in a phosphotyrosine-independent manner (28) .  ... 
doi:10.1074/jbc.m206041200 pmid:12176995 fatcat:jr6znx56p5fnrdvqz3pvkfm5bu

Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells

Erik Arner, Carsten O. Daub, Kristoffer Vitting-Seerup, Robin Andersson, Berit Lilje, Finn Drabløs, Andreas Lennartsson, Michelle Rönnerblad, Olga Hrydziuszko, Morana Vitezic, Tom C. Freeman, Ahmad M. N. Alhendi (+97 others)
2015 Science  
33. The use of microarray data sets to identify alternative mechanisms of TERT reactivation employed by those cell lines that were WT at positions -124 and -146 was unsuccessful. Average mRNA levels were roughly similar for (i) the ETS1 and ETS2 transcription factors (~1.1-fold higher in the WT group), (ii) the c-MYC transcription factor (~1.4-fold higher in the WT group), and (iii) the core components of the Polycomb repressive complex 2 (between~0.91-fold and~1.3-fold higher in the WT group).
more » ... 34. J. Nandakumar et al., Nature 492, 285-289 (2012). ACKNOWLEDGMENTS We thank C. Owens for providing the UC23, as well as detailed information on their origins and growth conditions. This work was supported by NIH grants CA075115 and CA104106 to D.T., Although it is generally accepted that cellular differentiation requires changes to transcriptional networks, dynamic regulation of promoters and enhancers at specific sets of genes has not been previously studied en masse. Exploiting the fact that active promoters and enhancers are transcribed, we simultaneously measured their activity in 19 human and 14 mouse time courses covering a wide range of cell types and biological stimuli. Enhancer RNAs, then messenger RNAs encoding transcription factors, dominated the earliest responses. Binding sites for key lineage transcription factors were simultaneously overrepresented in enhancers and promoters active in each cellular system. Our data support a highly generalizable model in which enhancer transcription is the earliest event in successive waves of transcriptional change during cellular differentiation or activation.
doi:10.1126/science.1259418 pmid:25678556 pmcid:PMC4681433 fatcat:wzkowgz4avg6jmd4pu5rcbnxh4

FANTOM5 CAGE profiles of human and mouse samples

Shuhei Noguchi, Takahiro Arakawa, Shiro Fukuda, Masaaki Furuno, Akira Hasegawa, Fumi Hori, Sachi Ishikawa-Kato, Kaoru Kaida, Ai Kaiho, Mutsumi Kanamori-Katayama, Tsugumi Kawashima, Miki Kojima (+166 others)
2017 Scientific Data  
Peaks were given a name in the form pN@GENE, where GENE indicates gene symbol or transcript name and N indicates the rank in the ranked list of promoter activities for that gene.  ... 
doi:10.1038/sdata.2017.112 pmid:28850106 pmcid:PMC5574368 fatcat:cel5hhhtardinak67mbl2okvhe

ECM Depletion Is Required to Improve the Intratumoral Uptake of Iron Oxide Nanoparticles in Poorly Perfused Hepatocellular Carcinoma

Yen Ling Yeow, Jiansha Wu, Xiao Wang, Louise Winteringham, Kirk W. Feindel, Janina E. E. Tirnitz-Parker, Peter J. Leedman, Ruth Ganss, Juliana Hamzah
2022 Frontiers in Oncology  
A minimum of n = 3 mice per group were used in each study.  ...  Gillies RJ, Schornack PA, Secomb TW, Raghunand N. Causes and Effects of Heterogeneous Perfusion in Tumors.  ... 
doi:10.3389/fonc.2022.837234 pmid:35273916 pmcid:PMC8902243 fatcat:nw3yat34irfhxlvnhnfr3xl4q4

Nuclear stabilisation of p53 requires a functional nucleolar surveillance pathway [article]

Katherine M Hannan, Priscilla Soo, Mei S Wong, Justine K Lee, Nadine Hein, Maurits Evers, Kira D Wysoke, Tobias D Williams, Christian Montellese, Lorey Smith, Sheren J Al-Obaidi, Lorena Núñez-Villacís (+19 others)
2021 bioRxiv   pre-print
Scott, Adam 312 Stephenson, Adam Stevenson, Parvathy Venugopal, Amilia Wee, Louise N. Winteringham and Mei 313 Szin Wong.  ...  RPL11, we further validated a selection of candidates from the 182 screen including HEATR3, RXRA and CIRH1A as bone fide modulators of the p53 response ( Fig. 183 3b, Supplementary Fig. 4a , c-h & i-n)  ...  Alphascreen 531 analysis performed n=3-5 biological experiments; ribosome subunit/polysome profiles, minimum 532 n=3 biological experiments per candidate. 533 (which was not certified by peer review) is  ... 
doi:10.1101/2021.01.21.427535 fatcat:jypcqdoiabe33fhlj5t2rp3xgi

Enhanced Detection of Desmoplasia by Targeted Delivery of Iron Oxide Nanoparticles to the Tumour-Specific Extracellular Matrix

Meenu Chopra, Jiansha Wu, Yen Ling Yeow, Louise Winteringham, Tristan D. Clemons, Martin Saunders, Venkata Ramana Kotamraju, Ruth Ganss, Kirk W. Feindel, Juliana Hamzah
2021 Pharmaceutics  
N,N ,N -tetramethyl-O-(1Hbenzotriazol-1-yl) uronium hexafluorophosphate) activator (or O-(benzotriazol-1-yl)-N,N, N ,N -tetramethyluronium hexafluorophosphate), collidine activator base and 5% piperazine  ...  A minimum of n = 3 mice per group were used in each study.  ... 
doi:10.3390/pharmaceutics13101663 pmid:34683956 fatcat:ryge5eg25rhcpa4a727xuwe74m

An integrated expression atlas of miRNAs and their promoters in human and mouse

Derek de Rie, Imad Abugessaisa, Tanvir Alam, Erik Arner, Peter Arner, Haitham Ashoor, Gaby Åström, Magda Babina, Nicolas Bertin, A Maxwell Burroughs, Ailsa J Carlisle, Carsten O Daub (+58 others)
2017 Nature Biotechnology  
coding pri-miRNAs (containing intronic mature miRNAs; n = 415), transcription factor (TF)-coding transcripts (n = 1,651), other protein-coding transcripts (n = 15,350), and long non-coding RNAs (n = 1,461  ...  (c) Reverse cumulative distribution of the maximum expression across the FANTOM5 samples of human miRNAs in the robust set (n = 735), permissive set (n = 999), and robust candidate set (n = 279).  ... 
doi:10.1038/nbt.3947 pmid:28829439 pmcid:PMC5767576 fatcat:z2xrrdah4rdjdpbzlt75evqbka

Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network

Mathys Grapotte, Manu Saraswat, Chloé Bessière, Christophe Menichelli, Jordan A. Ramilowski, Jessica Severin, Yoshihide Hayashizaki, Masayoshi Itoh, Michihira Tagami, Mitsuyoshi Murata, Miki Kojima-Ishiyama, Shohei Noma (+480 others)
2021 Nature Communications  
and balanced ((CGG) n , (CCG) n ).  ...  In these cases, global and (T) n -specific models achieved better performance than (GTTTTT) n , (GTTT) n , or (CTTTT) n -specific models.  ... 
doi:10.1038/s41467-021-23143-7 pmid:34078885 pmcid:PMC8172540 fatcat:ctyfp77e2fcejlamqa7s5ni2tq