Tead2 Expression Levels Control the Subcellular Distribution Of
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Machine-Learning and Chemicogenomics Approach Defi Nes and Predicts Cross-Talk of Hippo and MAPK Pathways
Published OnlineFirst November 18, 2020; DOI: 10.1158/2159-8290.CD-20-0706 RESEARCH ARTICLE Machine -Learning and Chemicogenomics Approach Defi nes and Predicts Cross-Talk of Hippo and MAPK Pathways Trang H. Pham 1 , Thijs J. Hagenbeek 1 , Ho-June Lee 1 , Jason Li 2 , Christopher M. Rose 3 , Eva Lin 1 , Mamie Yu 1 , Scott E. Martin1 , Robert Piskol 2 , Jennifer A. Lacap 4 , Deepak Sampath 4 , Victoria C. Pham 3 , Zora Modrusan 5 , Jennie R. Lill3 , Christiaan Klijn 2 , Shiva Malek 1 , Matthew T. Chang 2 , and Anwesha Dey 1 ABSTRACT Hippo pathway dysregulation occurs in multiple cancers through genetic and non- genetic alterations, resulting in translocation of YAP to the nucleus and activation of the TEAD family of transcription factors. Unlike other oncogenic pathways such as RAS, defi ning tumors that are Hippo pathway–dependent is far more complex due to the lack of hotspot genetic alterations. Here, we developed a machine-learning framework to identify a robust, cancer type–agnostic gene expression signature to quantitate Hippo pathway activity and cross-talk as well as predict YAP/TEAD dependency across cancers. Further, through chemical genetic interaction screens and multiomics analyses, we discover a direct interaction between MAPK signaling and TEAD stability such that knockdown of YAP combined with MEK inhibition results in robust inhibition of tumor cell growth in Hippo dysregulated tumors. This multifaceted approach underscores how computational models combined with experimental studies can inform precision medicine approaches including predictive diagnostics and combination strategies. SIGNIFICANCE: An integrated chemicogenomics strategy was developed to identify a lineage- independent signature for the Hippo pathway in cancers. -
Glioblastoma Stem Cells Induce Quiescence in Surrounding Neural Stem Cells Via Notch Signalling
bioRxiv preprint doi: https://doi.org/10.1101/856062; this version posted November 29, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Glioblastoma stem cells induce quiescence in surrounding neural stem cells via Notch signalling. Katerina Lawlor1, Maria Angeles Marques-Torrejon2, Gopuraja Dharmalingham3, Yasmine El-Azhar1, Michael D. Schneider1, Steven M. Pollard2§ and Tristan A. Rodríguez1§ 1National Heart and Lung Institute, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, United Kingdom. 2 MRC Centre for Regenerative Medicine & Edinburgh Cancer Research UK Centre, University of Edinburgh, Edinburgh, UK. 3MRC London Institute of Medical Sciences, Institute of Clinical Sciences, Imperial College London, UK §Authors for correspondence: [email protected] and [email protected] Running title: Glioblastoma stem cell competition Keyword: Neural stem cells, quiescence, glioblastoma, Notch, cell competition 1 bioRxiv preprint doi: https://doi.org/10.1101/856062; this version posted November 29, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 1 Abstract 2 There is increasing evidence suggesting that adult neural stem cells (NSCs) are a cell of 3 origin of glioblastoma, the most aggressive form of malignant glioma. The earliest stages of 4 hyperplasia are not easy to explore, but likely involve a cross-talk between normal and 5 transformed NSCs. How normal cells respond to this cross-talk and if they expand or are 6 outcompeted is poorly understood. -
Glucocorticoid Receptor Signaling Activates TEAD4 to Promote Breast
Published OnlineFirst July 9, 2019; DOI: 10.1158/0008-5472.CAN-19-0012 Cancer Molecular Cell Biology Research Glucocorticoid Receptor Signaling Activates TEAD4 to Promote Breast Cancer Progression Lingli He1,2, Liang Yuan3,Yang Sun1,2, Pingyang Wang1,2, Hailin Zhang4, Xue Feng1,2, Zuoyun Wang1,2, Wenxiang Zhang1,2, Chuanyu Yang4,Yi Arial Zeng1,2,Yun Zhao1,2,3, Ceshi Chen4,5,6, and Lei Zhang1,2,3 Abstract The Hippo pathway plays a critical role in cell growth and to the TEAD4 promoter to boost its own expression. Func- tumorigenesis. The activity of TEA domain transcription factor tionally, the activation of TEAD4 by GC promoted breast 4 (TEAD4) determines the output of Hippo signaling; how- cancer stem cells maintenance, cell survival, metastasis, and ever, the regulation and function of TEAD4 has not been chemoresistance both in vitro and in vivo. Pharmacologic explored extensively. Here, we identified glucocorticoids (GC) inhibition of TEAD4 inhibited GC-induced breast cancer as novel activators of TEAD4. GC treatment facilitated gluco- chemoresistance. In conclusion, our study reveals a novel corticoid receptor (GR)-dependent nuclear accumulation and regulation and functional role of TEAD4 in breast cancer and transcriptional activation of TEAD4. TEAD4 positively corre- proposes a potential new strategy for breast cancer therapy. lated with GR expression in human breast cancer, and high expression of TEAD4 predicted poor survival of patients with Significance: This study provides new insight into the role breast cancer. Mechanistically, GC activation promoted GR of glucocorticoid signaling in breast cancer, with potential for interaction with TEAD4, forming a complex that was recruited clinical translation. -
Bioinformatics Studies Provide Insight Into Possible Target and Mechanisms of Action of Nobiletin Against Cancer Stem Cells
DOI:10.31557/APJCP.2020.21.3.611 Bioinformatics Studies Provide Insight into Possible Target and Mechanisms of Action of Nobiletin against Cancer Stem Cells RESEARCH ARTICLE Editorial Process: Submission:05/08/2019 Acceptance:03/06/2020 Bioinformatics Studies Provide Insight into Possible Target and Mechanisms of Action of Nobiletin against Cancer Stem Cells Adam Hermawan1*, Herwandhani Putri2 Abstract Objective: Nobiletin treatment on MDA-MB 231 cells reduces the expression of CXC chemokine receptor type 4 (CXCR4), which is highly expressed in cancer stem cell populations in tumor patients. However, the mechanisms of nobiletin in cancer stem cells (CSCs) remain elusive. This study was aimed to explore the potential target and mechanisms of nobiletin in cancer stem cells using bioinformatics approaches. Methods: Gene expression profiles by public COMPARE predicting the sensitivity of tumor cells to nobiletin. Functional annotations on gene lists are carried out with The Database for Annotation, Visualization and Integrated Discovery (DAVID) v6.8, and WEB-based GEne SeT Analysis Toolkit (WebGestalt). The protein-protein interaction (PPI) network was analyzed by STRING-DB and visualized by Cytoscape. Results: Microarray analyses reveal many genes involved in protein binding, transcriptional and translational activity. Pathway enrichment analysis revealed breast cancer regulation of estrogen signaling and Wnt/ß-catenin by nobiletin. Moreover, three hub genes, i.e. ESR1, NCOA3, and RPS6KB1 and one significant module were filtered out and selected from the PPI network. Conclusion: Nobiletin might serve as a lead compound for the development of CSCs-targeted drugs by targeting estrogen and Wnt/ß-catenin signaling. Further studies are needed to explore the full therapeutic potential of nobiletin in cancer stem cells. -
YAP Activation Drives Liver Regeneration After Cholestatic Damage Induced by Rbpj Deletion
International Journal of Molecular Sciences Article YAP Activation Drives Liver Regeneration after Cholestatic Damage Induced by Rbpj Deletion Umesh Tharehalli 1 , Michael Svinarenko 1, Johann M. Kraus 2, Silke D. Kühlwein 2 , Robin Szekely 2, Ute Kiesle 1, Annika Scheffold 3, Thomas F.E. Barth 4, Alexander Kleger 1, Reinhold Schirmbeck 1, Hans A. Kestler 2 , Thomas Seufferlein 1, Franz Oswald 1, Sarah-Fee Katz 1 and André Lechel 1,* 1 Department of Internal Medicine I, Ulm University, 89081 Ulm, Germany; [email protected] (U.T.); [email protected] (M.S.); [email protected] (U.K.); [email protected] (A.K.); [email protected] (R.S.); [email protected] (T.S.); [email protected] (F.O.); [email protected] (S.-F.K.) 2 Medical Systems Biology, Ulm University, 89081 Ulm, Germany; [email protected] (J.M.K.); [email protected] (S.D.K.); [email protected] (R.S.); [email protected] (H.A.K.) 3 Department of Internal Medicine III, Ulm University, 89081 Ulm, Germany; [email protected] 4 Department of Pathology, Ulm University, 89081 Ulm, Germany; [email protected] * Correspondence: [email protected]; Tel.: +49-731-500-44810 Received: 8 November 2018; Accepted: 26 November 2018; Published: 29 November 2018 Abstract: Liver cholestasis is a chronic liver disease and a major health problem worldwide. Cholestasis is characterised by a decrease in bile flow due to impaired secretion by hepatocytes or by obstruction of bile flow through intra- or extrahepatic bile ducts. -
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UC Irvine UC Irvine Previously Published Works Title Proteomic analyses reveal distinct chromatin-associated and soluble transcription factor complexes. Permalink https://escholarship.org/uc/item/1fz5r77k Journal Molecular systems biology, 11(1) ISSN 1744-4292 Authors Li, Xu Wang, Wenqi Wang, Jiadong et al. Publication Date 2015-01-21 DOI 10.15252/msb.20145504 License https://creativecommons.org/licenses/by/4.0/ 4.0 Peer reviewed eScholarship.org Powered by the California Digital Library University of California Article Proteomic analyses reveal distinct chromatin- associated and soluble transcription factor complexes Xu Li1,†, Wenqi Wang1,†, Jiadong Wang1, Anna Malovannaya2, Yuanxin Xi2,3, Wei Li2,3, Rudy Guerra4, David H Hawke5, Jun Qin2 & Junjie Chen1,* Abstract living organisms. Sophisticated signal transduction pathways are required for the development and survival of any organism, a minor The current knowledge on how transcription factors (TFs), the ulti- disruption of which may cause developmental defects and diseases mate targets and executors of cellular signalling pathways, are such as cancer (Fig 1A). The examples of these highly conserved regulated by protein–protein interactions remains limited. Here, signalling pathways include the Wnt (MacDonald et al,2009),TGF-b we performed proteomics analyses of soluble and chromatin- (Massague, 1998) and NF-jB (Hayden & Ghosh, 2004) pathways. associated complexes of 56 TFs, including the targets of many Many of these pathways function by ultimately regulating the signalling pathways involved in development and cancer, and 37 activity of certain transcription factors (TFs), often by changing their members of the Forkhead box (FOX) TF family. Using tandem affin- localizations. Reports on individual proteins suggested that the ity purification followed by mass spectrometry (TAP/MS), we chromatin association of TFs is tightly controlled by upstream signals. -
Engineered Type 1 Regulatory T Cells Designed for Clinical Use Kill Primary
ARTICLE Acute Myeloid Leukemia Engineered type 1 regulatory T cells designed Ferrata Storti Foundation for clinical use kill primary pediatric acute myeloid leukemia cells Brandon Cieniewicz,1* Molly Javier Uyeda,1,2* Ping (Pauline) Chen,1 Ece Canan Sayitoglu,1 Jeffrey Mao-Hwa Liu,1 Grazia Andolfi,3 Katharine Greenthal,1 Alice Bertaina,1,4 Silvia Gregori,3 Rosa Bacchetta,1,4 Norman James Lacayo,1 Alma-Martina Cepika1,4# and Maria Grazia Roncarolo1,2,4# Haematologica 2021 Volume 106(10):2588-2597 1Department of Pediatrics, Division of Stem Cell Transplantation and Regenerative Medicine, Stanford School of Medicine, Stanford, CA, USA; 2Stanford Institute for Stem Cell Biology and Regenerative Medicine, Stanford School of Medicine, Stanford, CA, USA; 3San Raffaele Telethon Institute for Gene Therapy, Milan, Italy and 4Center for Definitive and Curative Medicine, Stanford School of Medicine, Stanford, CA, USA *BC and MJU contributed equally as co-first authors #AMC and MGR contributed equally as co-senior authors ABSTRACT ype 1 regulatory (Tr1) T cells induced by enforced expression of interleukin-10 (LV-10) are being developed as a novel treatment for Tchemotherapy-resistant myeloid leukemias. In vivo, LV-10 cells do not cause graft-versus-host disease while mediating graft-versus-leukemia effect against adult acute myeloid leukemia (AML). Since pediatric AML (pAML) and adult AML are different on a genetic and epigenetic level, we investigate herein whether LV-10 cells also efficiently kill pAML cells. We show that the majority of primary pAML are killed by LV-10 cells, with different levels of sensitivity to killing. Transcriptionally, pAML sensitive to LV-10 killing expressed a myeloid maturation signature. -
Alternatively Constructed Estrogen Receptor Alpha-Driven Super-Enhancers Result in Similar Gene Expression in Breast and Endometrial Cell Lines
International Journal of Molecular Sciences Article Alternatively Constructed Estrogen Receptor Alpha-Driven Super-Enhancers Result in Similar Gene Expression in Breast and Endometrial Cell Lines 1,2, 3, 1, Dóra Bojcsuk y , Gergely Nagy y and Bálint László Bálint * 1 Genomic Medicine and Bioinformatic Core Facility, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary; [email protected] 2 Doctoral School of Molecular Cell and Immune Biology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary 3 Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary; [email protected] * Correspondence: [email protected] These authors contributed equally to this work. y Received: 22 January 2020; Accepted: 25 February 2020; Published: 27 February 2020 Abstract: Super-enhancers (SEs) are clusters of highly active enhancers, regulating cell type-specific and disease-related genes, including oncogenes. The individual regulatory regions within SEs might be simultaneously bound by different transcription factors (TFs) and co-regulators, which together establish a chromatin environment conducting to effective transcription. While cells with distinct TF profiles can have different functions, how different cells control overlapping genetic programs remains a question. In this paper, we show that the construction of estrogen receptor alpha-driven SEs is tissue-specific, both collaborating TFs and the active SE components greatly differ between human breast cancer-derived MCF-7 and endometrial cancer-derived Ishikawa cells; nonetheless, SEs common to both cell lines have similar transcriptional outputs. These results delineate that despite the existence of a combinatorial code allowing alternative SE construction, a single master regulator might be able to determine the overall activity of SEs. -
Cell Contact and Nf2/Merlin-Dependent Regulation of TEAD Palmitoylation and Activity
Cell contact and Nf2/Merlin-dependent regulation of TEAD palmitoylation and activity Nam-Gyun Kima,b and Barry M. Gumbinera,b,c,1 aCenter for Developmental Biology and Regenerative Medicine, Seattle Children’s Research Institute, Seattle, WA 98101; bDepartment of Pediatrics, University of Washington School of Medicine, Seattle, WA 98195; and cDepartment of Biochemistry, University of Washington School of Medicine, Seattle, WA 98195 Edited by Joan S. Brugge, Harvard Medical School, Boston, MA, and approved April 10, 2019 (received for review November 19, 2018) The Hippo pathway is involved in regulating contact inhibition of S-palmitoylation is a posttranslational modification of proteins in proliferation and organ size control and responds to various physical which a saturated fatty acid, palmitate, is attached via thioester and biochemical stimuli. It is a kinase cascade that negatively linkage to cysteine residue and, less frequently, to serine and regulates the activity of cotranscription factors YAP and TAZ, which threonine residues of protein (16, 17). Palmitate is supplied ex- interact with DNA binding transcription factors including TEAD and ogenously by diet or de novo biosynthesized by fatty acid syn- activate the expression of target genes. In this study, we show that thase (FASN) (18), the only mammalian enzyme that catalyzes the palmitoylation of TEAD, which controls the activity and stability palmitate from acetyl CoA, malonyl-CoA, and NADPH. Unlike of TEAD proteins, is actively regulated by cell density independent of other lipid modifications, such as prenylation and myristoylation, Lats, the key kinase of the Hippo pathway. The expression of fatty the palmitoylation process is reversible and can be dynamically acid synthase and acetyl-CoA carboxylase involved in de novo modulated in response to cell stimulation (16). -
Supplementary Table 1
Up-regulated accession # Development M93275 ADFP, adipose differentiation related protein D43694 MATH-1, homolog of atonal 1 M64068 Bmi-1, zinc finger protein AW124785 Midnolin, midbrain nucleolar protein AI843178 Cla3, Cerebellar ataxia 3 D10712 Nedd1, Neural precursor cell expressed, developmentally down-regulated gene 1 AB011678 Doublecortin, for neurogenesis M57683 mPDGF-alpha-R, PDGF alpha receptor U41626 DSS1, deleted in split hand/split foot 1 homolog (Dss1), for limb development AB010833 PTCH2, patched 2, Mouse homolog of yeast CDC46 NP_034226 Ebf3, early B-cell factor 3 AI846695 Qk, Quaking U63386 Edr1 Early development regulator 1 (homolog of polyhomeotic 1), Mph1 AI043016 Rnf2, Ring finger protein 2 X69942 Enhancer-trap-locus 1, for transcription regulation AF100694 Ruvbl1, Ruv-B like protein 1, DNA helicase AW123618 Fzd2, Frizzled homolog 2 U88566 Sfrp1, secreted frizzled related protein 1 AA681520 Geminin-pending, for embryogenesis and morphogenesis U88567 Sfrp2, secreted frizzled related protein 2 AB025922 Gli1, GLI-Kruppel family member 1 AF089721 Smo, Smoothened X99104 Gli2, GLI-Kruppel family member 2 AF009414 SOX11, SRY-box containing gene 11 U61362 Grg1, groucho-related gene 1, Tle1, transducin-like enhancer of split 1 U85614 SRG3, Smarcc1, SWI/SNF related, matrix associated, action dependent regulator of chromatin, subfamily, member 1 M97506 Hen1, helix-loop-helix protein AI837838 Tmeff1, Transmembrane protein with EGF-like and two follistatin-like domains 1 U79748 Madh4, MAD homolog 4, for transcription regulation -
Temporal Epigenomic Profiling Identifies AHR As a Dynamic Super-Enhancer Controlled Regulator of Mesenchymal Multipotency
bioRxiv preprint doi: https://doi.org/10.1101/183988; this version posted November 17, 2017. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. Gerard et al.: Time-series epigenomic profiles of mesenchymal differentiation 1 Temporal epigenomic profiling identifies AHR as a 2 dynamic super-enhancer controlled regulator of 3 mesenchymal multipotency 4 Deborah Gérard1, Florian Schmidt2,3, Aurélien Ginolhac1, Martine Schmitz1, 5 Rashi Halder4, Peter Ebert3, Marcel H. Schulz2,3, Thomas Sauter1 and Lasse 6 Sinkkonen1* 7 1Life Sciences Research Unit, University of Luxembourg, L-4367 Belvaux, 8 Luxembourg 9 2Excellence Cluster for Multimodal Computing and Interaction, Saarland Informatics 10 Campus, Germany 11 3Computational Biology & Applied Algorithmics, Max Planck Institute for 12 Informatics, Saarland Informatics Campus, Germany 13 4Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur- 14 Alzette, L-4362, Luxembourg 15 16 [email protected]; [email protected]; [email protected]; 17 [email protected]; [email protected]; [email protected]; 18 [email protected]; [email protected]; [email protected] 19 20 *Corresponding author: Dr. Lasse Sinkkonen 21 Life Sciences Research Unit, University of Luxembourg 22 6, Avenue du Swing, L-4367 Belvaux, Luxembourg 23 Tel.: +352-4666446839 24 E-mail: [email protected] 25 1 bioRxiv preprint doi: https://doi.org/10.1101/183988; this version posted November 17, 2017. -
Identification of Genomic Targets of Krüppel-Like Factor 9 in Mouse Hippocampal
Identification of Genomic Targets of Krüppel-like Factor 9 in Mouse Hippocampal Neurons: Evidence for a role in modulating peripheral circadian clocks by Joseph R. Knoedler A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy (Neuroscience) in the University of Michigan 2016 Doctoral Committee: Professor Robert J. Denver, Chair Professor Daniel Goldman Professor Diane Robins Professor Audrey Seasholtz Associate Professor Bing Ye ©Joseph R. Knoedler All Rights Reserved 2016 To my parents, who never once questioned my decision to become the other kind of doctor, And to Lucy, who has pushed me to be a better person from day one. ii Acknowledgements I have a huge number of people to thank for having made it to this point, so in no particular order: -I would like to thank my adviser, Dr. Robert J. Denver, for his guidance, encouragement, and patience over the last seven years; his mentorship has been indispensable for my growth as a scientist -I would also like to thank my committee members, Drs. Audrey Seasholtz, Dan Goldman, Diane Robins and Bing Ye, for their constructive feedback and their willingness to meet in a frequently cold, windowless room across campus from where they work -I am hugely indebted to Pia Bagamasbad and Yasuhiro Kyono for teaching me almost everything I know about molecular biology and bioinformatics, and to Arasakumar Subramani for his tireless work during the home stretch to my dissertation -I am grateful for the Neuroscience Program leadership and staff, in particular