Glioblastoma Stem Cells Induce Quiescence in Surrounding Neural Stem Cells Via Notch Signalling
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Core Transcriptional Regulatory Circuitries in Cancer
Oncogene (2020) 39:6633–6646 https://doi.org/10.1038/s41388-020-01459-w REVIEW ARTICLE Core transcriptional regulatory circuitries in cancer 1 1,2,3 1 2 1,4,5 Ye Chen ● Liang Xu ● Ruby Yu-Tong Lin ● Markus Müschen ● H. Phillip Koeffler Received: 14 June 2020 / Revised: 30 August 2020 / Accepted: 4 September 2020 / Published online: 17 September 2020 © The Author(s) 2020. This article is published with open access Abstract Transcription factors (TFs) coordinate the on-and-off states of gene expression typically in a combinatorial fashion. Studies from embryonic stem cells and other cell types have revealed that a clique of self-regulated core TFs control cell identity and cell state. These core TFs form interconnected feed-forward transcriptional loops to establish and reinforce the cell-type- specific gene-expression program; the ensemble of core TFs and their regulatory loops constitutes core transcriptional regulatory circuitry (CRC). Here, we summarize recent progress in computational reconstitution and biologic exploration of CRCs across various human malignancies, and consolidate the strategy and methodology for CRC discovery. We also discuss the genetic basis and therapeutic vulnerability of CRC, and highlight new frontiers and future efforts for the study of CRC in cancer. Knowledge of CRC in cancer is fundamental to understanding cancer-specific transcriptional addiction, and should provide important insight to both pathobiology and therapeutics. 1234567890();,: 1234567890();,: Introduction genes. Till now, one critical goal in biology remains to understand the composition and hierarchy of transcriptional Transcriptional regulation is one of the fundamental mole- regulatory network in each specified cell type/lineage. -
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. -
Supplemental Materials ZNF281 Enhances Cardiac Reprogramming
Supplemental Materials ZNF281 enhances cardiac reprogramming by modulating cardiac and inflammatory gene expression Huanyu Zhou, Maria Gabriela Morales, Hisayuki Hashimoto, Matthew E. Dickson, Kunhua Song, Wenduo Ye, Min S. Kim, Hanspeter Niederstrasser, Zhaoning Wang, Beibei Chen, Bruce A. Posner, Rhonda Bassel-Duby and Eric N. Olson Supplemental Table 1; related to Figure 1. Supplemental Table 2; related to Figure 1. Supplemental Table 3; related to the “quantitative mRNA measurement” in Materials and Methods section. Supplemental Table 4; related to the “ChIP-seq, gene ontology and pathway analysis” and “RNA-seq” and gene ontology analysis” in Materials and Methods section. Supplemental Figure S1; related to Figure 1. Supplemental Figure S2; related to Figure 2. Supplemental Figure S3; related to Figure 3. Supplemental Figure S4; related to Figure 4. Supplemental Figure S5; related to Figure 6. Supplemental Table S1. Genes included in human retroviral ORF cDNA library. Gene Gene Gene Gene Gene Gene Gene Gene Symbol Symbol Symbol Symbol Symbol Symbol Symbol Symbol AATF BMP8A CEBPE CTNNB1 ESR2 GDF3 HOXA5 IL17D ADIPOQ BRPF1 CEBPG CUX1 ESRRA GDF6 HOXA6 IL17F ADNP BRPF3 CERS1 CX3CL1 ETS1 GIN1 HOXA7 IL18 AEBP1 BUD31 CERS2 CXCL10 ETS2 GLIS3 HOXB1 IL19 AFF4 C17ORF77 CERS4 CXCL11 ETV3 GMEB1 HOXB13 IL1A AHR C1QTNF4 CFL2 CXCL12 ETV7 GPBP1 HOXB5 IL1B AIMP1 C21ORF66 CHIA CXCL13 FAM3B GPER HOXB6 IL1F3 ALS2CR8 CBFA2T2 CIR1 CXCL14 FAM3D GPI HOXB7 IL1F5 ALX1 CBFA2T3 CITED1 CXCL16 FASLG GREM1 HOXB9 IL1F6 ARGFX CBFB CITED2 CXCL3 FBLN1 GREM2 HOXC4 IL1F7 -
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. -
Tead2 Expression Levels Control the Subcellular Distribution Of
ß 2014. Published by The Company of Biologists Ltd | Journal of Cell Science (2014) 127, 1523–1536 doi:10.1242/jcs.139865 RESEARCH ARTICLE Tead2 expression levels control the subcellular distribution of Yap and Taz, zyxin expression and epithelial–mesenchymal transition Maren Diepenbruck1,*, Lorenz Waldmeier1,*, Robert Ivanek1, Philipp Berninger2, Phil Arnold2, Erik van Nimwegen2 and Gerhard Christofori1,` ABSTRACT tumor, but also results in the acquisition of stem-cell-like traits, which has implications for cancer therapy and might also be The cellular changes during an epithelial–mesenchymal transition important for colonization at distant organs (Chaffer and Weinberg, (EMT) largely rely on global changes in gene expression 2011; Magee et al., 2012; Polyak and Weinberg, 2009; Scheel and orchestrated by transcription factors. Tead transcription factors Weinberg, 2012). Among the many genes and signaling pathways and their transcriptional co-activators Yap and Taz have been active during EMT, transcription factors are the master coordinators previously implicated in promoting an EMT; however, their direct of the EMT program (Acloque et al., 2009; Moreno-Bueno et al., transcriptional target genes and their functional role during EMT 2008; Nieto, 2011). have remained elusive. We have uncovered a previously The Hippo tumor suppressor signaling pathway plays a critical unanticipated role of the transcription factor Tead2 during EMT. role in restricting organ size by antagonizing the oncogenic During EMT in mammary gland epithelial cells and breast cancer transcriptional co-activators Yap and Taz (Hong and Guan, 2012; cells, levels of Tead2 increase in the nucleus of cells, thereby Zhao et al., 2011). A complex network of cell adhesion and signaling directing a predominant nuclear localization of its co-factors molecules, including the tumor suppressor neurofibromin-2/ Yap and Taz via the formation of Tead2–Yap–Taz complexes. -
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. -
UNIVERSITY of CALIFORNIA, IRVINE Combinatorial Regulation By
UNIVERSITY OF CALIFORNIA, IRVINE Combinatorial regulation by maternal transcription factors during activation of the endoderm gene regulatory network DISSERTATION submitted in partial satisfaction of the requirements for the degree of DOCTOR OF PHILOSOPHY in Biological Sciences by Kitt D. Paraiso Dissertation Committee: Professor Ken W.Y. Cho, Chair Associate Professor Olivier Cinquin Professor Thomas Schilling 2018 Chapter 4 © 2017 Elsevier Ltd. © 2018 Kitt D. Paraiso DEDICATION To the incredibly intelligent and talented people, who in one way or another, helped complete this thesis. ii TABLE OF CONTENTS Page LIST OF FIGURES vii LIST OF TABLES ix LIST OF ABBREVIATIONS X ACKNOWLEDGEMENTS xi CURRICULUM VITAE xii ABSTRACT OF THE DISSERTATION xiv CHAPTER 1: Maternal transcription factors during early endoderm formation in 1 Xenopus Transcription factors co-regulate in a cell type-specific manner 2 Otx1 is expressed in a variety of cell lineages 4 Maternal otx1 in the endodermal conteXt 5 Establishment of enhancers by maternal transcription factors 9 Uncovering the endodermal gene regulatory network 12 Zygotic genome activation and temporal control of gene eXpression 14 The role of maternal transcription factors in early development 18 References 19 CHAPTER 2: Assembly of maternal transcription factors initiates the emergence 26 of tissue-specific zygotic cis-regulatory regions Introduction 28 Identification of maternal vegetally-localized transcription factors 31 Vegt and OtX1 combinatorially regulate the endodermal 33 transcriptome iii -
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. -
SUPPLEMENTARY MATERIAL Bone Morphogenetic Protein 4 Promotes
www.intjdevbiol.com doi: 10.1387/ijdb.160040mk SUPPLEMENTARY MATERIAL corresponding to: Bone morphogenetic protein 4 promotes craniofacial neural crest induction from human pluripotent stem cells SUMIYO MIMURA, MIKA SUGA, KAORI OKADA, MASAKI KINEHARA, HIROKI NIKAWA and MIHO K. FURUE* *Address correspondence to: Miho Kusuda Furue. Laboratory of Stem Cell Cultures, National Institutes of Biomedical Innovation, Health and Nutrition, 7-6-8, Saito-Asagi, Ibaraki, Osaka 567-0085, Japan. Tel: 81-72-641-9819. Fax: 81-72-641-9812. E-mail: [email protected] Full text for this paper is available at: http://dx.doi.org/10.1387/ijdb.160040mk TABLE S1 PRIMER LIST FOR QRT-PCR Gene forward reverse AP2α AATTTCTCAACCGACAACATT ATCTGTTTTGTAGCCAGGAGC CDX2 CTGGAGCTGGAGAAGGAGTTTC ATTTTAACCTGCCTCTCAGAGAGC DLX1 AGTTTGCAGTTGCAGGCTTT CCCTGCTTCATCAGCTTCTT FOXD3 CAGCGGTTCGGCGGGAGG TGAGTGAGAGGTTGTGGCGGATG GAPDH CAAAGTTGTCATGGATGACC CCATGGAGAAGGCTGGGG MSX1 GGATCAGACTTCGGAGAGTGAACT GCCTTCCCTTTAACCCTCACA NANOG TGAACCTCAGCTACAAACAG TGGTGGTAGGAAGAGTAAAG OCT4 GACAGGGGGAGGGGAGGAGCTAGG CTTCCCTCCAACCAGTTGCCCCAAA PAX3 TTGCAATGGCCTCTCAC AGGGGAGAGCGCGTAATC PAX6 GTCCATCTTTGCTTGGGAAA TAGCCAGGTTGCGAAGAACT p75 TCATCCCTGTCTATTGCTCCA TGTTCTGCTTGCAGCTGTTC SOX9 AATGGAGCAGCGAAATCAAC CAGAGAGATTTAGCACACTGATC SOX10 GACCAGTACCCGCACCTG CGCTTGTCACTTTCGTTCAG Suppl. Fig. S1. Comparison of the gene expression profiles of the ES cells and the cells induced by NC and NC-B condition. Scatter plots compares the normalized expression of every gene on the array (refer to Table S3). The central line -
The Camp Signaling System Regulates Lhβ Gene Expression: Roles of Early
291 The cAMP signaling system regulates LH gene expression: roles of early growth response protein-1, SP1 and steroidogenic factor-1 C D Horton and L M Halvorson Division of Reproductive Endocrinology, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9032, USA (Requests for offprints should be addressed to L M Halvorson; Email: [email protected]) Abstract Expression of the gonadotropin genes has been shown to be modulated by pharmacological or physiological activators of both the protein kinase C (PKC) and the cAMP second messenger signaling pathways. Over the past few years, a substantial amount of progress has been made in the identification and characterization of the transcription factors and cognate cis-elements which mediate the PKC response in the LH -subunit (LH) gene. In contrast, little is known regarding the molecular mechanisms which mediate cAMP-mediated regulation of this gene. Using pituitary cell lines, we now demonstrate that rat LH gene promoter activity is stimulated following activation of the cAMP system by the adenylate cyclase activating agent, forskolin, or by the peptide, pituitary adenylate cyclase-activating peptide. The forskolin response was eliminated with mutation of a previously identified 3′ cis-acting element for the early growth response protein-1 (Egr-1) when evaluated in the context of region −207/+5 of the LH gene. Activation of the cAMP system increased Egr-1 gene promoter activity, Egr-1 protein levels and Egr-1 binding to the LH gene promoter, supporting the role of this transcription factor in mediating the cAMP response. Analysis of a longer LH promoter construct (−797/+5) revealed additional contribution by upstream Sp1 DNA-regulatory regions. -
Otx1 and Otx2 in Inner Ear Development 2337 by BMP4 Expression (Lc in Fig
Development 126, 2335-2343 (1999) 2335 Printed in Great Britain © The Company of Biologists Limited 1999 DEV1416 Otx1 and Otx2 activities are required for the normal development of the mouse inner ear Hakim Morsli1, Francesca Tuorto2, Daniel Choo1,*, Maria Pia Postiglione2, Antonio Simeone2 and Doris K. Wu1,‡ 1National Institute on Deafness and Other Communication Disorders, 5 Research Ct., Rockville, MD 20850, USA 2International Institute of Genetics and Biophysics, CNR, Via G. Marconi, 12, 80125 Naples, Italy *Present address: Children’s Hospital Medical Center of Cincinnati, Department of Otolaryngology, 3333 Burnet Ave., Cincinnati, OH 45229, USA ‡Author for correspondence (e-mail: [email protected]) Accepted 12 March; published on WWW 4 May 1999 SUMMARY The Otx1 and Otx2 genes are two murine orthologues of variable in Otx1−/− mice and were much more severe the Orthodenticle (Otd) gene in Drosophila. In the in an Otx1−/−;Otx2+/− background. Histological and in developing mouse embryo, both Otx genes are expressed situ hybridization experiments of both Otx1−/− and in the rostral head region and in certain sense organs such Otx1−/−;Otx2+/− mutants revealed that the lateral crista as the inner ear. Previous studies have shown that mice was absent. In addition, the maculae of the utricle and lacking Otx1 display abnormal patterning of the brain, saccule were partially fused. In mutant mice in which whereas embryos lacking Otx2 develop without heads. In both copies of the Otx1 gene were replaced with a human this study, we examined, at different developmental Otx2 cDNA (hOtx21/ hOtx21), most of the defects stages, the inner ears of mice lacking both Otx1 and Otx2 associated with Otx1−/− mutants were rescued. -
Supplement-Molecular Sys Biology
Supplementary Material for: Iwona Stelniec-Klotz, Stefan Legewie, Oleg Tchernitsa, Franziska Witzel, Bertram Klinger, Christine Sers, Hanspeter Herzel, Nils Blüthgen and Reinhold Schäfer: Reverse-engineering a hierarchical regulatory network downstream of oncogenic KRAS Content (9 Figures, 3 Tables, 1 Text, 1 List of References) Supplementary Figures S1: Nuclear protein levels of Fosl1, Hmga2, Klf6, JunB, Otx1, Gfi1, RelA after silencing in KRAS-transformed RAS-ROSE cells. S2: Impact of transcription factor knock-down on the KRAS pathway-mediated mRNA expression profile S3: RNA expression of Fosl1, Hmga2, Klf6, JunB, Otx1, Gfi1, RelA after silencing in KRAS- transformed RAS-ROSE cells S4: Effects of Fosl1, Hmga2, Klf6, JunB, Otx1, Gfi1, RelA knock-down in RAS-ROSE cells on the activity of cytoplasmic signaling downstream of RAS S5: Effect of Fosl1 overepxression and Otx1 knockdown on Fosl1mRNA and phospho-Erk. S6: Effects on growth characteristics of RAS-ROSE cells after silencing Fosl1, Hmga2, Klf6, JunB S7: Effects on growth characteristics of RAS-ROSE cells after silencing Otx1, Gfi1, RelA S8: Effects on distribution of cell cycle phases in KRAS-transformed RAS-ROSE cells after silencing of Fosl1, Hmga2, Klf6, JunB, Otx1, Gfi1, RelA S9: Effect of perturbation strength and noise on algorithm performance. Supplementary Tables S1: Rules for finding transcription factor-related patterns in genome-wide expression data (related to Fig. 3B and C). S2: Known interaction (related to Fig. 4) S3: Quantification of the network. Supplementary Texts Generation of artificial data sets Supplementary References Supplementary Fig. 1 Nuclear protein levels of Fosl1, Hmga2, Klf6, JunB, Otx1, Gfi1, RelA after silencing in KRAS-transformed RAS-ROSE cells.