Hippo Pathway and YAP Signaling Alterations in Squamous Cancer of the Head and Neck
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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. -
Common and Distinctive Functions of the Hippo Effectors Taz and Yap In
TISSUE-SPECIFIC STEM CELLS aRandall Division of Cell and Common and Distinctive Functions of the Hippo Molecular Biophysics, King’s College London, London, UK; Effectors Taz and Yap in Skeletal Muscle Stem Cell bSchool of Medicine, Medical Sciences & Nutrition, Function University of Aberdeen, Foresterhill, Aberdeen, a b b a Scotland, UK; cSystems CONGSHAN SUN, VANESSA DE MELLO, ABDALLA MOHAMED, HUASCAR P. O RTUSTE QUIROGA, c b d,e,f Biology Ireland, Conway AMAYA GARCIA-MUNOZ, ABDULLAH AL BLOSHI, ANNIE M. TREMBLAY, c g b c Institute, Dublin, Ireland; ALEXANDER VON KRIEGSHEIM, ELAINA COLLIE-DUGUID, NEIL VARGESSON, DAVID MATALLANAS, d b,h a Stem Cell Program, HENNING WACKERHAGE, PETER S. ZAMMIT Children’s Hospital, Boston, Massachusetts, USA; Key Words. Taz • Yap • Tead • Satellite cells • Muscle stem cells eDepartment of Stem Cell and Regenerative Biology, Harvard University, ABSTRACT Cambridge, Massachusetts, USA; fHarvard Stem Cell Hippo pathway downstream effectors Yap and Taz play key roles in cell proliferation and regen- Institute, Cambridge, eration, regulating gene expression especially via Tead transcription factors. To investigate their Massachusetts, USA; gCentre role in skeletal muscle stem cells, we analyzed Taz in vivo and ex vivo in comparison with Yap. for Genome Enabled Biology Small interfering RNA knockdown or retroviral-mediated expression of wild-type human or con- and Medicine, School of stitutively active TAZ mutants in satellite cells showed that TAZ promoted proliferation, a func- Medicine, Medical Sciences tion shared with YAP. However, at later stages of myogenesis, TAZ also enhanced myogenic and Nutrition, University of differentiation of myoblasts, whereas YAP inhibits such differentiation. Functionally, while mus- Aberdeen, Foresterhill, cle growth was mildly affected in Taz (gene Wwtr1–/–) knockout mice, there were no overt Aberdeen, Scotland, UK; effects on regeneration. -
The Legionella Kinase Legk7 Exploits the Hippo Pathway Scaffold Protein MOB1A for Allostery and Substrate Phosphorylation
The Legionella kinase LegK7 exploits the Hippo pathway scaffold protein MOB1A for allostery and substrate phosphorylation Pei-Chung Leea,b,1, Ksenia Beyrakhovac,1, Caishuang Xuc, Michal T. Bonieckic, Mitchell H. Leea, Chisom J. Onub, Andrey M. Grishinc, Matthias P. Machnera,2, and Miroslaw Cyglerc,2 aDivision of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD 20892; bDepartment of Biological Sciences, College of Liberal Arts and Sciences, Wayne State University, Detroit, MI 48202; and cDepartment of Biochemistry, University of Saskatchewan, Saskatoon, SK S7N5E5, Canada Edited by Ralph R. Isberg, Tufts University School of Medicine, Boston, MA, and approved May 1, 2020 (received for review January 12, 2020) During infection, the bacterial pathogen Legionella pneumophila Active LATS1/2 phosphorylate the cotranscriptional regulator manipulates a variety of host cell signaling pathways, including YAP1 (yes-associated protein 1) and its homolog TAZ (tran- the Hippo pathway which controls cell proliferation and differen- scriptional coactivator with PDZ-binding motif). Phosphorylated tiation in eukaryotes. Our previous studies revealed that L. pneu- YAP1 and TAZ are prevented from entering the nucleus by being mophila encodes the effector kinase LegK7 which phosphorylates either sequestered in the cytosol through binding to 14-3-3 pro- MOB1A, a highly conserved scaffold protein of the Hippo path- teins or targeted for proteolytic degradation (6, 8). Consequently, way. Here, we show that MOB1A, in addition to being a substrate the main outcome of signal transduction along the Hippo pathway of LegK7, also functions as an allosteric activator of its kinase is changes in gene expression (6). -
DNA-Damage Induced Cell Death in Yap1;Wwtr1 Mutant Epidermal Basal Cells
bioRxiv preprint doi: https://doi.org/10.1101/2021.07.23.453490; this version posted July 23, 2021. 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. 1 DNA-damage induced cell death in yap1;wwtr1 mutant epidermal basal cells 2 Jason K. H. Lai1,*, Pearlyn J. Y. Toh1, Hamizah A. Cognart1, Geetika Chouhan2 & Timothy 3 E. Saunders1,3,4,5,* 4 1 Mechanobiology Institute, National University of Singapore, Singapore 117411 5 2 Department of Biological Sciences, Tata Institute of Fundamental Research, Colaba, 6 Mumbai, India 7 3 Department of Biological Sciences, National University of Singapore, Singapore 117558 8 4 Institute of Molecular and Cell Biology, A*Star, Singapore 9 5 Warwick Medical School, University of Warwick, United Kingdom 10 * Corresponding authors: J. K. H. L. ([email protected]), T. E. S. 11 ([email protected]) 12 1 bioRxiv preprint doi: https://doi.org/10.1101/2021.07.23.453490; this version posted July 23, 2021. 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. 13 ABSTRACT 14 In a previous study, it was reported that Yap1 and Wwtr1 in zebrafish regulates the 15 morphogenesis of the posterior body and epidermal fin fold (Kimelman, D., et al. -
The Role of the C-Terminus Merlin in Its Tumor Suppressor Function Vinay Mandati
The role of the C-terminus Merlin in its tumor suppressor function Vinay Mandati To cite this version: Vinay Mandati. The role of the C-terminus Merlin in its tumor suppressor function. Agricultural sciences. Université Paris Sud - Paris XI, 2013. English. NNT : 2013PA112140. tel-01124131 HAL Id: tel-01124131 https://tel.archives-ouvertes.fr/tel-01124131 Submitted on 19 Mar 2015 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. 1 TABLE OF CONTENTS Abbreviations ……………………………………………………………………………...... 8 Resume …………………………………………………………………………………… 10 Abstract …………………………………………………………………………………….. 11 1. Introduction ………………………………………………………………………………12 1.1 Neurofibromatoses ……………………………………………………………………….14 1.2 NF2 disease ………………………………………………………………………………15 1.3 The NF2 gene …………………………………………………………………………….17 1.4 Mutational spectrum of NF2 gene ………………………………………………………..18 1.5 NF2 in other cancers ……………………………………………………………………...20 2. ERM proteins and Merlin ……………………………………………………………….21 2.1 ERMs ……………………………………………………………………………………..21 2.1.1 Band 4.1 Proteins and ERMs …………………………………………………………...21 2.1.2 ERMs structure ………………………………………………………………………....23 2.1.3 Sub-cellular localization and tissue distribution of ERMs ……………………………..25 2.1.4 ERM proteins and their binding partners ……………………………………………….25 2.1.5 Assimilation of ERMs into signaling pathways ………………………………………...26 2.1.5. A. ERMs and Ras signaling …………………………………………………...26 2.1.5. B. ERMs in membrane transport ………………………………………………29 2.1.6 ERM functions in metastasis …………………………………………………………...30 2.1.7 Regulation of ERM proteins activity …………………………………………………...31 2.1.7. -
Whole-Exome Sequencing of Metastatic Cancer and Biomarkers of Treatment Response
Supplementary Online Content Beltran H, Eng K, Mosquera JM, et al. Whole-exome sequencing of metastatic cancer and biomarkers of treatment response. JAMA Oncol. Published online May 28, 2015. doi:10.1001/jamaoncol.2015.1313 eMethods eFigure 1. A schematic of the IPM Computational Pipeline eFigure 2. Tumor purity analysis eFigure 3. Tumor purity estimates from Pathology team versus computationally (CLONET) estimated tumor purities values for frozen tumor specimens (Spearman correlation 0.2765327, p- value = 0.03561) eFigure 4. Sequencing metrics Fresh/frozen vs. FFPE tissue eFigure 5. Somatic copy number alteration profiles by tumor type at cytogenetic map location resolution; for each cytogenetic map location the mean genes aberration frequency is reported eFigure 6. The 20 most frequently aberrant genes with respect to copy number gains/losses detected per tumor type eFigure 7. Top 50 genes with focal and large scale copy number gains (A) and losses (B) across the cohort eFigure 8. Summary of total number of copy number alterations across PM tumors eFigure 9. An example of tumor evolution looking at serial biopsies from PM222, a patient with metastatic bladder carcinoma eFigure 10. PM12 somatic mutations by coverage and allele frequency (A) and (B) mutation correlation between primary (y- axis) and brain metastasis (x-axis) eFigure 11. Point mutations across 5 metastatic sites of a 55 year old patient with metastatic prostate cancer at time of rapid autopsy eFigure 12. CT scans from patient PM137, a patient with recurrent platinum refractory metastatic urothelial carcinoma eFigure 13. Tracking tumor genomics between primary and metastatic samples from patient PM12 eFigure 14. -
Αe-Catenin Inhibits a Src–YAP1 Oncogenic Module That Couples Tyrosine Kinases and the Effector of Hippo Signaling Pathway
Downloaded from genesdev.cshlp.org on September 30, 2021 - Published by Cold Spring Harbor Laboratory Press αE-catenin inhibits a Src–YAP1 oncogenic module that couples tyrosine kinases and the effector of Hippo signaling pathway Peng Li,1,4 Mark R. Silvis,1,4 Yuchi Honaker,1,4 Wen-Hui Lien,1,3 Sarah T. Arron,2 and Valeri Vasioukhin1 1Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA; 2Department of Dermatology, University of California at San Fricisco, San Francisco, California, 94143, USA Cell–cell adhesion protein αE-catenin inhibits skin squamous cell carcinoma (SCC) development; however, the mechanisms responsible for this function are not completely understood. We report here that αE-catenin inhibits β4 integrin-mediated activation of SRC tyrosine kinase. SRC is the first discovered oncogene, but the protein substrate critical for SRC-mediated transformation has not been identified. We found that YAP1, the pivotal effector of the Hippo signaling pathway, is a direct SRC phosphorylation target, and YAP1 phosphorylation at three sites in its transcription activation domain is necessary for SRC–YAP1-mediated transformation. We uncovered a marked in- crease in this YAP1 phosphorylation in human and mouse SCC tumors with low/negative expression of αE-catenin. We demonstrate that the tumor suppressor function of αE-catenin involves negative regulation of the β4 integrin– SRC signaling pathway and that SRC-mediated phosphorylation and activation of YAP1 are an alternative to the canonical Hippo signaling pathway that directly connect oncogenic tyrosine kinase signaling with YAP1. [Keywords: αE-catenin; SRC; YAP1; SCC; keratinocytes; skin] Supplemental material is available for this article. -
YAP1 Monoclonal Antibody
For Research Use Only YAP1 Monoclonal antibody Catalog Number:66900-1-Ig Featured Product 10 Publications www.ptgcn.com Catalog Number: GenBank Accession Number: CloneNo.: Basic Information 66900-1-Ig BC038235 3A7A9 Size: GeneID (NCBI): Recommended Dilutions: 1000 μg/ml 10413 WB 1:2000-1:8000 Source: Full Name: IHC 1:1000-1:4000 Mouse Yes-associated protein 1, 65kDa IF 1:50-1:500 Isotype: Calculated MW: IgG1 504 aa, 54 kDa Purification Method: Observed MW: Protein G purification 70 kDa Immunogen Catalog Number: AG28194 Applications Tested Applications: Positive Controls: IF, IHC, WB,ELISA WB : HeLa cells; HSC-T6 cells, NIH/3T3 cells, MCF-7 Cited Applications: cells, HUVEC cells IF, IHC, WB IHC : human lung cancer tissue; human colon cancer Species Specificity: tissue, human liver cancer tissue, human ovary tumor Human, mouse, rat tissue Cited Species: IF : HepG2 cells; human, mouse, rat Note-IHC: suggested antigen retrieval with TE buffer pH 9.0; (*) Alternatively, antigen retrieval may be performed with citrate buffer pH 6.0 Yes-associated protein 1 (YAP1) is a transcriptional regulator which can act both as a coactivator and a corepressor Background Information and is the critical downstream regulatory target in the Hippo signaling pathway that plays a pivotal role in organ size control and tumor suppression by restricting proliferation and promoting apoptosis. The core of this pathway is composed of a kinase cascade wherein STK3/MST2 and STK4/MST1, in complex with its regulatory protein SAV1, phosphorylates and activates LATS1/2 in complex with its regulatory protein MOB1, which in turn phosphorylates and inactivates YAP1 oncoprotein and WWTR1/TAZ. -
YAP OFF, YAP on by Michael Leviten, Senior Writer Vivace Therapeutics Inc
REPRINT FROM NOVEMBER 16, 2017 EMERGING COMPANY PROFILE YAP OFF, YAP ON By Michael Leviten, Senior Writer Vivace Therapeutics Inc. exploits opposite angles of the Hippo-YAP pathway, with first-in-class inhibitors that turn VIVACE THERAPEUTICS INC., San Mateo, Calif. it off in cancers with activating mutations and activators Technology: Hippo-YAP pathway modulators as targeted therapies or that turn it on to enhance tumor immunogenicity in other immuno-oncology agents Disease focus: Cancer cancers. The newco emerged from stealth mode this summer Clinical status: Preclinical after closing a $25 million Series B led by China-based Founded: 2015 by Sofie Qiao, Tim Shannon, Edward Hu, Kun-Liang Guan, Bin Cenova Capital. Liu, Sheng Ding The Hippo-YAP pathway regulates cell growth and survival. University collaborators: University of California San Diego, University of Under normal conditions, Hippo signaling phosphorylates California San Francisco Corporate partners: None YAP1 and silences it. But under cellular stress, G-protein Number of employees: Five signaling dephosphorylates YAP1, triggering its Funds raised: $40 million translocation to the nucleus where it induces expression of Investors: Canaan Partners, WuXi Healthcare Ventures, Mission Bay Capital, survival genes. Cenova Capital and Sequoia Capital China Several cancers co-opt the pathway for survival and proliferation. CEO: Sofie Qiao About 85% of uveal melanomas have activating mutations in Patents: None issued the G-proteins GαQ and GNA11, 70% of mesotheliomas have activated YAP1, and YAP1 gene amplifications occur in about 25% of all lung, cervical and thyroid cancers. ReliTrexed, an injectable formulation of pemetrexed, for Because the pathway has been difficult to drug, Vivace took a mesothelioma, with at least 30 more compounds in the target-agnostic approach in undisclosed cancer cell lines to clinic. -
Human Induced Pluripotent Stem Cell–Derived Podocytes Mature Into Vascularized Glomeruli Upon Experimental Transplantation
BASIC RESEARCH www.jasn.org Human Induced Pluripotent Stem Cell–Derived Podocytes Mature into Vascularized Glomeruli upon Experimental Transplantation † Sazia Sharmin,* Atsuhiro Taguchi,* Yusuke Kaku,* Yasuhiro Yoshimura,* Tomoko Ohmori,* ‡ † ‡ Tetsushi Sakuma, Masashi Mukoyama, Takashi Yamamoto, Hidetake Kurihara,§ and | Ryuichi Nishinakamura* *Department of Kidney Development, Institute of Molecular Embryology and Genetics, and †Department of Nephrology, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan; ‡Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Hiroshima, Japan; §Division of Anatomy, Juntendo University School of Medicine, Tokyo, Japan; and |Japan Science and Technology Agency, CREST, Kumamoto, Japan ABSTRACT Glomerular podocytes express proteins, such as nephrin, that constitute the slit diaphragm, thereby contributing to the filtration process in the kidney. Glomerular development has been analyzed mainly in mice, whereas analysis of human kidney development has been minimal because of limited access to embryonic kidneys. We previously reported the induction of three-dimensional primordial glomeruli from human induced pluripotent stem (iPS) cells. Here, using transcription activator–like effector nuclease-mediated homologous recombination, we generated human iPS cell lines that express green fluorescent protein (GFP) in the NPHS1 locus, which encodes nephrin, and we show that GFP expression facilitated accurate visualization of nephrin-positive podocyte formation in -
Recurrent YAP1-MAML2 and YAP1-NUTM1 Fusions in Poroma and Porocarcinoma
Recurrent YAP1-MAML2 and YAP1-NUTM1 fusions in poroma and porocarcinoma Shigeki Sekine, … , Naoya Yamazaki, Taisuke Mori J Clin Invest. 2019;129(9):3827-3832. https://doi.org/10.1172/JCI126185. Concise Communication Dermatology Oncology Poroma is a benign skin tumor exhibiting terminal sweat gland duct differentiation. The present study aimed to explore the potential role of gene fusions in the tumorigenesis of poromas. RNA sequencing and reverse transcription PCR identified highly recurrent YAP1-MAML2 and YAP1-NUTM1 fusions in poromas (92/104 lesions, 88.5%) and their rare malignant counterpart, porocarcinomas (7/11 lesions, 63.6%). A WWTR1-NUTM1 fusion was identified in a single lesion of poroma. Fluorescence in situ hybridization confirmed genomic rearrangements involving these genetic loci. Immunohistochemical staining could readily identify the YAP1 fusion products as nuclear expression of the N-terminal portion of YAP1 with a lack of the C-terminal portion. YAP1 and WWTR1, also known as YAP and TAZ, respectively, encode paralogous transcriptional activators of TEAD, which are negatively regulated by the Hippo signaling pathway. The YAP1 and WWTR1 fusions strongly transactivated a TEAD reporter and promoted anchorage-independent growth, confirming their tumorigenic roles. Our results demonstrate the frequent presence of transforming YAP1 fusions in poromas and porocarcinomas and suggest YAP1/TEAD-dependent transcription as a candidate therapeutic target against porocarcinoma. Find the latest version: https://jci.me/126185/pdf The Journal of Clinical Investigation CONCISE COMMUNICATION Recurrent YAP1-MAML2 and YAP1-NUTM1 fusions in poroma and porocarcinoma Shigeki Sekine,1,2 Tohru Kiyono,3,4 Eijitsu Ryo,2 Reiko Ogawa,2 Susumu Wakai,1 Hitoshi Ichikawa,5 Koyu Suzuki,6 Satoru Arai,7 Koji Tsuta,8 Mitsuaki Ishida,8 Yuko Sasajima,9 Naoki Goshima,10 Naoya Yamazaki,11 and Taisuke Mori1,2 1Department of Diagnostic Pathology, National Cancer Center Hospital, Tokyo, Japan. -
Systematic Morphological Profiling of Human Gene and Allele Function Via
TOOLS AND RESOURCES Systematic morphological profiling of human gene and allele function via Cell Painting Mohammad Hossein Rohban1, Shantanu Singh1, Xiaoyun Wu1, Julia B Berthet2, Mark-Anthony Bray1†, Yashaswi Shrestha1, Xaralabos Varelas2, Jesse S Boehm1, Anne E Carpenter1* 1Broad Institute of MIT and Harvard, Cambridge, United States; 2Department of Biochemistry, Boston University School of Medicine, Boston, United States Abstract We hypothesized that human genes and disease-associated alleles might be systematically functionally annotated using morphological profiling of cDNA constructs, via a microscopy-based Cell Painting assay. Indeed, 50% of the 220 tested genes yielded detectable morphological profiles, which grouped into biologically meaningful gene clusters consistent with known functional annotation (e.g., the RAS-RAF-MEK-ERK cascade). We used novel subpopulation- based visualization methods to interpret the morphological changes for specific clusters. This unbiased morphologic map of gene function revealed TRAF2/c-REL negative regulation of YAP1/ WWTR1-responsive pathways. We confirmed this discovery of functional connectivity between the NF-kB pathway and Hippo pathway effectors at the transcriptional level, thereby expanding knowledge of these two signaling pathways that critically regulate tumor initiation and progression. We make the images and raw data publicly available, providing an initial morphological map of *For correspondence: anne@ major biological pathways for future study. broadinstitute.org DOI: 10.7554/eLife.24060.001 Present address: †Novartis Institutes for BioMedical Research, Cambridge, United States Introduction Competing interests: The The dramatic increase in human genome sequence data has created a significant bottleneck. The authors declare that no number of genes and variants known to be associated with most human diseases has increased dra- competing interests exist.