Ascl1 and Helt Act Combinatorially to Specify Thalamic Neuronal Identity by Repressing Dlxs Activation
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Uncovering the Signaling Landscape Controlling Breast Cancer Cell Migration Identifies Novel Metastasis Driver Genes
ARTICLE https://doi.org/10.1038/s41467-019-11020-3 OPEN Uncovering the signaling landscape controlling breast cancer cell migration identifies novel metastasis driver genes Esmee Koedoot1,4, Michiel Fokkelman 1,4, Vasiliki-Maria Rogkoti1,4, Marcel Smid2, Iris van de Sandt1, Hans de Bont1, Chantal Pont1, Janna E. Klip1, Steven Wink 1, Mieke A. Timmermans2, Erik A.C. Wiemer2, Peter Stoilov3, John A. Foekens2, Sylvia E. Le Dévédec 1, John W.M. Martens 2 & Bob van de Water1 1234567890():,; Ttriple-negative breast cancer (TNBC) is an aggressive and highly metastatic breast cancer subtype. Enhanced TNBC cell motility is a prerequisite of TNBC cell dissemination. Here, we apply an imaging-based RNAi phenotypic cell migration screen using two highly motile TNBC cell lines (Hs578T and MDA-MB-231) to provide a repository of signaling determinants that functionally drive TNBC cell motility. We have screened ~4,200 target genes individually and discovered 133 and 113 migratory modulators of Hs578T and MDA-MB-231, respectively, which are linked to signaling networks predictive for breast cancer progression. The splicing factors PRPF4B and BUD31 and the transcription factor BPTF are essential for cancer cell migration, amplified in human primary breast tumors and associated with metastasis-free survival. Depletion of PRPF4B, BUD31 and BPTF causes primarily down regulation of genes involved in focal adhesion and ECM-interaction pathways. PRPF4B is essential for TNBC metastasis formation in vivo, making PRPF4B a candidate for further drug development. 1 Division of Drug Discovery and Safety, LACDR, Leiden University, Einsteinweg 55, Leiden 2333 CC, Netherlands. 2 Department of Medical Oncology and Cancer Genomics Netherlands, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam 3008 AE, Netherlands. -
A Computational Approach for Defining a Signature of Β-Cell Golgi Stress in Diabetes Mellitus
Page 1 of 781 Diabetes A Computational Approach for Defining a Signature of β-Cell Golgi Stress in Diabetes Mellitus Robert N. Bone1,6,7, Olufunmilola Oyebamiji2, Sayali Talware2, Sharmila Selvaraj2, Preethi Krishnan3,6, Farooq Syed1,6,7, Huanmei Wu2, Carmella Evans-Molina 1,3,4,5,6,7,8* Departments of 1Pediatrics, 3Medicine, 4Anatomy, Cell Biology & Physiology, 5Biochemistry & Molecular Biology, the 6Center for Diabetes & Metabolic Diseases, and the 7Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202; 2Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, 46202; 8Roudebush VA Medical Center, Indianapolis, IN 46202. *Corresponding Author(s): Carmella Evans-Molina, MD, PhD ([email protected]) Indiana University School of Medicine, 635 Barnhill Drive, MS 2031A, Indianapolis, IN 46202, Telephone: (317) 274-4145, Fax (317) 274-4107 Running Title: Golgi Stress Response in Diabetes Word Count: 4358 Number of Figures: 6 Keywords: Golgi apparatus stress, Islets, β cell, Type 1 diabetes, Type 2 diabetes 1 Diabetes Publish Ahead of Print, published online August 20, 2020 Diabetes Page 2 of 781 ABSTRACT The Golgi apparatus (GA) is an important site of insulin processing and granule maturation, but whether GA organelle dysfunction and GA stress are present in the diabetic β-cell has not been tested. We utilized an informatics-based approach to develop a transcriptional signature of β-cell GA stress using existing RNA sequencing and microarray datasets generated using human islets from donors with diabetes and islets where type 1(T1D) and type 2 diabetes (T2D) had been modeled ex vivo. To narrow our results to GA-specific genes, we applied a filter set of 1,030 genes accepted as GA associated. -
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 -
Drosophila Valosin-Containing Protein Is Required for Dendrite Pruning Through a Regulatory Role in Mrna Metabolism
Drosophila Valosin-Containing Protein is required for dendrite pruning through a regulatory role in mRNA metabolism Sebastian Rumpfa,b,c,1,2, Joshua A. Bagleya,b,c, Katherine L. Thompson-Peera,b,c, Sijun Zhua,b,c,3, David Gorczycaa,b,c, Robert B. Becksteadd, Lily Yeh Jana,b,c, and Yuh Nung Jana,b,c,2 aHoward Hughes Medical Institute and Departments of bPhysiology and cBiochemistry, University of California, San Francisco, CA 94158; and dPoultry Science Department, University of Georgia, Athens, GA 30602 Contributed by Yuh Nung Jan, April 16, 2014 (sent for review December 20, 2013) The dendritic arbors of the larval Drosophila peripheral class IV for pruning (2, 7, 8), as well as the ATPase associated with di- dendritic arborization neurons degenerate during metamorphosis verse cellular activities (AAA) ATPase Valosin-Containing in an ecdysone-dependent manner. This process—also known as Protein (VCP) (CDC48 in yeast, p97 in vertebrates, also known dendrite pruning—depends on the ubiquitin–proteasome system as TER94 in Drosophila) (11), which acts as a chaperone for (UPS), but the specific processes regulated by the UPS during prun- ubiquitylated proteins (12). Interestingly, autosomal dominant ing have been largely elusive. Here, we show that mutation or mutations in the human VCP gene cause hereditary forms of inhibition of Valosin-Containing Protein (VCP), a ubiquitin-depen- ubiquitin-positive frontotemporal dementia (FTLD-U) (13) and dent ATPase whose human homolog is linked to neurodegenera- amyotrophic lateral sclerosis (ALS) (14). A hallmark of these tive disease, leads to specific defects in mRNA metabolism and that diseases is the occurrence of both cytosolic and nuclear ubiq- this role of VCP is linked to dendrite pruning. -
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 -
Exclusion of Dlx5/6 Expression from the Distal-Most Mandibular Arches Enables BMP-Mediated Specification of the Distal Cap
Exclusion of Dlx5/6 expression from the distal-most mandibular arches enables BMP-mediated specification of the distal cap Joshua W. Vincentza, Jose J. Casasnovasa, Ralston M. Barnesb, Jianwen Quec, David E. Clouthierd, Jun Wange, and Anthony B. Firullia,1 aRiley Heart Research Center, Herman B. Wells Center for Pediatric Research Division of Pediatric Cardiology, Departments of Anatomy, Biochemistry, and Medical and Molecular Genetics, Indiana University Medical School, Indianapolis, IN 46202; bBiologics Discovery California, Bristol-Myers Squibb, Redwood City, CA 94063; cDepartment of Medicine, Columbia University Medical Center, New York, NY 10032; dDepartment of Craniofacial Biology, University of Colorado Anschutz Medical Campus, Aurora, CO 80108; and eDepartment of Molecular Physiology and Biophysics, Texas Heart Institute, Baylor College of Medicine, Houston, TX 77030 Edited by Clifford J. Tabin, Harvard Medical School, Boston, MA, and approved May 26, 2016 (received for review March 8, 2016) Cranial neural crest cells (crNCCs) migrate from the neural tube to Smads, H2, and GATA2/3 provide positive transcriptional inputs the pharyngeal arches (PAs) of the developing embryo and, sub- that serve to counteract the activity of Dlx proteins, thereby re- sequently, differentiate into bone and connective tissue to form the lieving EDN1-meditated repression. Together, these findings in- mandible. Within the PAs, crNCCs respond to local signaling cues to tegrate the communication between BMP and EDN1 signaling partition into the proximo-distally oriented subdomains that convey that establishes the distal cap of the mandible. positional information to these developing tissues. Here, we show that the distal-most of these subdomains, the distal cap, is marked Results by expression of the transcription factor Hand1 (H1) and gives rise to The H1Cre Lineage Gives Rise to the Lower Incisors, in a HAND Factor- the ectomesenchymal derivatives of the lower incisors. -
Dlx5 and Dlx6 Expression in Gabaergic Neurons Controls Behavior, Metabolism, Healthy Aging and Lifespan
Dlx5 and Dlx6 expression in GABAergic neurons controls behavior, metabolism, healthy aging and lifespan. Camille de Lombares, Eglantine Heude, Gladys Alfama, Anastasia Fontaine, Rim Hassouna, Cecile Vernochet, Fabrice de Chaumont, Christophe Olivo-Marin, Elodie Ey, Sebastien Parnaudeau, et al. To cite this version: Camille de Lombares, Eglantine Heude, Gladys Alfama, Anastasia Fontaine, Rim Hassouna, et al.. Dlx5 and Dlx6 expression in GABAergic neurons controls behavior, metabolism, healthy aging and lifespan.. Aging, Impact Journals, 2019, 11 (17), pp.6638-6656. 10.18632/aging.102141. mnhn- 02295464 HAL Id: mnhn-02295464 https://hal-mnhn.archives-ouvertes.fr/mnhn-02295464 Submitted on 4 Feb 2020 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. Distributed under a Creative Commons Attribution| 4.0 International License www.aging-us.com AGING 2019, Vol. 11, No. 17 Research Paper Dlx5 and Dlx6 expression in GABAergic neurons controls behavior, metabolism, healthy aging and lifespan Camille de Lombares1, Eglantine Heude1, Gladys Alfama1, Anastasia Fontaine1, -
SOX2 and SOX12 Are Predictive of Prognosis in Patients with Clear Cell Renal Cell Carcinoma
4564 ONCOLOGY LETTERS 15: 4564-4570, 2018 SOX2 and SOX12 are predictive of prognosis in patients with clear cell renal cell carcinoma WEIJIE GU1,2*, BEIHE WANG1,2*, FANGNING WAN1,2*, JUNLONG WU1,2, XIAOLIN LU1,2, HONGKAI WANG1,2, YAO ZHU1,2, HAILIANG ZHANG1,2, GUOHAI SHI1,2, BO DAI1,2 and DINGWEI YE1,2 1Department of Urology, Fudan University Shanghai Cancer Center; 2Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, P.R. China Received October 21, 2016; Accepted September 28, 2017 DOI: 10.3892/ol.2018.7828 Abstract. Sex-determining region Y-box protein (SOX) genes were associated with poor prognosis for OS (log-rank test, all serve an important role in cancer growth and metastasis. P<0.05). SOX2 and SOX12 were identified as independent The present study aimed to determine the predictive ability prognostic factors of OS in clear cell RCC. of SOX and associated genes identified through molecular network in clear cell renal cell carcinoma (RCC). A total of Introduction 505 patients with clear cell RCC from The Cancer Genome Atlas (TCGA) cohorts were collected in this study. The Renal cell carcinoma (RCC) accounts for ~2-3% of all malig- expression profile of SOX and associated genes were obtained nancies worldwide (1). Despite an increasing proportion of from the TCGA RNAseq database. Clinicopathological patients with early stage tumors at diagnosis and the develop- characteristics, including age, gender, tumor grade, stage, ment of novel treatment strategies, a quarter still present with laterality disease-free-survival and overall survival (OS) were locally advanced or metastatic disease, and eventually, one collected. -
Loss of the Neural-Specific BAF Subunit ACTL6B Relieves Repression of Early Response Genes and Causes Recessive Autism
Loss of the neural-specific BAF subunit ACTL6B relieves repression of early response genes and causes recessive autism Wendy Wenderskia,b,c,d, Lu Wange,f,g,1, Andrey Krokhotina,b,c,d,1, Jessica J. Walshh, Hongjie Lid,i, Hirotaka Shojij, Shereen Ghoshe,f,g, Renee D. Georgee,f,g, Erik L. Millera,b,c,d, Laura Eliasa,b,c,d, Mark A. Gillespiek, Esther Y. Sona,b,c,d, Brett T. Staahla,b,c,d, Seung Tae Baeke,f,g, Valentina Stanleye,f,g, Cynthia Moncadaa,b,c,d, Zohar Shiponya,b,c,d, Sara B. Linkerl, Maria C. N. Marchettol, Fred H. Gagel, Dillon Chene,f,g, Tipu Sultanm, Maha S. Zakin, Jeffrey A. Ranishk, Tsuyoshi Miyakawaj, Liqun Luod,i, Robert C. Malenkah, Gerald R. Crabtreea,b,c,d,2, and Joseph G. Gleesone,f,g,2 aDepartment of Pathology, Stanford Medical School, Palo Alto, CA 94305; bDepartment of Genetics, Stanford Medical School, Palo Alto, CA 94305; cDepartment of Developmental Biology, Stanford Medical School, Palo Alto, CA 94305; dHoward Hughes Medical Institute, Stanford University, Palo Alto, CA 94305; eDepartment of Neuroscience, University of California San Diego, La Jolla, CA 92037; fHoward Hughes Medical Institute, University of California San Diego, La Jolla, CA 92037; gRady Children’s Institute of Genomic Medicine, University of California San Diego, La Jolla, CA 92037; hNancy Pritztker Laboratory, Department of Psychiatry and Behavioral Sciences, Stanford Medical School, Palo Alto, CA 94305; iDepartment of Biology, Stanford University, Palo Alto, CA 94305; jDivision of Systems Medical Science, Institute for Comprehensive Medical Science, Fujita Health University, 470-1192 Toyoake, Aichi, Japan; kInstitute for Systems Biology, Seattle, WA 98109; lLaboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA 92037; mDepartment of Pediatric Neurology, Institute of Child Health, Children Hospital Lahore, 54000 Lahore, Pakistan; and nClinical Genetics Department, Human Genetics and Genome Research Division, National Research Centre, 12311 Cairo, Egypt Edited by Arthur L. -
DLX Genes: Roles in Development and Cancer
cancers Review DLX Genes: Roles in Development and Cancer Yinfei Tan 1,* and Joseph R. Testa 1,2,* 1 Genomics Facility, Fox Chase Cancer Center, Philadelphia, PA 19111, USA 2 Cancer Signaling and Epigenetics Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA * Correspondence: [email protected] (Y.T.); [email protected] (J.R.T.) Simple Summary: DLX homeobox family genes encode transcription factors that have indispensable roles in embryonic and postnatal development. These genes are critically linked to the morphogene- sis of craniofacial structures, branchial arches, forebrain, and sensory organs. DLX genes are also involved in postnatal homeostasis, particularly hematopoiesis and, when dysregulated, oncogen- esis. DLX1/2, DLX3/4, and DLX5/6 exist as bigenes on different chromosomes, sharing intergenic enhancers between gene pairs, which allows orchestrated spatiotemporal expression. Genomic alterations of human DLX gene enhancers or coding sequences result in congenital disorders such as split-hand/foot malformation. Aberrant postnatal expression of DLX genes is associated with hematological malignancies, including leukemias and lymphomas. In several mouse models of T-cell lymphoma, Dlx5 has been shown to act as an oncogene by cooperating with activated Akt, Notch1/3, and/or Wnt to drive tumor formation. In humans, DLX5 is aberrantly expressed in lung and ovarian carcinomas and holds promise as a therapeutic target. Abstract: Homeobox genes control body patterning and cell-fate decisions during development. The homeobox genes consist of many families, only some of which have been investigated regarding a possible role in tumorigenesis. Dysregulation of HOX family genes have been widely implicated in cancer etiology. -
GATA Transcription Factors and Their Co-Regulators Guide the Development Of
GATA transcription factors and their co-regulators guide the development of GABAergic and serotonergic neurons in the anterior brainstem Laura Tikker Molecular and Integrative Biosciences Research Programme Faculty of Biological and Environmental Sciences Doctoral Programme Integrative Life Science University of Helsinki ACADEMIC DISSERTATION Doctoral thesis, to be presented for public examination, with the permission of the Faculty of Biological and Environmental Sciences of the University of Helsinki, in Raisio Hall (LS B2) in Forest Sciences building, Latokartanonkaari 7, Helsinki, on the 3rd of April, 2020 at 12 noon. Supervisor Professor Juha Partanen University of Helsinki (Finland) Thesis Committee members Docent Mikko Airavaara University of Helsinki (Finland) Professor Timo Otonkoski University of Helsinki (Finland) Pre-examinators Docent Satu Kuure University of Helsinki (Finland) Research Scientist Siew-Lan Ang, PhD The Francis Crick Institute (United Kingdom) Opponent Research Scientist Johan Holmberg, PhD Karolinska Institutet (Sweden) Custos Professor Juha Partanen University of Helsinki (Finland) The Faculty of Biological and Environmental Sciences, University of Helsinki, uses the Urkund system for plagiarism recognition to examine all doctoral dissertations. ISBN: 978-951-51-5930-4 (paperback) ISBN: 978-951-51-5931-1 (PDF) ISSN: 2342-3161 (paperback) ISSN: 2342-317X (PDF) Printing house: Painosalama Oy Printing location: Turku, Finland Printed on: 03.2020 Cover artwork: Serotonergic neurons in adult dorsal raphe (mouse). -
Transcriptional Profiling of Mesc-Derived Tendon And
ARTICLE https://doi.org/10.1038/s41467-021-24535-5 OPEN Transcriptional profiling of mESC-derived tendon and fibrocartilage cell fate switch ✉ Deepak A. Kaji1, Angela M. Montero1, Roosheel Patel2 & Alice H. Huang 1 The transcriptional regulators underlying induction and differentiation of dense connective tissues such as tendon and related fibrocartilaginous tissues (meniscus and annulus fibrosus) remain largely unknown. Using an iterative approach informed by developmental cues and 1234567890():,; single cell RNA sequencing (scRNA-seq), we establish directed differentiation models to generate tendon and fibrocartilage cells from mouse embryonic stem cells (mESCs) by activation of TGFβ and hedgehog pathways, achieving 90% induction efficiency. Transcrip- tional signatures of the mESC-derived cells recapitulate embryonic tendon and fibrocartilage signatures from the mouse tail. scRNA-seq further identify retinoic acid signaling as a critical regulator of cell fate switch between TGFβ-induced tendon and fibrocartilage lineages. Tra- jectory analysis by RNA sequencing define transcriptional modules underlying tendon and fibrocartilage fate induction and identify molecules associated with lineage-specific differ- entiation. Finally, we successfully generate 3-dimensional engineered tissues using these differentiation protocols and show activation of mechanotransduction markers with dynamic tensile loading. These findings provide a serum-free approach to generate tendon and fibrocartilage cells and tissues at high efficiency for modeling development and