Non-Coding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies

Total Page:16

File Type:pdf, Size:1020Kb

Non-Coding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies Author Manuscript Published OnlineFirst on March 18, 2020; DOI: 10.1158/2159-8290.CD-19-1128 Author manuscripts have been peer reviewed and accepted for publication but have not yet been edited. Non-Coding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies Kailong Li1,2,5, Yuannyu Zhang1,2,5, Xin Liu1,2,5, Yuxuan Liu1,2,5, Zhimin Gu1,2, Hui Cao1,2, Kathryn E. Dickerson1,2, Mingyi Chen3, Weina Chen3, Zhen Shao4, Min Ni1, Jian Xu1,2,* 1Children’s Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA 2Department of Pediatrics, Harold C. Simmons Comprehensive Cancer Center, and Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA 3Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA 4Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China 5These authors contributed equally *Corresponding Author: [email protected] (J.X.) Mailing address: 6000 Harry Hines Blvd. C. Kern Wildenthal Research Building – NL12.138B UT Southwestern Medical Center Dallas, Texas 75390-8502 Phone: 214-648-6125 Running Title: Non-Coding Variants in Hematopoietic Malignancies Keywords: Non-Coding Variants, Enhancers, Epigenetics, Leukemia, Nuclear Receptor Disclosure of Potential Conflicts of Interest: No potential conflicts of interest were disclosed. 1 Downloaded from cancerdiscovery.aacrjournals.org on September 30, 2021. © 2020 American Association for Cancer Research. Author Manuscript Published OnlineFirst on March 18, 2020; DOI: 10.1158/2159-8290.CD-19-1128 Author manuscripts have been peer reviewed and accepted for publication but have not yet been edited. ABSTRACT Mutations in protein-coding genes are well established as the basis for human cancer, yet it remains elusive how alterations within non-coding genome, a substantial fraction of which contain cis-regulatory elements (CREs), contribute to cancer pathophysiology. Here, we developed an integrative approach to systematically identify and characterize non-coding regulatory variants with functional consequences in human hematopoietic malignancies. Combining targeted resequencing of hematopoietic lineage-associated CREs and mutation discovery, we uncovered 1,836 recurrently mutated CREs containing leukemia-associated non- coding variants. By enhanced CRISPR/dCas9-based CRE perturbation screening and functional analyses, we identified 218 variant-associated oncogenic or tumor suppressive CREs in human leukemia. Non-coding variants at KRAS and PER2 enhancers reside in proximity to nuclear receptor (NR) binding regions and modulate transcriptional activities in response to NR signaling in leukemia cells. NR binding sites frequently co-localize with non-coding variants across cancer types. Hence, recurrent non-coding variants connect enhancer dysregulation with nuclear receptor signaling in hematopoietic malignancies. SIGNIFICANCE We describe an integrative approach to identify non-coding variants in human leukemia, and reveal cohorts of variant-associated oncogenic and tumor suppressive cis-elements including KRAS and PER2 enhancers. Our findings support a model that non-coding regulatory variants connect enhancer dysregulation with nuclear receptor signaling to modulate gene programs in hematopoietic malignancies. 2 Downloaded from cancerdiscovery.aacrjournals.org on September 30, 2021. © 2020 American Association for Cancer Research. Author Manuscript Published OnlineFirst on March 18, 2020; DOI: 10.1158/2159-8290.CD-19-1128 Author manuscripts have been peer reviewed and accepted for publication but have not yet been edited. INTRODUCTION Advances in genome sequencing have provided critical insights into the role of pathogenic DNA alterations as cancer drivers. However, current efforts are focused on protein-coding sequences (or exomes) consisting of only about 1% of human genome. It remains unclear how alterations within non-coding genome contribute to cancer pathophysiology. Similarly, genome-wide genotype-phenotype association studies continue to reveal non-coding sequences that are altered in human diseases, although identification of causal elements remains difficult impeding drug development and therapeutics. Enhancers are non-coding cis-regulatory elements (CREs) that determine cell identity by coordinating spatiotemporal gene expression. Major progress has been made to identify candidate enhancers by genome-wide mapping of enhancer-associated histone modifications including H3-Lys27 acetylation (H3K27ac) and H3-Lys4 mono-methylation (H3K4me1), transcription factors (TFs), and chromatin features (1-4). The biological significance of enhancers is underscored by gene expression studies showing the deterministic role of enhancers in directing cell-type-specific transcription (2,5-7). Highly marked clusters of enhancers or super-enhancers associated with developmental or cancer-related genes have been identified in various cell types (8-11). These studies suggest a model that a small set of lineage-defining enhancers determine cell identity in development and cancer. Emerging evidence points to a critical role of non-coding regulatory variants as cancer drivers (12,13). For instance, recurrent mutations in the TERT promoter create new binding motifs for ETS family TFs to enhance gene transcription in familial and sporadic melanoma (14,15). In the context of leukemia, recurrent non-coding mutations upstream of the TAL1 proto-oncogene introduce de novo binding sites for the MYB oncoprotein in T-cell leukemia. MYB associates with these sites with CBP, RUNX1 and TAL1 to create an oncogenic super-enhancer and activates TAL1 expression (16). In another example, a single chromosomal rearrangement repositions a GATA2 enhancer to ectopically activate EVI1 and confer GATA2 haploinsufficiency in inv(3)/t(3;3) acute myeloid leukemia (AML) (17). These studies raise important questions about the extent to which non-coding variants contribute to cancer development, and how they work. Moreover, the functional impact of non-coding somatic mutations found in cancer genome sequencing has not been systematically investigated or validated. The main challenges are to distinguish candidate non-coding cancer drivers from numerous non-functional passenger mutations and to establish causality of non-coding variants in cancer pathophysiology. Human nuclear receptors (NRs) are a family of signaling-activated TFs that play integral roles in development and cancer (18). The peroxisome proliferator-activated receptors (PPARα, β/δ, and γ) function as obligate heterodimers with the retinoid X receptors (RXRα, β, and γ) in the absence of ligands and bind to hormone response elements together with corepressor proteins. The retinoic acid receptors (RARα, β, and γ) also heterodimerize with RXRs and bind 3 Downloaded from cancerdiscovery.aacrjournals.org on September 30, 2021. © 2020 American Association for Cancer Research. Author Manuscript Published OnlineFirst on March 18, 2020; DOI: 10.1158/2159-8290.CD-19-1128 Author manuscripts have been peer reviewed and accepted for publication but have not yet been edited. constitutively to DNA in the absence of ligands. Binding of agonist ligands to PPAR/RXR or RAR/RXR complexes leads to dissociation of corepressors and recruitment of coactivator proteins, resulting in transcriptional activation of downstream target genes. The ability of NRs to rapidly and dynamically respond to various developmental and environmental clues by modulating gene programs makes them versatile cellular ‘sensors’. As such, NRs have historically served as biomarkers for classification of several solid tumors including breast and prostate cancers and targets for hormone therapy (19). In the hematopoietic system, the fusion oncogene PML-RARA provides a diagnostic biomarker for acute promyelocytic leukemia (APL) and the molecular basis for oncoprotein-targeted therapy (20). In this work, we developed an integrative approach to identify recurrent non-coding variants by targeted resequencing of cis-regulatory elements in human leukemia. A major limiting step towards understanding non-coding cancer variants is the lack of a high-throughput platform to assess their functional effects. To that end, we employed enhanced dCas9-based epigenetic editing and performed CRE perturbation screens. This revealed a cohort of variant-associated oncogenic and tumor suppressive CREs, and established a new molecular link between non- coding regulatory variants and nuclear receptor signaling in modifying gene programs in hematopoietic malignancies. RESULTS Identification of non-coding DNA alterations by targeted CRE resequencing To determine whether human leukemia genomes harbor recurrent non-coding alterations, we generated mutational landscapes of CREs by targeted resequencing (Fig. 1A; Fig. S1). We first annotated hematopoietic lineage-associated CREs based on genome-wide profiling of active enhancer or promoter-associated H3K27ac in various normal and diseased hematopoietic cell types, including CD34+ hematopoietic stem/progenitor cells (HSPCs), lymphocytes, macrophages, monocytes, erythroblasts, lymphoma, acute lymphoblastic leukemia (ALL), and AML (total 72 ChIP-seq datasets for 51 normal and 21 disease samples, respectively; Table S1 and Fig. S1A,B). We then designed a
Recommended publications
  • Table of Contents (PDF)
    July 26, 2011 u vol. 108 u no. 30 u 12187–12560 Cover image: Pictured is a Tasmanian devil (Sarcophilus harrisii), a carnivorous marsupial whose numbers are dwindling due to an infectious facial cancer called Devil Facial Tumor Disease. Webb Miller et al. sequenced the genome of devils from northwest and south- east Tasmania, spanning the range of this threatened species on the Australian island. The authors report that the sequences reveal a worrisome dearth of genetic diversity among devils, suggesting the need for genetically characterized stocks to help breed hardier devils that might be better equipped to fight diseases. See the article by Miller et al. on pages 12348–12353. Image courtesy of Stephan C. Schuster. From the Cover 12348 Decoding the Tasmanian devil genome 12283 Illuminating chromosomal architecture 12295 Symmetry of cultured cells 12319 Caloric restriction and infertility 12366 Genetic diversity among ants Contents COMMENTARIES 12189 Methyl fingerprinting of the nucleosome reveals the molecular mechanism of high-mobility group THIS WEEK IN PNAS nucleosomal-2 (HMGN2) association Catherine A. Musselman and Tatiana G. Kutateladze See companion article on page 12283 12187 In This Issue 12191 Examining the establishment of cellular axes using intrinsic chirality LETTERS (ONLINE ONLY) Jason C. McSheene and Rebecca D. Burdine See companion article on page 12295 E341 Difference between restoring and predicting 3D 12193 Secrets of palm oil biosynthesis revealed structures of the loops in G-protein–coupled Toni Voelker receptors by molecular modeling See companion article on page 12527 Gregory V. Nikiforovich, Christina M. Taylor, Garland R. Marshall, and Thomas J. Baranski E342 Reply to Nikiforovich et al.: Restoration of the loop regions of G-protein–coupled receptors Dahlia A.
    [Show full text]
  • Table S1 the Four Gene Sets Derived from Gene Expression Profiles of Escs and Differentiated Cells
    Table S1 The four gene sets derived from gene expression profiles of ESCs and differentiated cells Uniform High Uniform Low ES Up ES Down EntrezID GeneSymbol EntrezID GeneSymbol EntrezID GeneSymbol EntrezID GeneSymbol 269261 Rpl12 11354 Abpa 68239 Krt42 15132 Hbb-bh1 67891 Rpl4 11537 Cfd 26380 Esrrb 15126 Hba-x 55949 Eef1b2 11698 Ambn 73703 Dppa2 15111 Hand2 18148 Npm1 11730 Ang3 67374 Jam2 65255 Asb4 67427 Rps20 11731 Ang2 22702 Zfp42 17292 Mesp1 15481 Hspa8 11807 Apoa2 58865 Tdh 19737 Rgs5 100041686 LOC100041686 11814 Apoc3 26388 Ifi202b 225518 Prdm6 11983 Atpif1 11945 Atp4b 11614 Nr0b1 20378 Frzb 19241 Tmsb4x 12007 Azgp1 76815 Calcoco2 12767 Cxcr4 20116 Rps8 12044 Bcl2a1a 219132 D14Ertd668e 103889 Hoxb2 20103 Rps5 12047 Bcl2a1d 381411 Gm1967 17701 Msx1 14694 Gnb2l1 12049 Bcl2l10 20899 Stra8 23796 Aplnr 19941 Rpl26 12096 Bglap1 78625 1700061G19Rik 12627 Cfc1 12070 Ngfrap1 12097 Bglap2 21816 Tgm1 12622 Cer1 19989 Rpl7 12267 C3ar1 67405 Nts 21385 Tbx2 19896 Rpl10a 12279 C9 435337 EG435337 56720 Tdo2 20044 Rps14 12391 Cav3 545913 Zscan4d 16869 Lhx1 19175 Psmb6 12409 Cbr2 244448 Triml1 22253 Unc5c 22627 Ywhae 12477 Ctla4 69134 2200001I15Rik 14174 Fgf3 19951 Rpl32 12523 Cd84 66065 Hsd17b14 16542 Kdr 66152 1110020P15Rik 12524 Cd86 81879 Tcfcp2l1 15122 Hba-a1 66489 Rpl35 12640 Cga 17907 Mylpf 15414 Hoxb6 15519 Hsp90aa1 12642 Ch25h 26424 Nr5a2 210530 Leprel1 66483 Rpl36al 12655 Chi3l3 83560 Tex14 12338 Capn6 27370 Rps26 12796 Camp 17450 Morc1 20671 Sox17 66576 Uqcrh 12869 Cox8b 79455 Pdcl2 20613 Snai1 22154 Tubb5 12959 Cryba4 231821 Centa1 17897
    [Show full text]
  • Analysis and Characterisation of the Mouse Hic2 Gene
    Aus dem Institut für Entwicklungsgenetik des GSF-Forschungszentrums für Umwelt und Gesundheit, GmbH Direktor: Prof. Dr. Wolfgang Wurst Anfertigung unter der Leitung von Prof. Dr. Jochen Graw Vorgelegt über den Lehrstuhl für Molekulare Tierzucht und Biotechnologie Der Tierärztlichen Fakultät der Ludwig-Maximilians-Universität München Vorstand: Prof. Dr. Eckhard Wolf Untersuchung und Charakterisierung des Hic2-Gens der Maus Inaugural-Dissertation Zur Erlangung der tiermedizinischen Doktorwürde der Tierärztlichen Fakultät der Ludwig-Maximilians-Universität München von Aleksandra Terzic aus Sarajevo/Bosnia und Herzegowina München 2004 II Aus dem Institut für Entwicklungsgenetik des GSF-Forschungszentrums für Umwelt und Gesundheit, GmbH Direktor: Prof. Dr. Wolfgang Wurst Anfertigung unter der Leitung von Prof. Dr. Jochen Graw Vorgelegt über den Lehrstuhl für Molekulare Tierzucht und Biotechnologie Der Tierärztlichen Fakultät der Ludwig-Maximilians-Universität München Vorstand: Prof. Dr. Eckhard Wolf Analysis and characterisation of the mouse Hic2 gene Inaugural-Dissertation Zur Erlangung der tiermedizinischen Doktorwürde der Tierärztlichen Fakultät der Ludwig-Maximilians-Universität München von Aleksandra Terzic aus Sarajevo/Bosnia und Herzegowina München 2004 III Gedruckt mit Genehmigung der Tierärztlichen Fakultät der Ludwig-Maximilians-Universität München Dekan: Univ.-Prof. Dr. A.Stolle Referent: Univ.-Prof. Dr. E. Wolf Korreferent: Univ.-Prof. Dr. K. Heinritzi Tag der Promotion: 13. Februar 2004 IV List of contents 1 INTRODUCTION.............................................................................................................1
    [Show full text]
  • 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.
    [Show full text]
  • NPAS2 As a Transcriptional Regulator of Non-Rapid Eye Movement Sleep: Genotype and Sex Interactions
    NPAS2 as a transcriptional regulator of non-rapid eye movement sleep: Genotype and sex interactions Paul Franken*†‡, Carol A. Dudley§, Sandi Jo Estill§, Monique Barakat*, Ryan Thomason¶, Bruce F. O’Hara¶, and Steven L. McKnight‡§ §Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390; *Department of Biological Sciences, Stanford University, Stanford, CA 94305; ¶Department of Biology, University of Kentucky, Lexington, KY 40506; and †Center for Integrative Genomics, University of Lausanne, CH-1015 Lausanne-Dorigny, Switzerland Contributed by Steven L. McKnight, March 13, 2006 Because the transcription factor neuronal Per-Arnt-Sim-type sig- delta frequency range is a sensitive marker of time spent awake (4, nal-sensor protein-domain protein 2 (NPAS2) acts both as a sensor 7) and local cortical activation (8) and is therefore widely used as and an effector of intracellular energy balance, and because sleep an index of NREMS need and intensity. is thought to correct an energy imbalance incurred during waking, The PAS-domain proteins, CLOCK, BMAL1, PERIOD-1 we examined NPAS2’s role in sleep homeostasis using npas2 (PER1), and PER2, play crucial roles in circadian rhythm gener- knockout (npas2؊/؊) mice. We found that, under conditions of ation (9). The NPAS2 paralog CLOCK, like NPAS2, can induce the increased sleep need, i.e., at the end of the active period or after transcription of per1, per2, cryptochrome-1 (cry1), and cry2. PER and sleep deprivation (SD), NPAS2 allows for sleep to occur at times CRY proteins, in turn, inhibit CLOCK- and NPAS2-induced when mice are normally awake. Lack of npas2 affected electroen- transcription, thereby closing a negative-feedback loop that is cephalogram activity of thalamocortical origin; during non-rapid thought to underlie circadian rhythm generation.
    [Show full text]
  • Modeling the Phenotype of Spinal Muscular Atrophy by the Direct Conversion of Human Fibroblasts to Motor Neurons
    www.impactjournals.com/oncotarget/ Oncotarget, 2017, Vol. 8, (No. 7), pp: 10945-10953 Research Paper Modeling the phenotype of spinal muscular atrophy by the direct conversion of human fibroblasts to motor neurons Qi-Jie Zhang1,*, Jin-Jing Li1,*, Xiang Lin1, Ying-Qian Lu1, Xin-Xin Guo1, En-Lin Dong1, Miao Zhao1, Jin He1, Ning Wang1,2 and Wan-Jin Chen1,2 1 Department of Neurology and Institute of Neurology, First Affiliated Hospital, Fujian Medical University, Fuzhou, China 2 Fujian Key Laboratory of Molecular Neurology, Fuzhou, China * These authors have contributed equally to this work Correspondence to: Wan-Jin Chen, email: [email protected] Keywords: direct reprogramming; fibroblast; induced motor neuron; spinal muscular atrophy Received: June 08, 2016 Accepted: November 22, 2016 Published: January 13, 2017 ABSTRACT Spinal muscular atrophy (SMA) is a lethal autosomal recessive neurological disease characterized by selective degeneration of motor neurons in the spinal cord. In recent years, the development of cellular reprogramming technology has provided an alternative and effective method for obtaining patient-specific neuronsin vitro. In the present study, we applied this technology to the field of SMA to acquire patient- specific induced motor neurons that were directly converted from fibroblasts via the forced expression of 8 defined transcription factors. The infected fibroblasts began to grow in a dipolar manner, and the nuclei gradually enlarged. Typical Tuj1-positive neurons were generated at day 23. After day 35, induced neurons with multiple neurites were observed, and these neurons also expressed the hallmarks of Tuj1, HB9, ISL1 and CHAT. The conversion efficiencies were approximately 5.8% and 5.5% in the SMA and control groups, respectively.
    [Show full text]
  • Integrated Analysis of Differentially Expressed Genes in Breast Cancer Pathogenesis
    2560 ONCOLOGY LETTERS 9: 2560-2566, 2015 Integrated analysis of differentially expressed genes in breast cancer pathogenesis DAOBAO CHEN and HONGJIAN YANG Department of Breast Surgery, Zhejiang Cancer Hospital, Hangzhou, Zhejiang 310022, P.R. China Received October 20, 2014; Accepted March 10, 2015 DOI: 10.3892/ol.2015.3147 Abstract. The present study aimed to detect the differences ducts or from the lobules that supply the ducts (1). Breast between breast cancer cells and normal breast cells, and inves- cancer affects ~1.2 million women worldwide and accounts tigate the potential pathogenetic mechanisms of breast cancer. for ~50,000 mortalities every year (2). Despite major advances The sample GSE9574 series was downloaded, and the micro- in surgical and nonsurgical management of the disease, breast array data was analyzed to identify differentially expressed cancer metastasis remains a significant clinical challenge genes (DEGs). Gene Ontology (GO) cluster analysis using affecting numerous of patients (3). The prognosis and survival the GO Enrichment Analysis Software Toolkit platform and rates for breast cancer are highly variable, and depend on Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway the cancer type, treatment strategy, stage of the disease and analysis for DEGs was conducted using the Gene Set Analysis geographical location of the patient (4). Toolkit V2. In addition, a protein-protein interaction (PPI) Microarray technology, which may be used to simultane- network was constructed, and target sites of potential transcrip- ously interrogate 10,000-40,000 genes, has provided new tion factors and potential microRNA (miRNA) molecules were insight into the molecular classification of different cancer screened.
    [Show full text]
  • 2016 Joint Meeting Program
    April 15 – 17, 2016 Fairmont Chicago Millennium Park • Chicago, Illinois The AAP/ASCI/APSA conference is jointly provided by Boston University School of Medicine and AAP/ASCI/APSA. Meeting Program and Abstracts www.jointmeeting.org www.jointmeeting.org Special Events at the 2016 AAP/ASCI/APSA Joint Meeting Friday, April 15 Saturday, April 16 ASCI President’s Reception ASCI Food and Science Evening 6:15 – 7:15 p.m. 6:30 – 9:00 p.m. Gold Room The Mid-America Club, Aon Center ASCI Dinner & New Member AAP Member Banquet Induction Ceremony (Ticketed guests only) (Ticketed guests only) 7:00 – 10:00 p.m. 7:30 – 9:45 p.m. Imperial Ballroom, Level B2 Rouge, Lobby Level How to Solve a Scientific Puzzle: Speaker: Clara D. Bloomfield, MD Clues from Stockholm and Broadway The Ohio State University Comprehensive Cancer Center Speaker: Joe Goldstein, MD APSA Welcome Reception & University of Texas Southwestern Medical Center at Dallas Presidential Address APSA Dinner (Ticketed guests only) 9:00 p.m. – Midnight Signature Room, 360 Chicago, 7:30 – 9:00 p.m. John Hancock Center (off-site) Rouge, Lobby Level Speaker: Daniel DelloStritto, APSA President Finding One’s Scientific Niche: Musings from a Clinical Neuroscientist Speaker: Helen Mayberg, MD, Emory University Dessert Reception (open to all attendees) 10:00 p.m. – Midnight Imperial Foyer, Level B2 Sunday, April 17 APSA Future of Medicine and www.jointmeeting.org Residency Luncheon Noon – 2:00 p.m. Rouge, Lobby Level 2 www.jointmeeting.org Program Contents General Program Information 4 Continuing Medical Education Information 5 Faculty and Speaker Disclosures 7 Scientific Program Schedule 9 Speaker Biographies 16 Call for Nominations: 2017 Harrington Prize for Innovation in Medicine 26 AAP/ASCI/APSA Joint Meeting Faculty 27 Award Recipients 29 Call for Nominations: 2017 Harrington Scholar-Innovator Award 31 Call for Nominations: George M.
    [Show full text]
  • Regulation of Adult Neurogenesis in Mammalian Brain
    International Journal of Molecular Sciences Review Regulation of Adult Neurogenesis in Mammalian Brain 1,2, 3, 3,4 Maria Victoria Niklison-Chirou y, Massimiliano Agostini y, Ivano Amelio and Gerry Melino 3,* 1 Centre for Therapeutic Innovation (CTI-Bath), Department of Pharmacy & Pharmacology, University of Bath, Bath BA2 7AY, UK; [email protected] 2 Blizard Institute of Cell and Molecular Science, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London E1 2AT, UK 3 Department of Experimental Medicine, TOR, University of Rome “Tor Vergata”, 00133 Rome, Italy; [email protected] (M.A.); [email protected] (I.A.) 4 School of Life Sciences, University of Nottingham, Nottingham NG7 2HU, UK * Correspondence: [email protected] These authors contributed equally to this work. y Received: 18 May 2020; Accepted: 7 July 2020; Published: 9 July 2020 Abstract: Adult neurogenesis is a multistage process by which neurons are generated and integrated into existing neuronal circuits. In the adult brain, neurogenesis is mainly localized in two specialized niches, the subgranular zone (SGZ) of the dentate gyrus and the subventricular zone (SVZ) adjacent to the lateral ventricles. Neurogenesis plays a fundamental role in postnatal brain, where it is required for neuronal plasticity. Moreover, perturbation of adult neurogenesis contributes to several human diseases, including cognitive impairment and neurodegenerative diseases. The interplay between extrinsic and intrinsic factors is fundamental in regulating neurogenesis. Over the past decades, several studies on intrinsic pathways, including transcription factors, have highlighted their fundamental role in regulating every stage of neurogenesis. However, it is likely that transcriptional regulation is part of a more sophisticated regulatory network, which includes epigenetic modifications, non-coding RNAs and metabolic pathways.
    [Show full text]
  • E Proteins and ID Proteins: Helix-Loop-Helix Partners in Development and Disease
    View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Elsevier - Publisher Connector Developmental Cell Review E Proteins and ID Proteins: Helix-Loop-Helix Partners in Development and Disease Lan-Hsin Wang1 and Nicholas E. Baker1,2,3,* 1Department of Genetics, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA 2Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA 3Department of Ophthalmology and Visual Sciences, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA *Correspondence: [email protected] http://dx.doi.org/10.1016/j.devcel.2015.10.019 The basic Helix-Loop-Helix (bHLH) proteins represent a well-known class of transcriptional regulators. Many bHLH proteins act as heterodimers with members of a class of ubiquitous partners, the E proteins. A widely expressed class of inhibitory heterodimer partners—the Inhibitor of DNA-binding (ID) proteins—also exists. Genetic and molecular analyses in humans and in knockout mice implicate E proteins and ID proteins in a wide variety of diseases, belying the notion that they are non-specific partner proteins. Here, we explore relationships of E proteins and ID proteins to a variety of disease processes and highlight gaps in knowledge of disease mechanisms. E proteins and Inhibitor of DNA-binding (ID) proteins are widely conferring DNA-binding specificity and transcriptional activation expressed transcriptional regulators with very general functions. on heterodimers with the ubiquitous E proteins (Figure 1). They are implicated in diseases by evidence ranging from Another class of pervasive HLH proteins acts in opposition to confirmed Mendelian inheritance, association studies, and E proteins.
    [Show full text]
  • Supplementary Data
    SUPPLEMENTARY DATA A cyclin D1-dependent transcriptional program predicts clinical outcome in mantle cell lymphoma Santiago Demajo et al. 1 SUPPLEMENTARY DATA INDEX Supplementary Methods p. 3 Supplementary References p. 8 Supplementary Tables (S1 to S5) p. 9 Supplementary Figures (S1 to S15) p. 17 2 SUPPLEMENTARY METHODS Western blot, immunoprecipitation, and qRT-PCR Western blot (WB) analysis was performed as previously described (1), using cyclin D1 (Santa Cruz Biotechnology, sc-753, RRID:AB_2070433) and tubulin (Sigma-Aldrich, T5168, RRID:AB_477579) antibodies. Co-immunoprecipitation assays were performed as described before (2), using cyclin D1 antibody (Santa Cruz Biotechnology, sc-8396, RRID:AB_627344) or control IgG (Santa Cruz Biotechnology, sc-2025, RRID:AB_737182) followed by protein G- magnetic beads (Invitrogen) incubation and elution with Glycine 100mM pH=2.5. Co-IP experiments were performed within five weeks after cell thawing. Cyclin D1 (Santa Cruz Biotechnology, sc-753), E2F4 (Bethyl, A302-134A, RRID:AB_1720353), FOXM1 (Santa Cruz Biotechnology, sc-502, RRID:AB_631523), and CBP (Santa Cruz Biotechnology, sc-7300, RRID:AB_626817) antibodies were used for WB detection. In figure 1A and supplementary figure S2A, the same blot was probed with cyclin D1 and tubulin antibodies by cutting the membrane. In figure 2H, cyclin D1 and CBP blots correspond to the same membrane while E2F4 and FOXM1 blots correspond to an independent membrane. Image acquisition was performed with ImageQuant LAS 4000 mini (GE Healthcare). Image processing and quantification were performed with Multi Gauge software (Fujifilm). For qRT-PCR analysis, cDNA was generated from 1 µg RNA with qScript cDNA Synthesis kit (Quantabio). qRT–PCR reaction was performed using SYBR green (Roche).
    [Show full text]
  • Melatonin Synthesis and Clock Gene Regulation in the Pineal Organ Of
    General and Comparative Endocrinology 279 (2019) 27–34 Contents lists available at ScienceDirect General and Comparative Endocrinology journal homepage: www.elsevier.com/locate/ygcen Review article Melatonin synthesis and clock gene regulation in the pineal organ of teleost fish compared to mammals: Similarities and differences T ⁎ Saurav Saha, Kshetrimayum Manisana Singh, Braj Bansh Prasad Gupta Environmental Endocrinology Laboratory, Department of Zoology, North-Eastern Hill University, Shillong 793022, India ARTICLE INFO ABSTRACT Keywords: The pineal organ of all vertebrates synthesizes and secretes melatonin in a rhythmic manner due to the circadian Aanat gene rhythm in the activity of arylalkylamine N-acetyltransferase (AANAT) – the rate-limiting enzyme in melatonin Circadian rhythm synthesis pathway. Nighttime increase in AANAT activity and melatonin synthesis depends on increased ex- Clock genes pression of aanat gene (a clock-controlled gene) and/or post-translation modification of AANAT protein. In Melatonin synthesis mammalian and avian species, only one aanat gene is expressed. However, three aanat genes (aanat1a, aanat1b, Pineal organ and aanat2) are reported in fish species. While aanat1a and aanat1b genes are expressed in the fish retina, the Photoperiod fi Temperature nervous system and other peripheral tissues, aanat2 gene is expressed exclusively in the sh pineal organ. Clock genes form molecular components of the clockwork, which regulates clock-controlled genes like aanat gene. All core clock genes (i.e., clock, bmal1, per1, per2, per3, cry1 and cry2) and aanat2 gene (a clock-controlled gene) are expressed in the pineal organ of several fish species. There is a large body of information on regulation of clock genes, aanat gene and melatonin synthesis in the mammalian pineal gland.
    [Show full text]