The Roles of ERK1 and ERK2 MAP Kinase in Neural Development and Disease
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PARSANA-DISSERTATION-2020.Pdf
DECIPHERING TRANSCRIPTIONAL PATTERNS OF GENE REGULATION: A COMPUTATIONAL APPROACH by Princy Parsana A dissertation submitted to The Johns Hopkins University in conformity with the requirements for the degree of Doctor of Philosophy Baltimore, Maryland July, 2020 © 2020 Princy Parsana All rights reserved Abstract With rapid advancements in sequencing technology, we now have the ability to sequence the entire human genome, and to quantify expression of tens of thousands of genes from hundreds of individuals. This provides an extraordinary opportunity to learn phenotype relevant genomic patterns that can improve our understanding of molecular and cellular processes underlying a trait. The high dimensional nature of genomic data presents a range of computational and statistical challenges. This dissertation presents a compilation of projects that were driven by the motivation to efficiently capture gene regulatory patterns in the human transcriptome, while addressing statistical and computational challenges that accompany this data. We attempt to address two major difficulties in this domain: a) artifacts and noise in transcriptomic data, andb) limited statistical power. First, we present our work on investigating the effect of artifactual variation in gene expression data and its impact on trans-eQTL discovery. Here we performed an in-depth analysis of diverse pre-recorded covariates and latent confounders to understand their contribution to heterogeneity in gene expression measurements. Next, we discovered 673 trans-eQTLs across 16 human tissues using v6 data from the Genotype Tissue Expression (GTEx) project. Finally, we characterized two trait-associated trans-eQTLs; one in Skeletal Muscle and another in Thyroid. Second, we present a principal component based residualization method to correct gene expression measurements prior to reconstruction of co-expression networks. -
Hidden Targets in RAF Signalling Pathways to Block Oncogenic RAS Signalling
G C A T T A C G G C A T genes Review Hidden Targets in RAF Signalling Pathways to Block Oncogenic RAS Signalling Aoife A. Nolan 1, Nourhan K. Aboud 1, Walter Kolch 1,2,* and David Matallanas 1,* 1 Systems Biology Ireland, School of Medicine, University College Dublin, Belfield, Dublin 4, Ireland; [email protected] (A.A.N.); [email protected] (N.K.A.) 2 Conway Institute of Biomolecular & Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland * Correspondence: [email protected] (W.K.); [email protected] (D.M.) Abstract: Oncogenic RAS (Rat sarcoma) mutations drive more than half of human cancers, and RAS inhibition is the holy grail of oncology. Thirty years of relentless efforts and harsh disappointments have taught us about the intricacies of oncogenic RAS signalling that allow us to now get a pharma- cological grip on this elusive protein. The inhibition of effector pathways, such as the RAF-MEK-ERK pathway, has largely proven disappointing. Thus far, most of these efforts were aimed at blocking the activation of ERK. Here, we discuss RAF-dependent pathways that are regulated through RAF functions independent of catalytic activity and their potential role as targets to block oncogenic RAS signalling. We focus on the now well documented roles of RAF kinase-independent functions in apoptosis, cell cycle progression and cell migration. Keywords: RAF kinase-independent; RAS; MST2; ASK; PLK; RHO-α; apoptosis; cell cycle; cancer therapy Citation: Nolan, A.A.; Aboud, N.K.; Kolch, W.; Matallanas, D. Hidden Targets in RAF Signalling Pathways to Block Oncogenic RAS Signalling. -
Prioritization and Comprehensive Analysis of Genes Associated with Melanoma
ONCOLOGY LETTERS 18: 127-136, 2019 Prioritization and comprehensive analysis of genes associated with melanoma CHENG FENG, MING BAI, HAILIN ZHANG, ANG ZENG and WENCHAO ZHANG Department of Plastic Surgery, Peking Union Medical College Hospital, Beijing 100730, P.R. China Received August 13, 2018; Accepted February 28, 2019 DOI: 10.3892/ol.2019.10284 Abstract. Melanoma is a malignant tumor derived from accuracy and appropriate treatment due to medical advances, melanocytes, which occurs mostly in the skin. A major chal- its pathogenesis and natural course remain unclear. lenge in cancer research is the biological interpretation of the Melanoma is a malignant type of tumor, which may be complexity of cancer somatic mutation profiles. The aim of the composed of epidermal melanocytes, nevocytes or dermal present study was to obtain a comprehensive understanding of melanocytes. Epidemiology studies revealed that melanoma the formation and development of melanoma and to identify its is likely to be caused by hereditary factors and environmental associated genes. In the present study, a pipeline was proposed risk factors, including sex, age, ethnicity and geographic loca- for investigating key genes associated with melanoma based tion (6,7). This is in line with the most vital and potentially on the Online Mendelian Inheritance in Man and Search Tool reversible risk factor of malignant melanoma arising from for the Retrieval of Interacting Genes/Proteins databases an interaction between environmental exposure and genetic through a random walk model. Additionally, functional enrich- susceptibility. Gandini et al (8) revealed the association ment analysis was performed for key genes associated with between melanoma and ultraviolet (UV)-irradiation, and melanoma. -
Significant Shortest Paths for the Detection of Putative Disease Modules
bioRxiv preprint doi: https://doi.org/10.1101/2020.04.01.019844; this version posted April 2, 2020. 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-NC-ND 4.0 International license. SIGNIFICANT SHORTEST PATHS FOR THE DETECTION OF PUTATIVE DISEASE MODULES Daniele Pepe1 1Department of Oncology, KU Leuven, LKI–Leuven Cancer Institute, Leuven, Belgium Email address: DP: [email protected] bioRxiv preprint doi: https://doi.org/10.1101/2020.04.01.019844; this version posted April 2, 2020. 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-NC-ND 4.0 International license. Keywords Structural equation modeling, significant shortest paths, pathway analysis, disease modules. Abstract Background The characterization of diseases in terms of perturbated gene modules was recently introduced for the analysis of gene expression data. Some approaches were proposed in literature, but many times they are inductive approaches. This means that starting directly from data, they try to infer key gene networks potentially associated to the biological phenomenon studied. However they ignore the biological information already available to characterize the gene modules. Here we propose the detection of perturbed gene modules using the combination of data driven and hypothesis-driven approaches relying on biological metabolic pathways and significant shortest paths tested by structural equation modeling. -
MAPK1/MAPK3 Monoclonal Antibody, Clone Sb46b
MAPK1/MAPK3 monoclonal antibody, clone SB46b Catalog # : MAB3337 規格 : [ 500 ug ] List All Specification Application Image Product Mouse monoclonal antibody raised against recombinant Western Blot Description: MAPK1/MAPK3. Immunogen: Recombinant protein corresponding to human MAPK1/MAPK3. Host: Mouse enlarge Reactivity: Human Immunoprecipitation Specificity: human Erk 1 and human Erk2. Form: Liquid Isotype: IgG2a Recommend Western Blot (1-2 ug/mL) Usage: Immunoprecipitation (10-15ug) The optimal working dilution should be determined by the end user. Storage Buffer: In 100 mM BBS, pH 8.0 Storage Store at 4°C. Instruction: Datasheet: Download Publication Reference 1. Hydrophobic as well as charged residues in both MEK1 and ERK2 are important for their proper docking. Xu Be, Stippec S, Robinson FL, Cobb MH.J Biol Chem. 2001 Jul 13;276(28):26509-15. Epub 2001 May 14. 2. Mitogen-activated protein (MAP) kinase pathways: regulation and physiological functions. Pearson G, Robinson F, Beers Gibson T, Xu BE, Karandikar M, Berman K, Cobb MH.Endocr Rev. 2001 Apr;22(2):153-83. 3. Molecular cloning, expression, and characterization of the human mitogen-activated protein kinase p44erk1. Charest DL, Mordret G, Harder KW, Jirik F, Pelech SL.Mol Cell Biol. 1993 Aug;13(8):4679-90. Applications Western Blot Page 1 of 3 2021/6/20 Human PBMC (Lane 1) and spleen lysate (Lane 2) was stained with MAPK1/3 monoclonal antibody, clone SB46b (Cat # MAB3337). Goat anti-Mouse IgG2a was used to develop. Immunoprecipitation MAPK1 MAPK3 Gene Information Entrez GeneID: 5595 Gene Name: MAPK3 Gene Alias: ERK1,HS44KDAP,HUMKER1A,MGC20180,P44ERK1,P44MAPK,PRKM3 Gene mitogen-activated protein kinase 3 Description: Omim ID: 601795 Gene Ontology: Hyperlink Gene Summary: The protein encoded by this gene is a member of the MAP kinase family. -
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. -
N-Glycan Trimming in the ER and Calnexin/Calreticulin Cycle
Neurotransmitter receptorsGABA and A postsynapticreceptor activation signal transmission Ligand-gated ion channel transport GABAGABA Areceptor receptor alpha-5 alpha-1/beta-1/gamma-2 subunit GABA A receptor alpha-2/beta-2/gamma-2GABA receptor alpha-4 subunit GABAGABA receptor A receptor beta-3 subunitalpha-6/beta-2/gamma-2 GABA-AGABA receptor; A receptor alpha-1/beta-2/gamma-2GABA receptoralpha-3/beta-2/gamma-2 alpha-3 subunit GABA-A GABAreceptor; receptor benzodiazepine alpha-6 subunit site GABA-AGABA-A receptor; receptor; GABA-A anion site channel (alpha1/beta2 interface) GABA-A receptor;GABA alpha-6/beta-3/gamma-2 receptor beta-2 subunit GABAGABA receptorGABA-A receptor alpha-2receptor; alpha-1 subunit agonist subunit GABA site Serotonin 3a (5-HT3a) receptor GABA receptorGABA-C rho-1 subunitreceptor GlycineSerotonin receptor subunit3 (5-HT3) alpha-1 receptor GABA receptor rho-2 subunit GlycineGlycine receptor receptor subunit subunit alpha-2 alpha-3 Ca2+ activated K+ channels Metabolism of ingested SeMet, Sec, MeSec into H2Se SmallIntermediateSmall conductance conductance conductance calcium-activated calcium-activated calcium-activated potassium potassium potassiumchannel channel protein channel protein 2 protein 1 4 Small conductance calcium-activatedCalcium-activated potassium potassium channel alpha/beta channel 1 protein 3 Calcium-activated potassiumHistamine channel subunit alpha-1 N-methyltransferase Neuraminidase Pyrimidine biosynthesis Nicotinamide N-methyltransferase Adenosylhomocysteinase PolymerasePolymeraseHistidine basic -
Anti-EGFR Monoclonal Antibodies and EGFR Tyrosine Kinase Inhibitors As Combination Therapy for Triple-Negative Breast Cancer
www.impactjournals.com/oncotarget/ Oncotarget, Vol. 7, No. 45 Research Paper Anti-EGFR monoclonal antibodies and EGFR tyrosine kinase inhibitors as combination therapy for triple-negative breast cancer Abderrahim El Guerrab1,2, Mahchid Bamdad2,3, Fabrice Kwiatkowski1, Yves-Jean Bignon1,2,*, Frédérique Penault-Llorca1,2,*, Corinne Aubel1,2 1Centre Jean Perrin - ERTICa-EA4677, BP392, 63011 Clermont-Ferrand Cedex, France 2Clermont Université - Université d’Auvergne - ERTICa-EA4677, Faculté de Médecine, BP38, 63001 Clermont-Ferrand Cedex, France 3Clermont Université - Université d’Auvergne - ERTICa-EA4677, Institut Universitaire de Technologie, Département Génie Biologique, Ensemble Universitaire des Cézeaux, BP86, 63172 Aubière Cedex, France *These authors have contributed equally to this work Correspondence to: Yves-Jean Bignon, email: [email protected] Keywords: triple-negative breast cancer, epidermal growth factor receptor, anti-EGFR targeted therapy, cytotoxicity, cell cycle Received: November 09, 2015 Accepted: August 22, 2016 Published: September 15, 2016 ABSTRACT Triple-negative breast cancer (TNBC) is characterized by overexpression of epidermal growth factor receptor (EGFR) and activation of its downstream signaling pathways. Dual targeting of EGFR using one monoclonal antibody (mAb; cetuximab or panitumumab) and one tyrosine kinase inhibitor (EGFR-TKI; gefitinib or erlotinib) is a potential therapeutic approach. We investigated the effect of these therapies in EGFR-expressing TNBC cell lines that do or do not harbor the main activating mutations of EGFR pathways. Cell lines were sensitive to EGFR-TKIs, whereas mAbs were active only in MDA-MB-468 (EGFR amplification) and SUM-1315 (KRAS and PTEN wild-type) cells. MDA-MB-231 (KRAS mutated) and HCC-1937 (PTEN deletion) cells were resistant to mAbs. -
RAF Protein-Serine/Threonine Kinases: Structure and Regulation
Biochemical and Biophysical Research Communications 399 (2010) 313–317 Contents lists available at ScienceDirect Biochemical and Biophysical Research Communications journal homepage: www.elsevier.com/locate/ybbrc Mini Review RAF protein-serine/threonine kinases: Structure and regulation Robert Roskoski Jr. * Blue Ridge Institute for Medical Research, 3754 Brevard Road, Suite 116, Box 19, Horse Shoe, NC 28742, USA article info abstract Article history: A-RAF, B-RAF, and C-RAF are a family of three protein-serine/threonine kinases that participate in the Received 12 July 2010 RAS-RAF-MEK-ERK signal transduction cascade. This cascade participates in the regulation of a large vari- Available online 30 July 2010 ety of processes including apoptosis, cell cycle progression, differentiation, proliferation, and transforma- tion to the cancerous state. RAS mutations occur in 15–30% of all human cancers, and B-RAF mutations Keywords: occur in 30–60% of melanomas, 30–50% of thyroid cancers, and 5–20% of colorectal cancers. Activation 14-3-3 of the RAF kinases requires their interaction with RAS-GTP along with dephosphorylation and also phos- ERK phorylation by SRC family protein-tyrosine kinases and other protein-serine/threonine kinases. The for- GDC-0879 mation of unique side-to-side RAF dimers is required for full kinase activity. RAF kinase inhibitors are MEK Melanoma effective in blocking MEK1/2 and ERK1/2 activation in cells containing the oncogenic B-RAF Val600Glu PLX4032 activating mutation. RAF kinase inhibitors lead to the paradoxical increase in RAF kinase activity in cells PLX4720 containing wild-type B-RAF and wild-type or activated mutant RAS. -
Modulation of NF-Κb Signalling by Microbial Pathogens
REVIEWS Modulation of NF‑κB signalling by microbial pathogens Masmudur M. Rahman and Grant McFadden Abstract | The nuclear factor-κB (NF‑κB) family of transcription factors plays a central part in the host response to infection by microbial pathogens, by orchestrating the innate and acquired host immune responses. The NF‑κB proteins are activated by diverse signalling pathways that originate from many different cellular receptors and sensors. Many successful pathogens have acquired sophisticated mechanisms to regulate the NF‑κB signalling pathways by deploying subversive proteins or hijacking the host signalling molecules. Here, we describe the mechanisms by which viruses and bacteria micromanage the host NF‑κB signalling circuitry to favour the continued survival of the pathogen. The nuclear factor-κB (NF-κB) family of transcription Signalling targets upstream of NF‑κB factors regulates the expression of hundreds of genes that NF-κB proteins are tightly regulated in both the cyto- are associated with diverse cellular processes, such as pro- plasm and the nucleus6. Under normal physiological liferation, differentiation and death, as well as innate and conditions, NF‑κB complexes remain inactive in the adaptive immune responses. The mammalian NF‑κB cytoplasm through a direct interaction with proteins proteins are members of the Rel domain-containing pro- of the inhibitor of NF-κB (IκB) family, including IκBα, tein family: RELA (also known as p65), RELB, c‑REL, IκBβ and IκBε (also known as NF-κBIα, NF-κBIβ and the NF-κB p105 subunit (also known as NF‑κB1; which NF-κBIε, respectively); IκB proteins mask the nuclear is cleaved into the p50 subunit) and the NF-κB p100 localization domains in the NF‑κB complex, thus subunit (also known as NF‑κB2; which is cleaved into retaining the transcription complex in the cytoplasm. -
Aneuploidy: Using Genetic Instability to Preserve a Haploid Genome?
Health Science Campus FINAL APPROVAL OF DISSERTATION Doctor of Philosophy in Biomedical Science (Cancer Biology) Aneuploidy: Using genetic instability to preserve a haploid genome? Submitted by: Ramona Ramdath In partial fulfillment of the requirements for the degree of Doctor of Philosophy in Biomedical Science Examination Committee Signature/Date Major Advisor: David Allison, M.D., Ph.D. Academic James Trempe, Ph.D. Advisory Committee: David Giovanucci, Ph.D. Randall Ruch, Ph.D. Ronald Mellgren, Ph.D. Senior Associate Dean College of Graduate Studies Michael S. Bisesi, Ph.D. Date of Defense: April 10, 2009 Aneuploidy: Using genetic instability to preserve a haploid genome? Ramona Ramdath University of Toledo, Health Science Campus 2009 Dedication I dedicate this dissertation to my grandfather who died of lung cancer two years ago, but who always instilled in us the value and importance of education. And to my mom and sister, both of whom have been pillars of support and stimulating conversations. To my sister, Rehanna, especially- I hope this inspires you to achieve all that you want to in life, academically and otherwise. ii Acknowledgements As we go through these academic journeys, there are so many along the way that make an impact not only on our work, but on our lives as well, and I would like to say a heartfelt thank you to all of those people: My Committee members- Dr. James Trempe, Dr. David Giovanucchi, Dr. Ronald Mellgren and Dr. Randall Ruch for their guidance, suggestions, support and confidence in me. My major advisor- Dr. David Allison, for his constructive criticism and positive reinforcement. -
Mutation-Specific RAS Oncogenicity Explains NRAS Codon 61 Selection in Melanoma
Published OnlineFirst September 24, 2014; DOI: 10.1158/2159-8290.CD-14-0729 reseArch Article Mutation-Specific RAS Oncogenicity Explains NRAS Codon 61 Selection in Melanoma Christin E. Burd1,2, Wenjin Liu3,4, Minh V. Huynh5, Meriam A. Waqas1, James E. Gillahan1,2, Kelly S. Clark3,4, Kailing Fu3,4, Brit L. Martin1, William R. Jeck3,4,. George P Souroullas3,4, David B. Darr3,4, Daniel C. Zedek6, Michael J. Miley7, Bruce C. Baguley8, Sharon L. Campbell4,5, and Norman E. Sharpless3,4 Abstrt Ac NRAS mutation at codons 12, 13, or 61 is associated with transformation; yet, in melanoma, such alterations are nearly exclusive to codon 61. Here, we compared the melanoma susceptibility of an NrasQ61R knock-in allele to similarly designed KrasG12D and NrasG12D alleles. With concomitant p16INK4a inactivation, KrasG12D or NrasQ61R expression efficiently promoted melanoma in vivo, whereas NrasG12D did not. In addition, NrasQ61R mutation potently cooperated with Lkb1/Stk11 loss to induce highly metastatic disease. Functional comparisons of NrasQ61R and NrasG12D revealed little difference in the ability of these proteins to engage PI3K or RAF. Instead, NrasQ61R showed enhanced nucleotide binding, decreased intrinsic GTPase activity, and increased stability when compared with NrasG12D. This work identifies a faithful model of human NRAS-mutant melanoma, and suggests that the increased melanomagenecity of NrasQ61R over NrasG12D is due to heightened abundance of the active, GTP-bound form rather than differences in the engagement of downstream effector pathways. SIGNIFICANCE: This work explains the curious predominance in human melanoma of mutations of codon 61 of NRAS over other oncogenic NRAS mutations.