Macrophage Activation JUNB Is a Key Transcriptional Modulator Of
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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. -
DNA Breakpoint Assay Reveals a Majority of Gross Duplications Occur in Tandem Reducing VUS Classifications in Breast Cancer Predisposition Genes
© American College of Medical Genetics and Genomics ARTICLE Corrected: Correction DNA breakpoint assay reveals a majority of gross duplications occur in tandem reducing VUS classifications in breast cancer predisposition genes Marcy E. Richardson, PhD1, Hansook Chong, PhD1, Wenbo Mu, MS1, Blair R. Conner, MS1, Vickie Hsuan, MS1, Sara Willett, MS1, Stephanie Lam, MS1, Pei Tsai, CGMBS, MB (ASCP)1, Tina Pesaran, MS, CGC1, Adam C. Chamberlin, PhD1, Min-Sun Park, PhD1, Phillip Gray, PhD1, Rachid Karam, MD, PhD1 and Aaron Elliott, PhD1 Purpose: Gross duplications are ambiguous in terms of clinical cohort, while the remainder have unknown tandem status. Among interpretation due to the limitations of the detection methods that the tandem gross duplications that were eligible for reclassification, cannot infer their context, namely, whether they occur in tandem or 95% of them were upgraded to pathogenic. are duplicated and inserted elsewhere in the genome. We Conclusion: DBA is a novel, high-throughput, NGS-based method investigated the proportion of gross duplications occurring in that informs the tandem status, and thereby the classification of, tandem in breast cancer predisposition genes with the intent of gross duplications. This method revealed that most gross duplica- informing their classifications. tions in the investigated genes occurred in tandem and resulted in a Methods: The DNA breakpoint assay (DBA) is a custom, paired- pathogenic classification, which helps to secure the necessary end, next-generation sequencing (NGS) method designed to treatment options for their carriers. capture and detect deep-intronic DNA breakpoints in gross duplications in BRCA1, BRCA2, ATM, CDH1, PALB2, and CHEK2. Genetics in Medicine (2019) 21:683–693; https://doi.org/10.1038/s41436- Results: DBA allowed us to ascertain breakpoints for 44 unique 018-0092-7 gross duplications from 147 probands. -
GSK3 Is a Negative Regulator of the Thermogenic Program in Brown Adipocytes
GSK3 is a negative regulator of the thermogenic program in brown adipocytes Markussen, Lasse K.; Winther, Sally; Wicksteed, Barton; Hansen, Jacob B. Published in: Scientific Reports DOI: 10.1038/s41598-018-21795-y Publication date: 2018 Document version Publisher's PDF, also known as Version of record Document license: CC BY Citation for published version (APA): Markussen, L. K., Winther, S., Wicksteed, B., & Hansen, J. B. (2018). GSK3 is a negative regulator of the thermogenic program in brown adipocytes. Scientific Reports, 8, 1-12. [3469]. https://doi.org/10.1038/s41598- 018-21795-y Download date: 01. okt.. 2021 www.nature.com/scientificreports OPEN GSK3 is a negative regulator of the thermogenic program in brown adipocytes Received: 16 January 2017 Lasse K. Markussen1, Sally Winther1, Barton Wicksteed2 & Jacob B. Hansen 1 Accepted: 9 February 2018 Brown adipose tissue is a promising therapeutic target in metabolic disorders due to its ability to Published: xx xx xxxx dissipate energy and improve systemic insulin sensitivity and glucose homeostasis. β-Adrenergic stimulation of brown adipocytes leads to an increase in oxygen consumption and induction of a thermogenic gene program that includes uncoupling protein 1 (Ucp1) and fbroblast growth factor 21 (Fgf21). In kinase inhibitor screens, we have identifed glycogen synthase kinase 3 (GSK3) as a negative regulator of basal and β-adrenergically stimulated Fgf21 expression in cultured brown adipocytes. In addition, inhibition of GSK3 also caused increased Ucp1 expression and oxygen consumption. β-Adrenergic stimulation triggered an inhibitory phosphorylation of GSK3 in a protein kinase A (PKA)- dependent manner. Mechanistically, inhibition of GSK3 activated the mitogen activated protein kinase (MAPK) kinase 3/6-p38 MAPK-activating transcription factor 2 signaling module. -
Human Regulatory T Cells Mediate Transcriptional Modulation of Dendritic Cell Function
Human Regulatory T Cells Mediate Transcriptional Modulation of Dendritic Cell Function This information is current as Emily Mavin, Lindsay Nicholson, Syed Rafez Ahmed, Fei of September 24, 2021. Gao, Anne Dickinson and Xiao-nong Wang J Immunol published online 28 November 2016 http://www.jimmunol.org/content/early/2016/11/26/jimmun ol.1502487 Downloaded from Supplementary http://www.jimmunol.org/content/suppl/2016/11/26/jimmunol.150248 Material 7.DCSupplemental http://www.jimmunol.org/ Why The JI? Submit online. • Rapid Reviews! 30 days* from submission to initial decision • No Triage! Every submission reviewed by practicing scientists • Fast Publication! 4 weeks from acceptance to publication by guest on September 24, 2021 *average Subscription Information about subscribing to The Journal of Immunology is online at: http://jimmunol.org/subscription Permissions Submit copyright permission requests at: http://www.aai.org/About/Publications/JI/copyright.html Email Alerts Receive free email-alerts when new articles cite this article. Sign up at: http://jimmunol.org/alerts The Journal of Immunology is published twice each month by The American Association of Immunologists, Inc., 1451 Rockville Pike, Suite 650, Rockville, MD 20852 Copyright © 2016 by The American Association of Immunologists, Inc. All rights reserved. Print ISSN: 0022-1767 Online ISSN: 1550-6606. Published November 28, 2016, doi:10.4049/jimmunol.1502487 The Journal of Immunology Human Regulatory T Cells Mediate Transcriptional Modulation of Dendritic Cell Function Emily Mavin,*,1 Lindsay Nicholson,*,1 Syed Rafez Ahmed,* Fei Gao,† Anne Dickinson,* and Xiao-nong Wang* Regulatory T cells (Treg) attenuate dendritic cell (DC) maturation and stimulatory function. Current knowledge on the functional impact of semimature DC is limited to CD4+ T cell proliferation and cytokine production. -
Single-Cell RNA Sequencing Identifies Senescent Cerebromicrovascular Endothelial Cells in the Aged Mouse Brain
GeroScience (2020) 42:429–444 https://doi.org/10.1007/s11357-020-00177-1 ORIGINAL ARTICLE/UNDERSTANDING SENESCENCE IN BRAIN AGING AND ALZHEIMER’SDISEASE Single-cell RNA sequencing identifies senescent cerebromicrovascular endothelial cells in the aged mouse brain Tamas Kiss & Ádám Nyúl-Tóth & Priya Balasubramanian & Stefano Tarantini & Chetan Ahire & Jordan DelFavero & Andriy Yabluchanskiy & Tamas Csipo & Eszter Farkas & Graham Wiley & Lori Garman & Anna Csiszar & Zoltan Ungvari Received: 31 January 2020 /Accepted: 1 March 2020 /Published online: 31 March 2020 # American Aging Association 2020 Abstract Age-related phenotypic changes of therapeutic exploitation of senolytic drugs in preclinical cerebromicrovascular endothelial cells lead to dysregula- studies. However, difficulties with the detection of senes- tion of cerebral blood flow and blood-brain barrier dis- cent endothelial cells in wild type mouse models of aging ruption, promoting the pathogenesis of vascular cognitive hinder the assessment of the efficiency of senolytic treat- impairment (VCI). In recent years, endothelial cell senes- ments. To detect senescent endothelial cells in the aging cence has emerged as a potential mechanism contributing mouse brain, we analyzed 4233 cells in fractions enriched to microvascular pathologies opening the avenue to the for cerebromicrovascular endothelial cells and other cells Tamas Kiss, Ádám Nyúl-Tóth, Priya Balasubramanian and Stefano Tarantini contributed equally to this work. T. Kiss : Á. Nyúl-Tóth : P. Balasubramanian : S. Tarantini : S. Tarantini : A. Yabluchanskiy : Z. Ungvari C. Ahire : J. DelFavero : A. Yabluchanskiy : T. Csipo : Department of Public Health, International Training Program in A. Csiszar (*) : Z. Ungvari Geroscience, Doctoral School of Basic and Translational Medicine, Department of Biochemistry and Molecular Biology, Reynolds Semmelweis University, Budapest, Hungary Oklahoma Center on Aging/Center for Geroscience and Healthy Brain Aging, Vascular Cognitive Impairment and T. -
MAP3K4/CBP-Regulated H2B Acetylation Controls Epithelial-Mesenchymal Transition in Trophoblast Stem Cells
Cell Stem Cell Article MAP3K4/CBP-Regulated H2B Acetylation Controls Epithelial-Mesenchymal Transition in Trophoblast Stem Cells Amy N. Abell,1,2,7,* Nicole Vincent Jordan,1,2,7 Weichun Huang,6 Aleix Prat,2,4 Alicia A. Midland,5 Nancy L. Johnson,1,2 Deborah A. Granger,1,2 Piotr A. Mieczkowski,2,3 Charles M. Perou,2,4 Shawn M. Gomez,5 Leping Li,6 and Gary L. Johnson1,2,* 1Department of Pharmacology 2Lineberger Comprehensive Cancer Center 3Department of Genetics and Carolina Center for Genome Sciences 4Department of Genetics 5Department of Biomedical Engineering and Curriculum in Bioinformatics and Computational Biology University of North Carolina School of Medicine, Chapel Hill, NC 27599-7365, USA 6Biostatistics Branch, National Institute of Environmental Health Sciences RTP, NC 27709, USA 7These authors contributed equally to this work *Correspondence: [email protected] (A.N.A.), [email protected] (G.L.J.) DOI 10.1016/j.stem.2011.03.008 SUMMARY berg, 2008). During development, EMT is responsible for proper formation of the body plan and for differentiation of many tissues Epithelial stem cells self-renew while maintaining and organs. Examples of EMT in mammalian development multipotency, but the dependence of stem cell prop- include implantation, gastrulation, and neural crest formation erties on maintenance of the epithelial phenotype is (Thiery et al., 2009). Initiation of placenta formation regulated unclear. We previously showed that trophoblast by trophoectoderm differentiation is the first, and yet most poorly stem (TS) cells lacking the protein kinase MAP3K4 defined, developmental EMT. maintain properties of both stemness and epithelial- The commitment of stem cells to specialized cell types requires extensive reprogramming of gene expression, involving, in part, mesenchymal transition (EMT). -
Targeting the CDK4/6-Rb Pathway Enhances Response to PI3K
Published OnlineFirst August 9, 2018; DOI: 10.1158/1078-0432.CCR-18-0717 Translational Cancer Mechanisms and Therapy Clinical Cancer Research Targeting the CDK4/6-Rb Pathway Enhances Response to PI3K Inhibition in PIK3CA-Mutant Lung Squamous Cell Carcinoma Ruoshi Shi1,2, Ming Li1, Vibha Raghavan1, Shirley Tam1, Michael Cabanero1, Nhu-An Pham1, Frances A. Shepherd1,3, Nadeem Moghal1,2, and Ming-Sound Tsao1,2,4 Abstract Purpose: Lung squamous cell carcinoma (LUSC) is a major of LUSC PDX models identified PI3K pathway alterations in subtype of non–small cell lung cancer characterized by mul- over 50% of the models. In vivo screening using PI3K tiple genetic alterations, particularly PI3K pathway alterations inhibitors in 12 of these models identified PIK3CA mutation which have been identified in over 50% of LUSC cases. Despite as a predictive biomarker of response (<20% tumor growth being an attractive target, single-agent PI3K inhibitors have compared with baseline/vehicle). Combined inhibition of demonstrated modest response in LUSC. Thus, novel combi- PI3K and CDK4/6 in models with PIK3CA mutation resulted nation therapies targeting LUSC are needed. in greater antitumor effects compared with either mono- Experimental Design: PI3K inhibitors alone and in com- therapy alone. In addition, the combination of the two bination with CDK4/6 inhibitors were evaluated in previously drugs achieved targeted inhibition of the PI3K and cell-cycle established LUSC patient-derived xenografts (PDX) using an pathways. in vivo screening method. Screening results were validated with Conclusions: PIK3CA mutations predict response to PI3K in vivo expansion to 5 to 8 mice per arm. -
Human Receptor-Interacting Serine/Threonine-Protein Kinase 2 (RIPK2) a Target Enabling Package (TEP)
Human Receptor-Interacting Serine/Threonine-Protein Kinase 2 (RIPK2) A Target Enabling Package (TEP) Gene ID / UniProt ID / EC 8767 / O43353 / - Target Nominator SGC Internal Nomination SGC Authors Peter Canning, Daniel M. Pinkas, Joshua C. Bufton, Sarah Picaud, Jennifer A. Ward, Catherine Rogers, Benedict-Tilman Berger, Stefan Knapp, Susanne Muller-Knapp, Paul E. Brennan, Kilian V. M. Huber, Panagis Filippakopoulos, Alex N. Bullock Collaborating Authors Matous Hrdinka1, Qui Ruan2, Chalada Suebsuwong3, Lisa Schlicher1, Bing Dai2, Jenny L. Maki2, Soumya S. Ray4, Danish Saleh5, Sameer Nikhar6, Tobias Schwerd7, Holm H.Uhlig7, Gregory D. Cuny6, Alexei Degterev2, Mads Gyrd-Hansen1 Target PI Alex N. Bullock (SGC Oxford) Therapeutic Area(s) Inflammatory diseases Disease Relevance Mutations in the NOD2-RIPK2 pathway identify RIPK2 a potential therapeutic target in auto-immune and inflammatory conditions such as Crohn’s disease, Blau syndrome, early-onset osteoarthritis and multiple sclerosis. Date Approved by TEP Evaluation 13th June 2018 Group Document version Version 3 Document version date October 2020 Citation Peter Canning, Daniel M. Pinkas, Joshua C. Bufton, Sarah Picaud, Jennifer A. Ward, Catherine Rogers, … Alex N. Bullock. (2018). Human Receptor- Interacting Serine/Threonine-Protein Kinase 2 (RIPK2); A Target Enabling Package. Zenodo. http://doi.org/10.5281/zenodo.1344501 Affiliations 1. Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford 2. Department of Developmental, Molecular & Chemical Biology, Tufts University School of Medicine 3. Department of Chemistry, Science and Research Building 2, University of Houston 4. Center for Neurologic Diseases, Department of Neurology, Brigham & Women's Hospital and Harvard Medical School 5. Medical Scientist Training Program and Program in Neuroscience, Sackler School of Graduate Biomedical Sciences, Tufts University School of Medicine 6. -
Systems Consequences of Amplicon Formation in Human Breast Cancer
Downloaded from genome.cshlp.org on September 25, 2021 - Published by Cold Spring Harbor Laboratory Press Research Systems consequences of amplicon formation in human breast cancer Koichiro Inaki,1,2,9 Francesca Menghi,1,2,9 Xing Yi Woo,1,9 Joel P. Wagner,1,2,3 4,5 1 2 Pierre-Etienne Jacques, Yi Fang Lee, Phung Trang Shreckengast, Wendy WeiJia Soon,1 Ankit Malhotra,2 Audrey S.M. Teo,1 Axel M. Hillmer,1 Alexis Jiaying Khng,1 Xiaoan Ruan,6 Swee Hoe Ong,4 Denis Bertrand,4 Niranjan Nagarajan,4 R. Krishna Murthy Karuturi,4,7 Alfredo Hidalgo Miranda,8 andEdisonT.Liu1,2,7 1Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, Genome, Singapore 138672, Singapore; 2The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut 06030, USA; 3Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA; 4Computational and Systems Biology, Genome Institute of Singapore, Genome, Singapore 138672, Singapore; 5Universite de Sherbrooke, Sherbrooke, Quebec, J1K 2R1, Canada; 6Genome Technology and Biology, Genome Institute of Singapore, Genome, Singapore 138672, Singapore; 7The Jackson Laboratory, Bar Harbor, Maine 04609, USA; 8National Institute of Genomic Medicine, Periferico Sur 4124, Mexico City 01900, Mexico Chromosomal structural variations play an important role in determining the transcriptional landscape of human breast cancers. To assess the nature of these structural variations, we analyzed eight breast tumor samples with a focus on regions of gene amplification using mate-pair sequencing of long-insert genomic DNA with matched transcriptome profiling. We found that tandem duplications appear to be early events in tumor evolution, especially in the genesis of amplicons. -
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. -
(P -Value<0.05, Fold Change≥1.4), 4 Vs. 0 Gy Irradiation
Table S1: Significant differentially expressed genes (P -Value<0.05, Fold Change≥1.4), 4 vs. 0 Gy irradiation Genbank Fold Change P -Value Gene Symbol Description Accession Q9F8M7_CARHY (Q9F8M7) DTDP-glucose 4,6-dehydratase (Fragment), partial (9%) 6.70 0.017399678 THC2699065 [THC2719287] 5.53 0.003379195 BC013657 BC013657 Homo sapiens cDNA clone IMAGE:4152983, partial cds. [BC013657] 5.10 0.024641735 THC2750781 Ciliary dynein heavy chain 5 (Axonemal beta dynein heavy chain 5) (HL1). 4.07 0.04353262 DNAH5 [Source:Uniprot/SWISSPROT;Acc:Q8TE73] [ENST00000382416] 3.81 0.002855909 NM_145263 SPATA18 Homo sapiens spermatogenesis associated 18 homolog (rat) (SPATA18), mRNA [NM_145263] AA418814 zw01a02.s1 Soares_NhHMPu_S1 Homo sapiens cDNA clone IMAGE:767978 3', 3.69 0.03203913 AA418814 AA418814 mRNA sequence [AA418814] AL356953 leucine-rich repeat-containing G protein-coupled receptor 6 {Homo sapiens} (exp=0; 3.63 0.0277936 THC2705989 wgp=1; cg=0), partial (4%) [THC2752981] AA484677 ne64a07.s1 NCI_CGAP_Alv1 Homo sapiens cDNA clone IMAGE:909012, mRNA 3.63 0.027098073 AA484677 AA484677 sequence [AA484677] oe06h09.s1 NCI_CGAP_Ov2 Homo sapiens cDNA clone IMAGE:1385153, mRNA sequence 3.48 0.04468495 AA837799 AA837799 [AA837799] Homo sapiens hypothetical protein LOC340109, mRNA (cDNA clone IMAGE:5578073), partial 3.27 0.031178378 BC039509 LOC643401 cds. [BC039509] Homo sapiens Fas (TNF receptor superfamily, member 6) (FAS), transcript variant 1, mRNA 3.24 0.022156298 NM_000043 FAS [NM_000043] 3.20 0.021043295 A_32_P125056 BF803942 CM2-CI0135-021100-477-g08 CI0135 Homo sapiens cDNA, mRNA sequence 3.04 0.043389246 BF803942 BF803942 [BF803942] 3.03 0.002430239 NM_015920 RPS27L Homo sapiens ribosomal protein S27-like (RPS27L), mRNA [NM_015920] Homo sapiens tumor necrosis factor receptor superfamily, member 10c, decoy without an 2.98 0.021202829 NM_003841 TNFRSF10C intracellular domain (TNFRSF10C), mRNA [NM_003841] 2.97 0.03243901 AB002384 C6orf32 Homo sapiens mRNA for KIAA0386 gene, partial cds. -
TMEM33 (A-17): Sc-244421
SAN TA C RUZ BI OTEC HNOL OG Y, INC . TMEM33 (A-17): sc-244421 BACKGROUND PRODUCT TMEM33 (transmembrane protein 33), also known as protein DB83, is a 247 Each vial contains 200 µg IgG in 1.0 ml of PBS with < 0.1% sodium azide amino acid protein encoded by a gene mapping to human chromosome 4. and 0.1% gelatin. Representing approximately 6% of the human genome, chromosome 4 con - Blocking peptide available for competition studies, sc-244421 P, (100 µg tains nearly 900 genes. Notably, the Huntingtin gene, which is found to en- peptide in 0.5 ml PBS containing < 0.1% sodium azide and 0.2% BSA). code an expanded glutamine tract in cases of Huntington’s disease, is on chromosome 4. FGFR-3 is also encoded on chromosome 4 and has been asso - APPLICATIONS ciated with thanatophoric dwarfism, achondroplasia, Muenke syndrome and bladder cancer. Chromosome 4 is also tied to Ellis-van Creveld syndrome, TMEM33 (A-17) is recommended for detection of TMEM33 of mouse, rat methylmalonic acidemia and polycystic kidney disease. Chromosome 4 report - and human origin by Western Blotting (starting dilution 1:200, dilution range edly contains the largest gene deserts (regions of the genome with no protein 1:100-1:1000), immunofluorescence (starting dilution 1:50, dilution range encoding genes) and has one of the two lowest recombination frequencies 1:50-1:500) and solid phase ELISA (starting dilution 1:30, dilution range of the human chromosomes. 1:30-1:3000); non cross-reactive with other TMEM family members. TMEM33 (A-17) is also recommended for detection of TMEM33 in additional REFERENCES species, including equine, canine, bovine, porcine and avian.