Protein Quality Control in the Endoplasmic Reticulum and Cancer
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Activated Peripheral-Blood-Derived Mononuclear Cells
Transcription factor expression in lipopolysaccharide- activated peripheral-blood-derived mononuclear cells Jared C. Roach*†, Kelly D. Smith*‡, Katie L. Strobe*, Stephanie M. Nissen*, Christian D. Haudenschild§, Daixing Zhou§, Thomas J. Vasicek¶, G. A. Heldʈ, Gustavo A. Stolovitzkyʈ, Leroy E. Hood*†, and Alan Aderem* *Institute for Systems Biology, 1441 North 34th Street, Seattle, WA 98103; ‡Department of Pathology, University of Washington, Seattle, WA 98195; §Illumina, 25861 Industrial Boulevard, Hayward, CA 94545; ¶Medtronic, 710 Medtronic Parkway, Minneapolis, MN 55432; and ʈIBM Computational Biology Center, P.O. Box 218, Yorktown Heights, NY 10598 Contributed by Leroy E. Hood, August 21, 2007 (sent for review January 7, 2007) Transcription factors play a key role in integrating and modulating system. In this model system, we activated peripheral-blood-derived biological information. In this study, we comprehensively measured mononuclear cells, which can be loosely termed ‘‘macrophages,’’ the changing abundances of mRNAs over a time course of activation with lipopolysaccharide (LPS). We focused on the precise mea- of human peripheral-blood-derived mononuclear cells (‘‘macro- surement of mRNA concentrations. There is currently no high- phages’’) with lipopolysaccharide. Global and dynamic analysis of throughput technology that can precisely and sensitively measure all transcription factors in response to a physiological stimulus has yet to mRNAs in a system, although such technologies are likely to be be achieved in a human system, and our efforts significantly available in the near future. To demonstrate the potential utility of advanced this goal. We used multiple global high-throughput tech- such technologies, and to motivate their development and encour- nologies for measuring mRNA levels, including massively parallel age their use, we produced data from a combination of two distinct signature sequencing and GeneChip microarrays. -
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. -
4-6 Weeks Old Female C57BL/6 Mice Obtained from Jackson Labs Were Used for Cell Isolation
Methods Mice: 4-6 weeks old female C57BL/6 mice obtained from Jackson labs were used for cell isolation. Female Foxp3-IRES-GFP reporter mice (1), backcrossed to B6/C57 background for 10 generations, were used for the isolation of naïve CD4 and naïve CD8 cells for the RNAseq experiments. The mice were housed in pathogen-free animal facility in the La Jolla Institute for Allergy and Immunology and were used according to protocols approved by the Institutional Animal Care and use Committee. Preparation of cells: Subsets of thymocytes were isolated by cell sorting as previously described (2), after cell surface staining using CD4 (GK1.5), CD8 (53-6.7), CD3ε (145- 2C11), CD24 (M1/69) (all from Biolegend). DP cells: CD4+CD8 int/hi; CD4 SP cells: CD4CD3 hi, CD24 int/lo; CD8 SP cells: CD8 int/hi CD4 CD3 hi, CD24 int/lo (Fig S2). Peripheral subsets were isolated after pooling spleen and lymph nodes. T cells were enriched by negative isolation using Dynabeads (Dynabeads untouched mouse T cells, 11413D, Invitrogen). After surface staining for CD4 (GK1.5), CD8 (53-6.7), CD62L (MEL-14), CD25 (PC61) and CD44 (IM7), naïve CD4+CD62L hiCD25-CD44lo and naïve CD8+CD62L hiCD25-CD44lo were obtained by sorting (BD FACS Aria). Additionally, for the RNAseq experiments, CD4 and CD8 naïve cells were isolated by sorting T cells from the Foxp3- IRES-GFP mice: CD4+CD62LhiCD25–CD44lo GFP(FOXP3)– and CD8+CD62LhiCD25– CD44lo GFP(FOXP3)– (antibodies were from Biolegend). In some cases, naïve CD4 cells were cultured in vitro under Th1 or Th2 polarizing conditions (3, 4). -
Uncovering Ubiquitin and Ubiquitin-Like Signaling Networks Alfred C
REVIEW pubs.acs.org/CR Uncovering Ubiquitin and Ubiquitin-like Signaling Networks Alfred C. O. Vertegaal* Department of Molecular Cell Biology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, The Netherlands CONTENTS 8. Crosstalk between Post-Translational Modifications 7934 1. Introduction 7923 8.1. Crosstalk between Phosphorylation and 1.1. Ubiquitin and Ubiquitin-like Proteins 7924 Ubiquitylation 7934 1.2. Quantitative Proteomics 7924 8.2. Phosphorylation-Dependent SUMOylation 7935 8.3. Competition between Different Lysine 1.3. Setting the Scenery: Mass Spectrometry Modifications 7935 Based Investigation of Phosphorylation 8.4. Crosstalk between SUMOylation and the and Acetylation 7925 UbiquitinÀProteasome System 7935 2. Ubiquitin and Ubiquitin-like Protein Purification 9. Conclusions and Future Perspectives 7935 Approaches 7925 Author Information 7935 2.1. Epitope-Tagged Ubiquitin and Ubiquitin-like Biography 7935 Proteins 7925 Acknowledgment 7936 2.2. Traps Based on Ubiquitin- and Ubiquitin-like References 7936 Binding Domains 7926 2.3. Antibody-Based Purification of Ubiquitin and Ubiquitin-like Proteins 7926 1. INTRODUCTION 2.4. Challenges and Pitfalls 7926 Proteomes are significantly more complex than genomes 2.5. Summary 7926 and transcriptomes due to protein processing and extensive 3. Ubiquitin Proteomics 7927 post-translational modification (PTM) of proteins. Hundreds ff fi 3.1. Proteomic Studies Employing Tagged of di erent modi cations exist. Release 66 of the RESID database1 (http://www.ebi.ac.uk/RESID/) contains 559 dif- Ubiquitin 7927 ferent modifications, including small chemical modifications 3.2. Ubiquitin Binding Domains 7927 such as phosphorylation, acetylation, and methylation and mod- 3.3. Anti-Ubiquitin Antibodies 7927 ification by small proteins, including ubiquitin and ubiquitin- 3.4. -
1 Supporting Information for a Microrna Network Regulates
Supporting Information for A microRNA Network Regulates Expression and Biosynthesis of CFTR and CFTR-ΔF508 Shyam Ramachandrana,b, Philip H. Karpc, Peng Jiangc, Lynda S. Ostedgaardc, Amy E. Walza, John T. Fishere, Shaf Keshavjeeh, Kim A. Lennoxi, Ashley M. Jacobii, Scott D. Rosei, Mark A. Behlkei, Michael J. Welshb,c,d,g, Yi Xingb,c,f, Paul B. McCray Jr.a,b,c Author Affiliations: Department of Pediatricsa, Interdisciplinary Program in Geneticsb, Departments of Internal Medicinec, Molecular Physiology and Biophysicsd, Anatomy and Cell Biologye, Biomedical Engineeringf, Howard Hughes Medical Instituteg, Carver College of Medicine, University of Iowa, Iowa City, IA-52242 Division of Thoracic Surgeryh, Toronto General Hospital, University Health Network, University of Toronto, Toronto, Canada-M5G 2C4 Integrated DNA Technologiesi, Coralville, IA-52241 To whom correspondence should be addressed: Email: [email protected] (M.J.W.); yi- [email protected] (Y.X.); Email: [email protected] (P.B.M.) This PDF file includes: Materials and Methods References Fig. S1. miR-138 regulates SIN3A in a dose-dependent and site-specific manner. Fig. S2. miR-138 regulates endogenous SIN3A protein expression. Fig. S3. miR-138 regulates endogenous CFTR protein expression in Calu-3 cells. Fig. S4. miR-138 regulates endogenous CFTR protein expression in primary human airway epithelia. Fig. S5. miR-138 regulates CFTR expression in HeLa cells. Fig. S6. miR-138 regulates CFTR expression in HEK293T cells. Fig. S7. HeLa cells exhibit CFTR channel activity. Fig. S8. miR-138 improves CFTR processing. Fig. S9. miR-138 improves CFTR-ΔF508 processing. Fig. S10. SIN3A inhibition yields partial rescue of Cl- transport in CF epithelia. -
An Unbiased Reconstruction of the T Helper Cell Type 2 Differentiation Network
bioRxiv preprint doi: https://doi.org/10.1101/196022; this version posted October 4, 2017. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. An unbiased reconstruction of the T helper cell type 2 differentiation network 1,3 1 1 1 1 Authors: Johan Henriksson , Xi Chen , Tomás Gomes , Kerstin Meyer , Ricardo Miragaia , 4 1 4 1 1,2,* Ubaid Ullah , Jhuma Pramanik , Riita Lahesmaa , Kosuke Yusa , Sarah A Teichmann Affiliations: 1 Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom 2 EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom 3 Karolinska Institutet, Department. of Biosciences and Nutrition, Hälsovägen 7, Novum, SE-141 83, Huddinge, Sweden 4 Turku Centre for Biotechnology, Tykistokatu 6 FI-20520, Turku, Finland *To whom correspondence should be addressed: [email protected] Tomas: [email protected] Ricardo: [email protected] Ubaid Ullah: [email protected] Jhuma: [email protected] -
The Ire1a-XBP1 Pathway Promotes T Helper Cell Differentiation by Resolving Secretory Stress and Accelerating Proliferation
bioRxiv preprint doi: https://doi.org/10.1101/235010; this version posted December 15, 2017. 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. The IRE1a-XBP1 pathway promotes T helper cell differentiation by resolving secretory stress and accelerating proliferation Jhuma Pramanik1, Xi Chen1, Gozde Kar1,2, Tomás Gomes1, Johan Henriksson1, Zhichao Miao1,2, Kedar Natarajan1, Andrew N. J. McKenzie3, Bidesh Mahata1,2*, Sarah A. Teichmann1,2,4* 1. Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom 2. EMBL-European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom 3. MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 OQH, United Kingdom 4. Theory of Condensed Matter, Cavendish Laboratory, 19 JJ Thomson Ave, Cambridge CB3 0HE, United Kingdom. *To whom correspondence should be addressed: [email protected] and [email protected] Keywords: Th2 lymphocyte, XBP1, Genome wide XBP1 occupancy, Th2 lymphocyte proliferation, ChIP-seq, RNA-seq, Th2 transcriptome Summary The IRE1a-XBP1 pathway, a conserved adaptive mediator of the unfolded protein response, is indispensable for the development of secretory cells. It maintains endoplasmic reticulum homeostasis by facilitating protein folding and enhancing secretory capacity of the cells. Its role in immune cells is emerging. It is involved in dendritic cell, plasma cell and eosinophil development and differentiation. Using genome-wide approaches, integrating ChIPmentation and mRNA-sequencing data, we have elucidated the regulatory circuitry governed by the IRE1a-XBP1 pathway in type-2 T helper cells (Th2). -
Loss of Postnatal Quiescence of Neural Stem Cells Through Mtor Activation Upon Genetic Removal of Cysteine String Protein-Α
Loss of postnatal quiescence of neural stem cells through mTOR activation upon genetic removal of cysteine string protein-α Jose L. Nieto-Gonzáleza,b,c,1,2, Leonardo Gómez-Sáncheza,b,c,1, Fabiola Mavillarda,b,c, Pedro Linares-Clementea,b,c, María C. Riveroa,b,c, Marina Valenzuela-Villatoroa,b,c, José L. Muñoz-Bravoa,b,c, Ricardo Pardala,b,c, and Rafael Fernández-Chacóna,b,c,2 aInstituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/Consejo Superior de Investigaciones Científicas/Universidad de Sevilla, 41013 Sevilla, Spain; bDepartamento de Fisiología Médica y Biofísica, Universidad de Sevilla, 41009 Sevilla, Spain; and cCentro Investigación Biomédica en Red Enfermedades Neurodegenerativas, 41013 Sevilla, Spain Edited by Thomas C. Südhof, Stanford University School of Medicine, Stanford, CA, and approved March 4, 2019 (received for review October 9, 2018) Neural stem cells continuously generate newborn neurons that protein-A (SGTA) (13). Interestingly, CSP-α is required to maintain integrate into and modify neural circuitry in the adult hippocam- the stability of the SNARE protein SNAP25 at synaptic termi- pus. The molecular mechanisms that regulate or perturb neural nals (14–16). SNAP25 cannot maintain its function without a stem cell proliferation and differentiation, however, remain poorly chaperone, which is probably due to the molecular stress induced understood. Here, we have found that mouse hippocampal radial during cycles of assembly and disassembly of the SNARE com- glia-like (RGL) neural stem cells express the synaptic cochaperone plex (15, 17). Remarkably, knockout (KO) mice lacking CSP-α cysteine string protein-α (CSP-α). Remarkably, in CSP-α knockout suffer from a devastating and early synaptic degeneration (18) mice, RGL stem cells lose quiescence postnatally and enter into a that is particularly evident in highly active neurons (19). -
Gene and Protein Expression Profiling of Human Ovarian Cancer Cells Treated with the Heat Shock Protein 90 Inhibitor 17-Allylamino-17-Demethoxygeldanamycin
Research Article Gene and Protein Expression Profiling of Human Ovarian Cancer Cells Treated with the Heat Shock Protein 90 Inhibitor 17-Allylamino-17-Demethoxygeldanamycin Alison Maloney,1 Paul A. Clarke,1 Soren Naaby-Hansen,3,4 Rob Stein,3,5 Jens-Oliver Koopman,3,4 Akunna Akpan,3,4 Alice Yang,3,4 Marketa Zvelebil,3,4 Rainer Cramer,3,4 Lindsay Stimson,1 Wynne Aherne,1 Udai Banerji,1,2 Ian Judson,1,2 Swee Sharp,1 Marissa Powers,1 Emmanuel deBilly,1 Joanne Salmons,1 Michael Walton,1 Al Burlingame,3,4 Michael Waterfield,3,4 and Paul Workman1 1Haddow Laboratories, Cancer Research UK Centre for Cancer Therapeutics, The Institute of Cancer Research; 2Royal Marsden NHS Foundation Trust, Sutton, Surrey, United Kingdom; 3Ludwig Institute for Cancer Research and Departments of 4Biochemistry and Molecular Biology and 5Oncology, University College London, London, United Kingdom Abstract anticancer agents and provide a means of obtaining a detailed The promising antitumor activity of 17-allylamino-17-deme- molecular signature of drug action (1, 2). In addition, these thoxygeldanamycin (17AAG) results from inhibition of the methods may identify pharmacodynamic markers that can be used molecular chaperone heat shock protein 90(HSP90)and to evaluate drugs in clinical trials. Gene expression microarrays are subsequent degradation of multiple oncogenic client proteins. increasingly used to investigate the molecular responses to cancer Gene expression microarray and proteomic analysis were used drugs in tumor cells (1). Although valuable, analysis of gene to profile molecular changes in the A2780human ovarian expression at the mRNA level alone cannot adequately predict cancer cell line treated with 17AAG. -
Small Glutamine-Rich Tetratricopeptide Repeat
www.nature.com/scientificreports OPEN Small Glutamine-Rich Tetratricopeptide Repeat- Containing Protein Alpha (SGTA) Received: 04 January 2016 Accepted: 07 June 2016 Ablation Limits Offspring Viability Published: 30 June 2016 and Growth in Mice Lisa K. Philp1, Tanya K. Day1, Miriam S. Butler1, Geraldine Laven-Law1, Shalini Jindal1, Theresa E. Hickey1, Howard I. Scher2, Lisa M. Butler1,3,* & Wayne D. Tilley1,3,* Small glutamine-rich tetratricopeptide repeat-containing protein α (SGTA) has been implicated as a co-chaperone and regulator of androgen and growth hormone receptor (AR, GHR) signalling. We investigated the functional consequences of partial and full Sgta ablation in vivo using Cre-lox Sgta- null mice. Sgta+/− breeders generated viable Sgta−/− offspring, but at less than Mendelian expectancy. Sgta−/− breeders were subfertile with small litters and higher neonatal death (P < 0.02). Body size was significantly and proportionately smaller in male and femaleSgta −/− (vs WT, Sgta+/− P < 0.001) from d19. Serum IGF-1 levels were genotype- and sex-dependent. Food intake, muscle and bone mass and adiposity were unchanged in Sgta−/−. Vital and sex organs had normal relative weight, morphology and histology, although certain androgen-sensitive measures such as penis and preputial size, and testis descent, were greater in Sgta−/−. Expression of AR and its targets remained largely unchanged, although AR localisation was genotype- and tissue-dependent. Generally expression of other TPR- containing proteins was unchanged. In conclusion, this thorough investigation of SGTA-null mutation reports a mild phenotype of reduced body size. The model’s full potential likely will be realised by genetic crosses with other models to interrogate the role of SGTA in the many diseases in which it has been implicated. -
AL SERAIHI, a Phd Final 010519
The Genetics of Familial Leukaemia and Myelodysplasia __________________ Ahad Fahad H Al Seraihi A thesis submitted for the Degree of Doctor of Philosophy (PhD) at Queen Mary University of London January 2019 Centre for Haemato-Oncology Barts Cancer Institute Charterhouse Square London, UK EC1M 6BQ Statement of Originality Statement of Originality I, Ahad Fahad H Al Seraihi, confirm that the research included within this thesis is my own work or that where it has been carried out in collaboration with, or supported by others, that this is duly acknowledged below and my contribution indicated. Previously published material is also acknowledged below. I attest that I have exercised reasonable care to ensure that the work is original, and does not to the best of my knowledge break any UK law, infringe any third party’s copyright or other Intellectual Property Right, or contain any confidential material. I accept that the College has the right to use plagiarism detection software to check the electronic version of the thesis. I confirm that this thesis has not been previously submitted for the award of a degree by this or any other university. The copyright of this thesis rests with the author and no quotation from it or information derived from it may be published without the prior written consent of the author. Signature: Date: 30th January 2019 2 Details of Collaborations and Publications Details of Collaborations: Targeted deep sequencing detailed in Chapter 3 was carried out at King’s College Hospital NHS Foundation Trust, London, UK, in the laboratory for Molecular Haemato- Oncology led by Dr Nicholas Lea and bioinformatics analysis was performed by Dr Steven Best. -
Heat Shock Proteins in Vascular Diabetic Complications: Review and Future Perspective
International Journal of Molecular Sciences Review Heat Shock Proteins in Vascular Diabetic Complications: Review and Future Perspective Stefania Bellini 1,†, Federica Barutta 1,†, Raffaella Mastrocola 2 ID , Luigi Imperatore 1, Graziella Bruno 1 and Gabriella Gruden 1,* 1 Laboratory of Diabetic Nephropathy, Department of Medical Sciences, University of Turin, Corso Dogliotti 14, 10126 Turin, Italy; [email protected] (S.B.); [email protected] (F.B.); [email protected] (L.I.); [email protected] (G.B.) 2 Department of Clinical and Biological Sciences, University of Turin, Corso Raffaello 30, 10125 Turin, Italy; [email protected] * Correspondence: [email protected]; Tel.: +39-011-633-6035 † These authors contribute equally to this work. Received: 27 November 2017; Accepted: 11 December 2017; Published: 14 December 2017 Abstract: Heat shock proteins (HSPs) are a large family of proteins highly conserved throughout evolution because of their unique cytoprotective properties. Besides assisting protein refolding and regulating proteostasis under stressful conditions, HSPs also play an important role in protecting cells from oxidative stress, inflammation, and apoptosis. Therefore, HSPs are crucial in counteracting the deleterious effects of hyperglycemia in target organs of diabetes vascular complications. Changes in HSP expression have been demonstrated in diabetic complications and functionally related to hyperglycemia-induced cell injury. Moreover, associations between diabetic complications and altered circulating levels of both HSPs and anti-HSPs have been shown in clinical studies. HSPs thus represent an exciting therapeutic opportunity and might also be valuable as clinical biomarkers. However, this field of research is still in its infancy and further studies in both experimental diabetes and humans are required to gain a full understanding of HSP relevance.