The Role of Heat Shock Proteins in Regulating Receptor Signal Transduction
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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. -
Yichen – Structure and Allostery of the Chaperonin Groel. Allosteric
Literature Lunch 5-1-13 Yichen – J Mol Biol. 2013 May 13;425(9):1476-87. doi: 10.1016/j.jmb.2012.11.028. Epub 2012 Nov 24. Structure and Allostery of the Chaperonin GroEL. Saibil HR, Fenton WA, Clare DK, Horwich AL. Source Crystallography and Institute of Structural and Molecular Biology, Birkbeck College London, Malet Street, London WC1E 7HX, UK. Abstract Chaperonins are intricate allosteric machines formed of two back-to-back, stacked rings of subunits presenting end cavities lined with hydrophobic binding sites for nonnative polypeptides. Once bound, substrates are subjected to forceful, concerted movements that result in their ejection from the binding surface and simultaneous encapsulation inside a hydrophilic chamber that favors their folding. Here, we review the allosteric machine movements that are choreographed by ATP binding, which triggers concerted tilting and twisting of subunit domains. These movements distort the ring of hydrophobic binding sites and split it apart, potentially unfolding the multiply bound substrate. Then, GroES binding is accompanied by a 100° twist of the binding domains that removes the hydrophobic sites from the cavity lining and forms the folding chamber. ATP hydrolysis is not needed for a single round of binding and encapsulation but is necessary to allow the next round of ATP binding in the opposite ring. It is this remote ATP binding that triggers dismantling of the folding chamber and release of the encapsulated substrate, whether folded or not. The basis for these ordered actions is an elegant system of nested cooperativity of the ATPase machinery. ATP binds to a ring with positive cooperativity, and movements of the interlinked subunit domains are concerted. -
RGS22 Antibody (Pab)
21.10.2014RGS22 antibody (pAb) Rabbit Anti-Human/Mouse/Rat Regulator of G-protein signaling 22 (PRTD -NY2) Instruction Manual Catalog Number PK-AB718-7001 Synonyms RGS22 Antibody: Regulator of G-protein signaling 22, PRTD-NY2 Description Regulator of G-protein signaling (RGS) proteins contain an 120 amino acid conserved domain, termed the RGS domain, that acts as a GTPase-activating protein that acts to reduce the signal transmitted by the receptor-activated G-alpha subunit. RGS22 is a recently identified member of this family that localizes to the testis and can interact with guanine nucleotide binding proteins alpha 11, 12, and 13 (GNA11, GNA12, and GNA13). While RGS22 has been postulated to play a role in spermiogenesis in the testis, it is also expressed in several cancer cell lines with an epithelial origin and associated with cancer metastasis. Its overexpression in a highly metastatic cancer causes a decrease in cell migration and a reduction of the invasive potential of the cells, suggesting that RGS22 may be a potential prognostic biomarker for metastasis. Quantity 100 µg Source / Host Rabbit Immunogen RGS22 antibody was raised against a 19 amino acid synthetic peptide near the amino terminus of human RGS22. Purification Method Affinity chromatography purified via peptide column. Clone / IgG Subtype Polyclonal antibody Species Reactivity Human, Mouse, Rat Specificity At least four isoforms of RGS22 are known to exist; this antibody will detect the three longest isoforms. RGS22 antibody is predicted to not cross-react with other RGS proteins Formulation Antibody is supplied in PBS containing 0.02% sodium azide. Reconstitution During shipment, small volumes of antibody will occasionally become entrapped in the seal of the product vial. -
Deletion Variant Against Age-Related Macular Degeneration In
Laboratory Investigation (2017) 97, 43–52 © 2017 USCAP, Inc All rights reserved 0023-6837/17 Protective effects of an HTRA1 insertion–deletion variant against age-related macular degeneration in the Chinese populations Tsz Kin Ng1, Xiao Ying Liang1, Fang Lu2,3, David TL Liu1, Gary HF Yam1,LiMa1, Pancy OS Tam1, Haoyu Chen4, Ling Ping Cen4, Li Jia Chen1, Zhenglin Yang2,3 and Chi Pui Pang1 Age-related macular degeneration (AMD) is a leading cause of visual impairment and irreversible blindness in most developed countries, affecting about 50 million elderly people worldwide. Retinal pigment epithelial (RPE) cell degeneration is the pathophysiological cause of AMD, leading to geographic atrophy and choroidal neovascularization. We and others have previously identified several polymorphisms on chromosome 10q26 (HTRA1 rs11200638 as well as LOC387715 rs10490924 and c.372_815del443ins54) associated with AMD. In this study, we confirmed the association of our previously identified HTRA1 insertion–deletion (indel) variant (c.34delCinsTCCT) in 195 exudative AMD patients and 390 controls from the Hong Kong Chinese cohort with additional 168 patients and 210 controls from the Chengdu Chinese cohort and followed by studying its biological functions in RPE cells. Genetic analysis verified the higher prevalence of c.34delCinsTCCT allele in control subjects (8.0%) than in AMD patients (1.9%; P = 7.87 × 10 − 5, odds ratio = 0.229). This protective effect was validated as the haplotype of the c.34delCinsTCCT allele existed independent of the risk haplotype (P = 1.17 × 10 − 5). In vitro studies showed that recombinant HTRA1 c.34delCinsTCCT variant protein was more localized in the endoplasmic reticulum of RPE cells compared with the wild-type protein, and its secretion was delayed. -
Investigation of the Underlying Hub Genes and Molexular Pathogensis in Gastric Cancer by Integrated Bioinformatic Analyses
bioRxiv preprint doi: https://doi.org/10.1101/2020.12.20.423656; this version posted December 22, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Investigation of the underlying hub genes and molexular pathogensis in gastric cancer by integrated bioinformatic analyses Basavaraj Vastrad1, Chanabasayya Vastrad*2 1. Department of Biochemistry, Basaveshwar College of Pharmacy, Gadag, Karnataka 582103, India. 2. Biostatistics and Bioinformatics, Chanabasava Nilaya, Bharthinagar, Dharwad 580001, Karanataka, India. * Chanabasayya Vastrad [email protected] Ph: +919480073398 Chanabasava Nilaya, Bharthinagar, Dharwad 580001 , Karanataka, India bioRxiv preprint doi: https://doi.org/10.1101/2020.12.20.423656; this version posted December 22, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Abstract The high mortality rate of gastric cancer (GC) is in part due to the absence of initial disclosure of its biomarkers. The recognition of important genes associated in GC is therefore recommended to advance clinical prognosis, diagnosis and and treatment outcomes. The current investigation used the microarray dataset GSE113255 RNA seq data from the Gene Expression Omnibus database to diagnose differentially expressed genes (DEGs). Pathway and gene ontology enrichment analyses were performed, and a proteinprotein interaction network, modules, target genes - miRNA regulatory network and target genes - TF regulatory network were constructed and analyzed. Finally, validation of hub genes was performed. The 1008 DEGs identified consisted of 505 up regulated genes and 503 down regulated genes. -
Mom Identifies a Receptor for the Drosophila JAK/STAT Signal Transduction Pathway and Encodes a Protein Distantly Related to the Mammalian Cytokine Receptor Family
Downloaded from genesdev.cshlp.org on October 1, 2021 - Published by Cold Spring Harbor Laboratory Press mom identifies a receptor for the Drosophila JAK/STAT signal transduction pathway and encodes a protein distantly related to the mammalian cytokine receptor family Hua-Wei Chen,1,3 Xiu Chen,1,3 Su-Wan Oh,1 Maria J. Marinissen,2 J. Silvio Gutkind,2 and Steven X. Hou1,4 1The Laboratory of Immunobiology, National Institutes of Health, National Cancer Institute at Frederick, Frederick, Maryland 21702, USA; 2Oral and Pharyngeal Cancer Branch, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, Maryland 20892, USA The JAK/STAT signal transduction pathway controls numerous events in Drosophila melanogaster development. Receptors for the pathway have yet to be identified. Here we have identified a Drosophila gene that shows embryonic mutant phenotypes identical to those in the hopscotch (hop)/JAK kinase and marelle (mrl)/Stat92e mutations. We named this gene master of marelle (mom). Genetic analyses place mom’s function between upd (the ligand) and hop. We further show that cultured cells transfected with the mom gene bind UPD and activate the HOP/STAT92E signal transduction pathway. mom encodes a protein distantly related to the mammalian cytokine receptor family. These data show that mom functions as a receptor of the Drosophila JAK/STAT signal transduction pathway. [Key Words: Drosophila; JAK/STAT; signal transduction; cytokine receptor] Received October 19, 2001; revised version accepted December 6, 2001. The JAK/STAT signal transduction pathway was identi- (upd) secreted glycoprotein identifies an in vivo ligand fied through studies of the transcriptional activation re- activating the HOP/STAT92E pathway (Harrison et al. -
At Elevated Temperatures, Heat Shock Protein Genes Show Altered Ratios Of
EXPERIMENTAL AND THERAPEUTIC MEDICINE 22: 900, 2021 At elevated temperatures, heat shock protein genes show altered ratios of different RNAs and expression of new RNAs, including several novel HSPB1 mRNAs encoding HSP27 protein isoforms XIA GAO1,2, KEYIN ZHANG1,2, HAIYAN ZHOU3, LUCAS ZELLMER4, CHENGFU YUAN5, HAI HUANG6 and DEZHONG JOSHUA LIAO2,6 1Department of Pathology, Guizhou Medical University Hospital; 2Key Lab of Endemic and Ethnic Diseases of The Ministry of Education of China in Guizhou Medical University; 3Clinical Research Center, Guizhou Medical University Hospital, Guiyang, Guizhou 550004, P.R. China; 4Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA; 5Department of Biochemistry, China Three Gorges University, Yichang, Hubei 443002; 6Center for Clinical Laboratories, Guizhou Medical University Hospital, Guiyang, Guizhou 550004, P.R. China Received December 16, 2020; Accepted May 10, 2021 DOI: 10.3892/etm.2021.10332 Abstract. Heat shock proteins (HSP) serve as chaperones genes may engender multiple protein isoforms. These results to maintain the physiological conformation and function of collectively suggested that, besides increasing their expres‑ numerous cellular proteins when the ambient temperature is sion, certain HSP and associated genes also use alternative increased. To determine how accurate the general assumption transcription start sites to produce multiple RNA transcripts that HSP gene expression is increased in febrile situations is, and use alternative splicing of a transcript to produce multiple the RNA levels of the HSF1 (heat shock transcription factor 1) mature RNAs, as important mechanisms for responding to an gene and certain HSP genes were determined in three cell increased ambient temperature in vitro. lines cultured at 37˚C or 39˚C for three days. -
1 Supplemental Appendix Table of Contents Author
Supplemental Appendix Table of Contents Author Lists………………………………………………….…..2-3 Supplemental Figures …………………………………..……..4-20 Supplemental Tables …………………………………….…….21-41 Supplemental References……………………………………..42 ! 1! Brittany A. Goods, PhD1,2*, Michael H. Askenase, PhD3*, Erica Markarian4, Hannah E. Beatty3, Riley Drake1, Ira Fleming1, Jonathan H. DeLong3, Naomi H. Philip5, Charles C. Matouk, MD6, Issam A. Awad, MD7, Mario Zuccarello, MD8, Daniel F. Hanley, MD9, J. Christopher Love, PhD2,4,10,#, Alex K. Shalek, PhD1,2,4,11,12,13,14,#, and Lauren H. Sansing, MD, MS3,15,#, on behalf of the ICHseq Investigators 1Department of Chemistry and Institute for Medical Engineering & Science, Massachusetts Institute of Technology 2Broad Institute, Harvard University & Massachusetts Institute of Technology 3Department of Neurology, Yale University School of Medicine 4Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology 5Department of Immunobiology, Yale University School of Medicine 6Department of Neurosurgery, Yale University School of Medicine 7Department of Neurosurgery, University of Chicago 8Department of Neurosurgery, University of Cincinnati 9Brain Injury Outcomes Division, Johns Hopkins School of Medicine 10Department of Chemical Engineering, Massachusetts Institute of Technology 11Ragon Institute, Harvard University, Massachusetts Institute of Technology, & Massachusetts General Hospital 12Division of Health Science & Technology, Harvard Medical School 13Program in Computational & Systems Biology, Massachusetts -
A Chemical Proteomic Approach to Investigate Rab Prenylation in Living Systems
A chemical proteomic approach to investigate Rab prenylation in living systems By Alexandra Fay Helen Berry A thesis submitted to Imperial College London in candidature for the degree of Doctor of Philosophy of Imperial College. Department of Chemistry Imperial College London Exhibition Road London SW7 2AZ August 2012 Declaration of Originality I, Alexandra Fay Helen Berry, hereby declare that this thesis, and all the work presented in it, is my own and that it has been generated by me as the result of my own original research, unless otherwise stated. 2 Abstract Protein prenylation is an important post-translational modification that occurs in all eukaryotes; defects in the prenylation machinery can lead to toxicity or pathogenesis. Prenylation is the modification of a protein with a farnesyl or geranylgeranyl isoprenoid, and it facilitates protein- membrane and protein-protein interactions. Proteins of the Ras superfamily of small GTPases are almost all prenylated and of these the Rab family of proteins forms the largest group. Rab proteins are geranylgeranylated with up to two geranylgeranyl groups by the enzyme Rab geranylgeranyltransferase (RGGT). Prenylation of Rabs allows them to locate to the correct intracellular membranes and carry out their roles in vesicle trafficking. Traditional methods for probing prenylation involve the use of tritiated geranylgeranyl pyrophosphate which is hazardous, has lengthy detection times, and is insufficiently sensitive. The work described in this thesis developed systems for labelling Rabs and other geranylgeranylated proteins using a technique known as tagging-by-substrate, enabling rapid analysis of defective Rab prenylation in cells and tissues. An azide analogue of the geranylgeranyl pyrophosphate substrate of RGGT (AzGGpp) was applied for in vitro prenylation of Rabs by recombinant enzyme. -
1714 Gene Comprehensive Cancer Panel Enriched for Clinically Actionable Genes with Additional Biologically Relevant Genes 400-500X Average Coverage on Tumor
xO GENE PANEL 1714 gene comprehensive cancer panel enriched for clinically actionable genes with additional biologically relevant genes 400-500x average coverage on tumor Genes A-C Genes D-F Genes G-I Genes J-L AATK ATAD2B BTG1 CDH7 CREM DACH1 EPHA1 FES G6PC3 HGF IL18RAP JADE1 LMO1 ABCA1 ATF1 BTG2 CDK1 CRHR1 DACH2 EPHA2 FEV G6PD HIF1A IL1R1 JAK1 LMO2 ABCB1 ATM BTG3 CDK10 CRK DAXX EPHA3 FGF1 GAB1 HIF1AN IL1R2 JAK2 LMO7 ABCB11 ATR BTK CDK11A CRKL DBH EPHA4 FGF10 GAB2 HIST1H1E IL1RAP JAK3 LMTK2 ABCB4 ATRX BTRC CDK11B CRLF2 DCC EPHA5 FGF11 GABPA HIST1H3B IL20RA JARID2 LMTK3 ABCC1 AURKA BUB1 CDK12 CRTC1 DCUN1D1 EPHA6 FGF12 GALNT12 HIST1H4E IL20RB JAZF1 LPHN2 ABCC2 AURKB BUB1B CDK13 CRTC2 DCUN1D2 EPHA7 FGF13 GATA1 HLA-A IL21R JMJD1C LPHN3 ABCG1 AURKC BUB3 CDK14 CRTC3 DDB2 EPHA8 FGF14 GATA2 HLA-B IL22RA1 JMJD4 LPP ABCG2 AXIN1 C11orf30 CDK15 CSF1 DDIT3 EPHB1 FGF16 GATA3 HLF IL22RA2 JMJD6 LRP1B ABI1 AXIN2 CACNA1C CDK16 CSF1R DDR1 EPHB2 FGF17 GATA5 HLTF IL23R JMJD7 LRP5 ABL1 AXL CACNA1S CDK17 CSF2RA DDR2 EPHB3 FGF18 GATA6 HMGA1 IL2RA JMJD8 LRP6 ABL2 B2M CACNB2 CDK18 CSF2RB DDX3X EPHB4 FGF19 GDNF HMGA2 IL2RB JUN LRRK2 ACE BABAM1 CADM2 CDK19 CSF3R DDX5 EPHB6 FGF2 GFI1 HMGCR IL2RG JUNB LSM1 ACSL6 BACH1 CALR CDK2 CSK DDX6 EPOR FGF20 GFI1B HNF1A IL3 JUND LTK ACTA2 BACH2 CAMTA1 CDK20 CSNK1D DEK ERBB2 FGF21 GFRA4 HNF1B IL3RA JUP LYL1 ACTC1 BAG4 CAPRIN2 CDK3 CSNK1E DHFR ERBB3 FGF22 GGCX HNRNPA3 IL4R KAT2A LYN ACVR1 BAI3 CARD10 CDK4 CTCF DHH ERBB4 FGF23 GHR HOXA10 IL5RA KAT2B LZTR1 ACVR1B BAP1 CARD11 CDK5 CTCFL DIAPH1 ERCC1 FGF3 GID4 HOXA11 IL6R KAT5 ACVR2A -
Functional and Physical Interaction Between Yeast Hsp90 and Hsp70
Functional and physical interaction between yeast PNAS PLUS Hsp90 and Hsp70 Andrea N. Kravatsa, Joel R. Hoskinsa, Michael Reidyb, Jill L. Johnsonc, Shannon M. Doylea, Olivier Genesta,1, Daniel C. Masisonb, and Sue Wicknera,2 aLaboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892; bLaboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892; and cDepartment of Biological Sciences, University of Idaho, Moscow, ID 83844 Contributed by Sue Wickner, January 25, 2018 (sent for review November 17, 2017; reviewed by Daniel N. A. Bolon and Jeffrey L. Brodsky) Heat shock protein 90 (Hsp90) is a highly conserved ATP-dependent changes in response to ATP binding, hydrolysis, and ADP release molecular chaperone that is essential in eukaryotes. It is required for (1,3,6,14–16). In the absence of ATP, the Hsp90 dimer acquires the activation and stabilization of more than 200 client proteins, an open, V-shaped structure such that the protomers interact via including many kinases and steroid hormone receptors involved in the C-terminal dimerization domain (16). When ATP is bound, the cell-signaling pathways. Hsp90 chaperone activity requires collabo- protein takes on a closed conformation with the two N-domains of ration with a subset of the many Hsp90 cochaperones, including the the dimer interacting and a portion of the N-domain, the “lid,” Hsp70 chaperone. In higher eukaryotes, the collaboration between closing over the nucleotide in each protomer (16, 17). Additional Hsp90 and Hsp70 is indirect and involves Hop, a cochaperone that conformational changes occur upon ATP hydrolysis, resulting in a interacts with both Hsp90 and Hsp70. -
The Role of Stress-Derived Vesicles in the Bystander Effect and Cancer Related Cachexia
THE ROLE OF STRESS-DERIVED VESICLES IN THE BYSTANDER EFFECT AND CANCER RELATED CACHEXIA Thesis is submitted in partial fulfilment of the requirements of the award of Doctor of Philosophy FINDLAY REDVERS BEWICKE-COPLEY Department of Biological and Medical Sciences Degree awarded by Oxford Brookes University First submitted for examination: January 2018 ACKNOWLEDGEMENTS Thank you to Oxford Brookes for providing funding for my research, and especially to Professor Nigel Groome whose research and generosity has allowed so many to complete their PhDs. I would also like to say thank you to the Cancer and Polio trust for providing some of the funding for my PhD I would like to thank my Supervisors Dave and Ryan for their support throughout my PhD and for only occasionally saddling me with unrelated projects. Without your guidance and support I would have curled up into a ball in the corner of the office and gently sobbed to myself for the last 5 years. Thanks to Priya for her tireless work ensuring the lab functions correctly and supporting all other members of the lab. I’d also like to thank past members of the lab, Laura Jacobs and Laura Mulcahy for their support throughout both my MSc and my PhD. Sunny Vijen for chatting with me whilst he smoked and making me leave lunch early, so he could have another smoke before going back to work. Thank you to Robbie Crickley for all the lunch time chats. To Lia I would like to say χασμουριέμαι! Thanks to Bianca for all her help getting to know the world of immunocytochemistry.