Driver Mutations of the Adenoma-Carcinoma Sequence Govern the Intestinal Epithelial Global Translational Capacity

Total Page:16

File Type:pdf, Size:1020Kb

Driver Mutations of the Adenoma-Carcinoma Sequence Govern the Intestinal Epithelial Global Translational Capacity Driver mutations of the adenoma-carcinoma sequence govern the intestinal epithelial global translational capacity Wouter Laurentius Smita, Claudia Nanette Spaana, Ruben Johannes de Boera, Prashanthi Rameshb,c, Tânia Martins Garciaa, Bartolomeus Joannes Meijera, Jacqueline Ludovicus Maria Vermeulena, Marco Lezzerinid, Alyson Winfried MacInnesd, Jan Kostere, Jan Paul Medemab,c, Gijs Robert van den Brinka,f, Vanesa Muncana, and Jarom Heijmansa,g,1 aDepartment of Gastroenterology and Hepatology, Tytgat Institute for Liver and Intestinal Research, Amsterdam University Medical Center, University of Amsterdam, 1105 BK Amsterdam, The Netherlands; bLaboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, Cancer Center Amsterdam, Amsterdam University Medical Center, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands; cOncode Institute, Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands; dLaboratory for Genetic Metabolic Diseases, Amsterdam University Medical Center, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands; eDepartment of Oncogenomics, Amsterdam University Medical Center, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands; fRoche Innovation Center Basel, F. Hoffmann-La Roche AG, 4070 Basel, Switzerland; and gDepartment of Internal Medicine and Hematology, Amsterdam University Medical Center, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands Edited by Napoleone Ferrara, University of California San Diego, La Jolla, CA, and approved August 26, 2020 (received for review July 25, 2019) Deregulated global mRNA translation is an emerging feature of (4), ribosomal proteins and ribosomal RNA (rRNA) (5), and the cancer cells. Oncogenic transformation in colorectal cancer (CRC) is presence of oncogenes such as PIK3CA and c-MYC, that modu- driven by mutations in APC, KRAS, SMAD4, and TP53, known as late translational control (6). Thus, through aberrant signaling of the adenoma-carcinoma sequence (ACS). Here we introduce each pathways that converge on the translational apparatus, specific of these driver mutations into intestinal organoids to show that oncogenes may utilize entire proteomic programs in order to drive they are modulators of global translational capacity in intestinal oncogenic transformation of a normal cell (7). epithelial cells. Increased global translation resulting from loss of In the majority of sporadic CRCs, accumulation of a few driver Apc expression was potentiated by the presence of oncogenic mutations is considered to be sufficient in coordinating many of G12D Kras . Knockdown of Smad4 further enhanced global transla- the cell-intrinsic aspects of oncogenic transformation, which tion efficiency and was associated with a lower 4E-BP1-to-eIF4E epithelial cancer cells must adopt to clonally expand, invade, and ratio. Quadruple mutant cells with additional P53 loss displayed metastasize (8). Although the transcriptomic layers underpinning the highest global translational capacity, paralleled by high prolif- this complex process have been studied extensively, effects on eration and growth rates, indicating that the proteome is heavily specific translational programs, as well as the global translational geared toward cell division. Transcriptional reprogramming facili- capacity itself, are largely unknown. Recently, it has been shown tating global translation included elevated ribogenesis and activa- that Apc-deficient mouse intestinal cells harbor increased global tion of mTORC1 signaling. Accordingly, interfering with the translation rates via mTORC1-mediated modulation of transla- mTORC1/4E-BP/eIF4E axis inhibited the growth potential endowed tion elongation (9). This study clearly demonstrated that inter- by accumulation of multiple drivers. In conclusion, the ACS is char- fering with global translation through the mTORC1/S6K/eEF2K acterized by a strongly altered global translational landscape in axis strongly impaired intestinal epithelial hyperproliferation and epithelial cells, exposing a therapeutic potential for direct target- tumorigenesis caused by deficiency of Apc. Moreover, we have ing of the translational apparatus. Significance global translation | protein synthesis | colorectal cancer | driver mutations Deregulated global mRNA translation is a feature of various he adenoma-carcinoma sequence (ACS) is defined by a set of cancers and considered important in oncogenic transformation. Trecurrent driver mutations in APC, KRAS, SMAD4, and TP53 In colorectal cancer (CRC), the role of the most common driver genes, that accumulate during adenoma formation and pro- mutations in APC, KRAS, SMAD4, and TP53 on the global gression to sporadic colorectal cancer (CRC), often correlating translational capacity are incompletely understood. Here, using with specific stages of the developmental process (1). Since its mouse and human intestinal organoids, we found that each early description by Vogelstein and colleagues, a body of re- mutation governs the global translational capacity of the epi- search has further supported and elaborated on this well- thelial cell. Global translation is linked to known oncogenic established paradigm (2), and the putative oncogenic potential hallmarks, including cell proliferation and growth upon accu- of each mutation has been demonstrated in various genetic rodent mulation of these mutations, posing the translational appara- models (3). It is well known that driver mutations deregulate tus as a potential therapeutic target in CRC. specific cell signaling pathways, but how this ultimately leads to oncogenic transformation of a healthy intestinal cell remains to be Author contributions: W.L.S., A.W.M., G.R.v.d.B., V.M., and J.H. designed research; W.L.S., understood. Over the past decade, mounting evidence has indi- C.N.S., R.J.d.B., P.R., T.M.G., B.J.M., J.L.M.V., and M.L. performed research; J.K. and J.P.M. cated that quantitative and qualitative alterations in mRNA contributed new reagents/analytic tools; W.L.S. and C.N.S. analyzed data; and W.L.S. translation are a prominent feature of various cancers (4). Global wrote the paper. mRNA translation can be defined as the capacity of the cell’s The authors declare no competing interest. translation apparatus to produce nascent polypeptides in order to This article is a PNAS Direct Submission. maintain the cellular proteome. The translational apparatus con- Published under the PNAS license. sists of the mRNA transcripts, ribosomes, translation factors, and 1To whom correspondence may be addressed. Email: [email protected]. aminoacyl-tRNAs. Cancer cells exploit the translational apparatus This article contains supporting information online at https://www.pnas.org/lookup/suppl/ by deregulating these components, which is supported by multiple doi:10.1073/pnas.1912772117/-/DCSupplemental. lines of evidence, including altered expression translation factors First published September 28, 2020. 25560–25570 | PNAS | October 13, 2020 | vol. 117 | no. 41 www.pnas.org/cgi/doi/10.1073/pnas.1912772117 Downloaded by guest on September 30, 2021 recently shown that heterozygous expression of chaperone GRP78, affected global translation in wild-type cells, we withdrew canon- which leads to repression of p-eIF2α-mediated global translation, ical WNT agonist R-spondin for 24 h from the culture medium of reduced adenoma formation in Apc-deficient mice (10). Interest- wild-type organoids. As expected, when WNT signaling could not ingly, these studies have shown that genetically interfering with be sustained, the rate of global translation declined (SI Appendix, global translation predominantly affected Apc-deficient epithelium, Fig. S1E). with no obvious discernible phenotype of the epithelium during Clinically, human loss-of-function mutations in the APC gene homeostasis (9, 10). This suggests that epithelial cells that exhibit usually precede or coincide with gain-of-function mutations in functional loss of APC rely on ample global translational output the oncogene KRAS, as illustrated by KRAS point mutations during adenoma formation, displaying the importance of transla- present in 40 to 50% of CRCs at early stages (16). The most tional efficiency in transformed cells. Furthermore, efficient mRNA frequent mutation is a base substitution KRASG12D, a conversion translation, which mainly determines the mammalian cellular pro- of glycine (G) to aspartic acid (D), that renders RAS in an active teome (11), may be particularly important for maintaining the on- GTP‐bound state causing continuous activation of RAS signaling cogenic proteome in a cancer cell that must overcome repressed (17). To model this event, we studied whether KrasG12D modu- global translation when exposed to cellular stress (12). lated global translation in wild-type and Apc-deleted epithelium. It remains to be investigated whether the main driver muta- Using inducible heterozygous organoids from Villin-CreERT2- tions associated with CRC development affect the global trans- Kras+/G12D transgenic mice, we generated organoids that grew lational capacity of the intestinal epithelial cell. To address this, independent of culture factor EGF after in vitro recombination we studied the impact of oncogenic mutations in APC, KRAS, (SI Appendix, Fig. S1 A, Middle). Kras+/G12D organoids exhibited SMAD, and TP53 on the global translational capacity of primary an enlarged central lumen with maintained pericentral budding, − − intestinal epithelial cells. Our data reveal a highly altered
Recommended publications
  • Supplementary Materials: Evaluation of Cytotoxicity and Α-Glucosidase Inhibitory Activity of Amide and Polyamino-Derivatives of Lupane Triterpenoids
    Supplementary Materials: Evaluation of cytotoxicity and α-glucosidase inhibitory activity of amide and polyamino-derivatives of lupane triterpenoids Oxana B. Kazakova1*, Gul'nara V. Giniyatullina1, Akhat G. Mustafin1, Denis A. Babkov2, Elena V. Sokolova2, Alexander A. Spasov2* 1Ufa Institute of Chemistry of the Ufa Federal Research Centre of the Russian Academy of Sciences, 71, pr. Oktyabrya, 450054 Ufa, Russian Federation 2Scientific Center for Innovative Drugs, Volgograd State Medical University, Novorossiyskaya st. 39, Volgograd 400087, Russian Federation Correspondence Prof. Dr. Oxana B. Kazakova Ufa Institute of Chemistry of the Ufa Federal Research Centre of the Russian Academy of Sciences 71 Prospeсt Oktyabrya Ufa, 450054 Russian Federation E-mail: [email protected] Prof. Dr. Alexander A. Spasov Scientific Center for Innovative Drugs of the Volgograd State Medical University 39 Novorossiyskaya st. Volgograd, 400087 Russian Federation E-mail: [email protected] Figure S1. 1H and 13C of compound 2. H NH N H O H O H 2 2 Figure S2. 1H and 13C of compound 4. NH2 O H O H CH3 O O H H3C O H 4 3 Figure S3. Anticancer screening data of compound 2 at single dose assay 4 Figure S4. Anticancer screening data of compound 7 at single dose assay 5 Figure S5. Anticancer screening data of compound 8 at single dose assay 6 Figure S6. Anticancer screening data of compound 9 at single dose assay 7 Figure S7. Anticancer screening data of compound 12 at single dose assay 8 Figure S8. Anticancer screening data of compound 13 at single dose assay 9 Figure S9. Anticancer screening data of compound 14 at single dose assay 10 Figure S10.
    [Show full text]
  • RPL36 Antibody Kit
    Leader in Biomolecular Solutions for Life Science [One Step]RPL36 Antibody Kit Catalog No.: RK05700 Basic Information Background Catalog No. Ribosomes, the organelles that catalyze protein synthesis, consist of a small 40S subunit RK05700 and a large 60S subunit. Together these subunits are composed of 4 RNA species and approximately 80 structurally distinct proteins. This gene encodes a ribosomal protein Applications that is a component of the 60S subunit. The protein belongs to the L36E family of WB ribosomal proteins. It is located in the cytoplasm. Transcript variants derived from alternative splicing exist; they encode the same protein. As is typical for genes encoding Cross-Reactivity ribosomal proteins, there are multiple processed pseudogenes of this gene dispersed Human, Mouse, Rat through the genome. Observed MW 15kDa Calculated MW 12kDa Category Antibody kit Product Information Component & Recommended Dilutions Source Catalog No. Product Name Dilutions Rabbit RK05700-1 RPL36 Rabbit pAb 1:1000 dilution Purification RK05700-2 HRP Goat Anti-Rabbit IgG (H+L) 1:10000 dilution Affinity purification Storage Store at -20℃. Avoid freeze / thaw Immunogen Information cycles. Buffer: PBS with 0.02% sodium azide, Gene ID Swiss Prot 50% glycerol, pH7.3. 25873 Q9Y3U8 Avoid repeated freeze-thaw cycles. Immunogen Recombinant fusion protein containing a sequence corresponding to amino acids 1-105 Contact of human RPL36 (NP_056229.2). www.abclonal.com Synonyms RPL36;L36 Validation Data Western blot analysis of extracts of various cells, using RPL36 antibody (A7793) at 1:1000 dilution ratio through one-step method. Antibody | Protein | ELISA Kits | Enzyme | NGS | Service For research use only. Not for therapeutic or diagnostic purposes.
    [Show full text]
  • Bayesian Hierarchical Modeling of High-Throughput Genomic Data with Applications to Cancer Bioinformatics and Stem Cell Differentiation
    BAYESIAN HIERARCHICAL MODELING OF HIGH-THROUGHPUT GENOMIC DATA WITH APPLICATIONS TO CANCER BIOINFORMATICS AND STEM CELL DIFFERENTIATION by Keegan D. Korthauer A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy (Statistics) at the UNIVERSITY OF WISCONSIN–MADISON 2015 Date of final oral examination: 05/04/15 The dissertation is approved by the following members of the Final Oral Committee: Christina Kendziorski, Professor, Biostatistics and Medical Informatics Michael A. Newton, Professor, Statistics Sunduz Kele¸s,Professor, Biostatistics and Medical Informatics Sijian Wang, Associate Professor, Biostatistics and Medical Informatics Michael N. Gould, Professor, Oncology © Copyright by Keegan D. Korthauer 2015 All Rights Reserved i in memory of my grandparents Ma and Pa FL Grandma and John ii ACKNOWLEDGMENTS First and foremost, I am deeply grateful to my thesis advisor Christina Kendziorski for her invaluable advice, enthusiastic support, and unending patience throughout my time at UW-Madison. She has provided sound wisdom on everything from methodological principles to the intricacies of academic research. I especially appreciate that she has always encouraged me to eke out my own path and I attribute a great deal of credit to her for the successes I have achieved thus far. I also owe special thanks to my committee member Professor Michael Newton, who guided me through one of my first collaborative research experiences and has continued to provide key advice on my thesis research. I am also indebted to the other members of my thesis committee, Professor Sunduz Kele¸s,Professor Sijian Wang, and Professor Michael Gould, whose valuable comments, questions, and suggestions have greatly improved this dissertation.
    [Show full text]
  • Analysis of Gene Expression Data for Gene Ontology
    ANALYSIS OF GENE EXPRESSION DATA FOR GENE ONTOLOGY BASED PROTEIN FUNCTION PREDICTION A Thesis Presented to The Graduate Faculty of The University of Akron In Partial Fulfillment of the Requirements for the Degree Master of Science Robert Daniel Macholan May 2011 ANALYSIS OF GENE EXPRESSION DATA FOR GENE ONTOLOGY BASED PROTEIN FUNCTION PREDICTION Robert Daniel Macholan Thesis Approved: Accepted: _______________________________ _______________________________ Advisor Department Chair Dr. Zhong-Hui Duan Dr. Chien-Chung Chan _______________________________ _______________________________ Committee Member Dean of the College Dr. Chien-Chung Chan Dr. Chand K. Midha _______________________________ _______________________________ Committee Member Dean of the Graduate School Dr. Yingcai Xiao Dr. George R. Newkome _______________________________ Date ii ABSTRACT A tremendous increase in genomic data has encouraged biologists to turn to bioinformatics in order to assist in its interpretation and processing. One of the present challenges that need to be overcome in order to understand this data more completely is the development of a reliable method to accurately predict the function of a protein from its genomic information. This study focuses on developing an effective algorithm for protein function prediction. The algorithm is based on proteins that have similar expression patterns. The similarity of the expression data is determined using a novel measure, the slope matrix. The slope matrix introduces a normalized method for the comparison of expression levels throughout a proteome. The algorithm is tested using real microarray gene expression data. Their functions are characterized using gene ontology annotations. The results of the case study indicate the protein function prediction algorithm developed is comparable to the prediction algorithms that are based on the annotations of homologous proteins.
    [Show full text]
  • Identification of the Binding Partners for Hspb2 and Cryab Reveals
    Brigham Young University BYU ScholarsArchive Theses and Dissertations 2013-12-12 Identification of the Binding arP tners for HspB2 and CryAB Reveals Myofibril and Mitochondrial Protein Interactions and Non- Redundant Roles for Small Heat Shock Proteins Kelsey Murphey Langston Brigham Young University - Provo Follow this and additional works at: https://scholarsarchive.byu.edu/etd Part of the Microbiology Commons BYU ScholarsArchive Citation Langston, Kelsey Murphey, "Identification of the Binding Partners for HspB2 and CryAB Reveals Myofibril and Mitochondrial Protein Interactions and Non-Redundant Roles for Small Heat Shock Proteins" (2013). Theses and Dissertations. 3822. https://scholarsarchive.byu.edu/etd/3822 This Thesis is brought to you for free and open access by BYU ScholarsArchive. It has been accepted for inclusion in Theses and Dissertations by an authorized administrator of BYU ScholarsArchive. For more information, please contact [email protected], [email protected]. Identification of the Binding Partners for HspB2 and CryAB Reveals Myofibril and Mitochondrial Protein Interactions and Non-Redundant Roles for Small Heat Shock Proteins Kelsey Langston A thesis submitted to the faculty of Brigham Young University in partial fulfillment of the requirements for the degree of Master of Science Julianne H. Grose, Chair William R. McCleary Brian Poole Department of Microbiology and Molecular Biology Brigham Young University December 2013 Copyright © 2013 Kelsey Langston All Rights Reserved ABSTRACT Identification of the Binding Partners for HspB2 and CryAB Reveals Myofibril and Mitochondrial Protein Interactors and Non-Redundant Roles for Small Heat Shock Proteins Kelsey Langston Department of Microbiology and Molecular Biology, BYU Master of Science Small Heat Shock Proteins (sHSP) are molecular chaperones that play protective roles in cell survival and have been shown to possess chaperone activity.
    [Show full text]
  • Datasheet: VPA00491 Product Details
    Datasheet: VPA00491 Description: RABBIT ANTI RPLP0 Specificity: RPLP0 Format: Purified Product Type: PrecisionAb™ Polyclonal Isotype: Polyclonal IgG Quantity: 100 µl Product Details Applications This product has been reported to work in the following applications. This information is derived from testing within our laboratories, peer-reviewed publications or personal communications from the originators. Please refer to references indicated for further information. For general protocol recommendations, please visit www.bio-rad-antibodies.com/protocols. Yes No Not Determined Suggested Dilution Western Blotting 1/1000 PrecisionAb antibodies have been extensively validated for the western blot application. The antibody has been validated at the suggested dilution. Where this product has not been tested for use in a particular technique this does not necessarily exclude its use in such procedures. Further optimization may be required dependant on sample type. Target Species Human Species Cross Reacts with: Mouse, Rat Reactivity N.B. Antibody reactivity and working conditions may vary between species. Product Form Purified IgG - liquid Preparation Rabbit polyclonal antibody purified by affinity chromatography Buffer Solution Phosphate buffered saline Preservative 0.09% Sodium Azide (NaN3) Stabilisers 2% Sucrose Immunogen Synthetic peptide directed towards the N terminal region of human RPLP0 External Database Links UniProt: P05388 Related reagents Entrez Gene: 6175 RPLP0 Related reagents Specificity Rabbit anti Human RPLP0 antibody recognizes RPLP0 also known as 60S acidic ribosomal protein P0, 60S ribosomal protein L10E or acidic ribosomal phosphoprotein P0. Page 1 of 2 Ribosomes, the organelles that catalyze protein synthesis, consist of a small 40S subunit and a large 60S subunit. Together these subunits are composed of 4 RNA species and approximately 80 structurally distinct proteins.
    [Show full text]
  • Molecular Profile of Tumor-Specific CD8+ T Cell Hypofunction in a Transplantable Murine Cancer Model
    Downloaded from http://www.jimmunol.org/ by guest on September 25, 2021 T + is online at: average * The Journal of Immunology , 34 of which you can access for free at: 2016; 197:1477-1488; Prepublished online 1 July from submission to initial decision 4 weeks from acceptance to publication 2016; doi: 10.4049/jimmunol.1600589 http://www.jimmunol.org/content/197/4/1477 Molecular Profile of Tumor-Specific CD8 Cell Hypofunction in a Transplantable Murine Cancer Model Katherine A. Waugh, Sonia M. Leach, Brandon L. Moore, Tullia C. Bruno, Jonathan D. Buhrman and Jill E. Slansky J Immunol cites 95 articles Submit online. Every submission reviewed by practicing scientists ? is published twice each month by Receive free email-alerts when new articles cite this article. Sign up at: http://jimmunol.org/alerts http://jimmunol.org/subscription Submit copyright permission requests at: http://www.aai.org/About/Publications/JI/copyright.html http://www.jimmunol.org/content/suppl/2016/07/01/jimmunol.160058 9.DCSupplemental This article http://www.jimmunol.org/content/197/4/1477.full#ref-list-1 Information about subscribing to The JI No Triage! Fast Publication! Rapid Reviews! 30 days* Why • • • Material References Permissions Email Alerts Subscription Supplementary The Journal of Immunology 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. This information is current as of September 25, 2021. The Journal of Immunology Molecular Profile of Tumor-Specific CD8+ T Cell Hypofunction in a Transplantable Murine Cancer Model Katherine A.
    [Show full text]
  • Epithelial Delamination Is Protective During Pharmaceutical-Induced Enteropathy
    Epithelial delamination is protective during pharmaceutical-induced enteropathy Scott T. Espenschieda, Mark R. Cronana, Molly A. Mattya, Olaf Muellera, Matthew R. Redinbob,c,d, David M. Tobina,e,f, and John F. Rawlsa,e,1 aDepartment of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710; bDepartment of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599; cDepartment of Biochemistry, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599; dDepartment of Microbiology and Immunology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599; eDepartment of Medicine, Duke University School of Medicine, Durham, NC 27710; and fDepartment of Immunology, Duke University School of Medicine, Durham, NC 27710 Edited by Dennis L. Kasper, Harvard Medical School, Boston, MA, and approved July 15, 2019 (received for review February 12, 2019) Intestinal epithelial cell (IEC) shedding is a fundamental response to in mediating intestinal responses to injury remains poorly un- intestinal damage, yet underlying mechanisms and functions have derstood for most xenobiotics. been difficult to define. Here we model chronic intestinal damage in Gastrointestinal pathology is common in people using phar- zebrafish larvae using the nonsteroidal antiinflammatory drug maceuticals, including nonsteroidal antiinflammatory drugs (NSAID) Glafenine. Glafenine induced the unfolded protein response (NSAIDs) (11). While gastric ulceration has historically been a (UPR) and inflammatory pathways in IECs, leading to delamination. defining clinical presentation of NSAID-induced enteropathy, Glafenine-induced inflammation was augmented by microbial colo- small intestinal pathology has also been observed, although the nizationandassociatedwithchanges in intestinal and environmental incidence may be underreported due to diagnostic limitations microbiotas.
    [Show full text]
  • Global Analysis of Protein Folding Thermodynamics for Disease State Characterization
    Global Analysis of Protein Folding Thermodynamics for Disease State Characterization and Biomarker Discovery by Jagat Adhikari Department of Biochemistry Duke University Date:_______________________ Approved: ___________________________ Michael C. Fitzgerald, Supervisor ___________________________ Kenneth Kreuzer ___________________________ Terrence G. Oas ___________________________ Jiyong Hong ___________________________ Seok-Yong Lee Dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the Department of Biochemistry in the Graduate School of Duke University 2015 ABSTRACT Global Analysis of Protein Folding Thermodynamics for Disease State Characterization and Biomarker Discovery by Jagat Adhikari Department of Biochemistry Duke University Date:_______________________ Approved: ___________________________ Michael C. Fitzgerald, Supervisor ___________________________ Kenneth Kreuzer ___________________________ Terrence G. Oas ___________________________ Jiyong Hong ___________________________ Seok-Yong Lee An abstract of a dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the Department of Biochemistry in the Graduate School of Duke University 2015 Copyright by Jagat Adhikari 2015 Abstract Protein biomarkers can facilitate the diagnosis of many diseases such as cancer and they can be important for the development of effective therapeutic interventions. Current large-scale biomarker discovery and disease state characterization
    [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]
  • Proteomics Provides Insights Into the Inhibition of Chinese Hamster V79
    www.nature.com/scientificreports OPEN Proteomics provides insights into the inhibition of Chinese hamster V79 cell proliferation in the deep underground environment Jifeng Liu1,2, Tengfei Ma1,2, Mingzhong Gao3, Yilin Liu4, Jun Liu1, Shichao Wang2, Yike Xie2, Ling Wang2, Juan Cheng2, Shixi Liu1*, Jian Zou1,2*, Jiang Wu2, Weimin Li2 & Heping Xie2,3,5 As resources in the shallow depths of the earth exhausted, people will spend extended periods of time in the deep underground space. However, little is known about the deep underground environment afecting the health of organisms. Hence, we established both deep underground laboratory (DUGL) and above ground laboratory (AGL) to investigate the efect of environmental factors on organisms. Six environmental parameters were monitored in the DUGL and AGL. Growth curves were recorded and tandem mass tag (TMT) proteomics analysis were performed to explore the proliferative ability and diferentially abundant proteins (DAPs) in V79 cells (a cell line widely used in biological study in DUGLs) cultured in the DUGL and AGL. Parallel Reaction Monitoring was conducted to verify the TMT results. γ ray dose rate showed the most detectable diference between the two laboratories, whereby γ ray dose rate was signifcantly lower in the DUGL compared to the AGL. V79 cell proliferation was slower in the DUGL. Quantitative proteomics detected 980 DAPs (absolute fold change ≥ 1.2, p < 0.05) between V79 cells cultured in the DUGL and AGL. Of these, 576 proteins were up-regulated and 404 proteins were down-regulated in V79 cells cultured in the DUGL. KEGG pathway analysis revealed that seven pathways (e.g.
    [Show full text]
  • Ingenuity Pathway Analysis of Differentially Expressed Genes Involved in Signaling Pathways and Molecular Networks in Rhoe Gene‑Edited Cardiomyocytes
    INTERNATIONAL JOURNAL OF MOleCular meDICine 46: 1225-1238, 2020 Ingenuity pathway analysis of differentially expressed genes involved in signaling pathways and molecular networks in RhoE gene‑edited cardiomyocytes ZHONGMING SHAO1*, KEKE WANG1*, SHUYA ZHANG2, JIANLING YUAN1, XIAOMING LIAO1, CAIXIA WU1, YUAN ZOU1, YANPING HA1, ZHIHUA SHEN1, JUNLI GUO2 and WEI JIE1,2 1Department of Pathology, School of Basic Medicine Sciences, Guangdong Medical University, Zhanjiang, Guangdong 524023; 2Hainan Provincial Key Laboratory for Tropical Cardiovascular Diseases Research and Key Laboratory of Emergency and Trauma of Ministry of Education, Institute of Cardiovascular Research of The First Affiliated Hospital, Hainan Medical University, Haikou, Hainan 571199, P.R. China Received January 7, 2020; Accepted May 20, 2020 DOI: 10.3892/ijmm.2020.4661 Abstract. RhoE/Rnd3 is an atypical member of the Rho super- injury and abnormalities, cell‑to‑cell signaling and interaction, family of proteins, However, the global biological function and molecular transport. In addition, 885 upstream regulators profile of this protein remains unsolved. In the present study, a were enriched, including 59 molecules that were predicated RhoE‑knockout H9C2 cardiomyocyte cell line was established to be strongly activated (Z‑score >2) and 60 molecules that using CRISPR/Cas9 technology, following which differentially were predicated to be significantly inhibited (Z‑scores <‑2). In expressed genes (DEGs) between the knockout and wild‑type particular, 33 regulatory effects and 25 networks were revealed cell lines were screened using whole genome expression gene to be associated with the DEGs. Among them, the most signifi- chips. A total of 829 DEGs, including 417 upregulated and cant regulatory effects were ‘adhesion of endothelial cells’ and 412 downregulated, were identified using the threshold of ‘recruitment of myeloid cells’ and the top network was ‘neuro- fold changes ≥1.2 and P<0.05.
    [Show full text]