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Supplementary Table S1. Protein Identification Parameters Item Value

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Supplementary Table S1. Protein identification parameters Item Value Enzyme Trypsin Max Missed Cleavages 2 Carbamidomethyl (C), Fixed modifications TMT 10 plex (N-term), TMT 10 plex (K) Variable modifications Oxidation (M) Peptide Mass Tolerance ± 20 ppm Fragment Mass Tolerance 0.1Da Database uniprot_rat_36079_20170921.fasta Database pattern Decoy Peptide FDR ≤0.01 The protein ratios are calculated as the median of Protein Quantification only unique peptides of the protein Normalizes all peptide ratios by the median protein Experimental Bias ratio. The median protein ratio should be 1 after the normalization. Supplementary Table S2. List of protein quantification and differential analysis Accession Description HF/C t test p value Cytochrome P450 2C70 OS=Rattus norvegicus GN=Cyp2c70 P19225 1.808583525 9.953E-07 PE=2 SV=1 - [CP270_RAT] Carboxylic ester hydrolase OS=Rattus norvegicus G3V9D8 1.583811454 1.61313E-06 GN=LOC108348093 PE=1 SV=1 - [G3V9D8_RAT] Epoxide hydrolase 1 OS=Rattus norvegicus GN=Ephx1 PE=1 P07687 1.732555816 3.21041E-06 SV=1 - [HYEP_RAT] Cholesterol 7-alpha-monooxygenase OS=Rattus norvegicus P18125 1.398497925 4.77469E-06 GN=Cyp7a1 PE=1 SV=1 - [CP7A1_RAT] Methyltransferase-like protein 7B OS=Rattus norvegicus Q562C4 1.462168835 5.07554E-06 GN=Mettl7b PE=1 SV=1 - [MET7B_RAT] Serum paraoxonase/arylesterase 1 OS=Rattus norvegicus P55159 1.451799589 8.48466E-06 GN=Pon1 PE=1 SV=3 - [PON1_RAT] Estradiol 17-beta-dehydrogenase 11 OS=Rattus norvegicus Q6AYS8 1.652588897 1.39328E-05 GN=Hsd17b11 PE=2 SV=1 - [DHB11_RAT] Peroxisomal bifunctional enzyme OS=Rattus norvegicus P07896 1.221789306 1.92615E-05 GN=Ehhadh PE=1 SV=2 - [ECHP_RAT] Cytochrome P450 3A2 OS=Rattus norvegicus GN=Cyp3a2 P05183 1.588862955 1.98411E-05 PE=1 SV=2 - [CP3A2_RAT] Aldehyde oxidase 1 OS=Rattus norvegicus GN=Aox1 PE=1 F1LRQ1 1.283524072 2.20966E-05 SV=3 - [F1LRQ1_RAT] Receptor expression-enhancing protein 5 OS=Rattus norvegicus B2RZ37 1.539226349 2.31705E-05 GN=Reep5 PE=1 SV=1 - [REEP5_RAT] Carboxylesterase 1D OS=Rattus norvegicus GN=Ces1d PE=1 P16303 1.408036765 2.75019E-05 SV=2 - [CES1D_RAT] Dehydrogenase/reductase (SDR family) member 1 OS=Rattus Q6AXY8 1.536302694 2.83349E-05 norvegicus GN=Dhrs1 PE=1 SV=1 - [Q6AXY8_RAT] Retinal dehydrogenase 1 OS=Rattus norvegicus GN=Aldh1a1 P51647 1.840092428 3.4716E-05 PE=1 SV=3 - [AL1A1_RAT] Carboxylic ester hydrolase OS=Rattus norvegicus GN=Ces2a Q8K3R0 1.419675339 4.56731E-05 PE=2 SV=1 - [Q8K3R0_RAT] Ras-related protein Rab-18 OS=Rattus norvegicus GN=Rab18 Q5EB77 1.384447664 5.65736E-05 PE=2 SV=1 - [RAB18_RAT] Perilipin OS=Rattus norvegicus GN=Plin2 PE=2 SV=1 - Q5U2U5 2.013776015 5.94017E-05 [Q5U2U5_RAT] UDP-glucuronosyltransferase 1-1 OS=Rattus norvegicus Q64550 1.493772264 8.17548E-05 GN=Ugt1a1 PE=1 SV=1 - [UD11_RAT] Acyl-coenzyme A oxidase OS=Rattus norvegicus GN=Acox2 F1LNW3 1.203005945 8.86563E-05 PE=1 SV=1 - [F1LNW3_RAT] Carboxylic ester hydrolase OS=Rattus norvegicus GN=Ces2h Q32Q55 1.240199167 0.000107193 PE=1 SV=1 - [Q32Q55_RAT] Lysosome membrane protein 2 OS=Rattus norvegicus P27615 1.278903221 0.000111769 GN=Scarb2 PE=1 SV=2 - [SCRB2_RAT] Hypoxanthine-guanine phosphoribosyltransferase OS=Rattus P27605 1.2186336 0.000123457 norvegicus GN=Hprt1 PE=1 SV=1 - [HPRT_RAT] UDP-glucuronosyltransferase OS=Rattus norvegicus D3ZLR6 1.225683241 0.000140185 GN=Ugt2b15 PE=1 SV=3 - [D3ZLR6_RAT] UDP-glucuronosyltransferase OS=Rattus norvegicus Q8VD45 1.399046982 0.000144338 GN=Ugt1a5 PE=2 SV=1 - [Q8VD45_RAT] Cytochrome P-450 OS=Rattus norvegicus GN=Cyp3a23/3a1 Q06884 1.511835628 0.000147063 PE=1 SV=1 - [Q06884_RAT] Bile acid-CoA:amino acid N-acyltransferase OS=Rattus Q63276 1.200113485 0.000148178 norvegicus GN=Baat PE=1 SV=2 - [BAAT_RAT] Liver carboxylesterase 4 OS=Rattus norvegicus PE=2 SV=2 - Q64573 1.260627651 0.000159303 [EST4_RAT] Cytochrome P450 2C23 OS=Rattus norvegicus GN=Cyp2c23 P24470 1.318079504 0.000165039 PE=2 SV=2 - [CP2CN_RAT] Glutathione S-transferase, theta 3 OS=Rattus norvegicus D3Z8I7 1.239882511 0.000232724 GN=Gstt3 PE=1 SV=1 - [D3Z8I7_RAT] Aflatoxin B1 aldehyde reductase member 3 OS=Rattus P38918 1.494791392 0.0002348 norvegicus GN=Akr7a3 PE=1 SV=2 - [ARK73_RAT] Cytochrome b5 OS=Rattus norvegicus GN=Cyb5a PE=1 SV=2 P00173 1.227719353 0.000270095 - [CYB5_RAT] Very long-chain acyl-CoA synthetase OS=Rattus norvegicus P97524 1.249642255 0.000280848 GN=Slc27a2 PE=1 SV=1 - [S27A2_RAT] Enoyl-[acyl-carrier-protein] reductase, mitochondrial A0A140TAE6 OS=Rattus norvegicus GN=Mecr PE=1 SV=1 - 1.222638422 0.000332009 [A0A140TAE6_RAT] Cytochrome P450 3A18 OS=Rattus norvegicus GN=Cyp3a18 G3V635 1.372231059 0.000353707 PE=1 SV=1 - [G3V635_RAT] NADPH--cytochrome P450 reductase OS=Rattus norvegicus P00388 1.227318458 0.000406763 GN=Por PE=1 SV=3 - [NCPR_RAT] Glutathione S-transferase alpha-5 OS=Rattus norvegicus P46418 1.676939556 0.000423909 GN=Gsta5 PE=1 SV=2 - [GSTA5_RAT] Methyltransferase like 7A, isoform CRA_b OS=Rattus Q3KRE2 1.362230744 0.000447562 norvegicus GN=Mettl7a PE=1 SV=1 - [Q3KRE2_RAT] CCZ1 homolog B, vacuolar protein-trafficking and biogenesis- A0A140UHX9 associated OS=Rattus norvegicus GN=Ccz1b PE=1 SV=1 - 1.260979136 0.000471004 [A0A140UHX9_RAT] Membrane-associated progesterone receptor component 1 P70580 OS=Rattus norvegicus GN=Pgrmc1 PE=1 SV=3 - 1.250193271 0.00048953 [PGRC1_RAT] Acyl-coenzyme A synthetase ACSM5, mitochondrial Q6AYT9 OS=Rattus norvegicus GN=Acsm5 PE=2 SV=1 - 1.34807686 0.000492078 [ACSM5_RAT] Alcohol dehydrogenase 4 OS=Rattus norvegicus GN=Adh4 A1L128 1.203832432 0.000524367 PE=1 SV=1 - [A1L128_RAT] RGD1563250 (Predicted), isoform CRA_a OS=Rattus D3ZJZ0 1.26805429 0.000604991 norvegicus GN=Tmem205 PE=1 SV=1 - [D3ZJZ0_RAT] Solute carrier organic anion transporter family member 1A4 O35913 OS=Rattus norvegicus GN=Slco1a4 PE=2 SV=1 - 1.316493831 0.000627043 [SO1A4_RAT] Peroxisomal multifunctional enzyme type 2 OS=Rattus P97852 1.212332672 0.00066838 norvegicus GN=Hsd17b4 PE=1 SV=3 - [DHB4_RAT] Myosin, heavy chain 15 OS=Rattus norvegicus GN=Myh15 A0A0G2JY53 1.279298327 0.000676785 PE=3 SV=1 - [A0A0G2JY53_RAT] UDP-glucuronosyltransferase OS=Rattus norvegicus D4A147 1.313522947 0.000686365 GN=Ugt2a3 PE=1 SV=3 - [D4A147_RAT] Translation initiation factor eIF-2B subunit beta OS=Rattus Q62818 2.16653058 0.000718203 norvegicus GN=Eif2b2 PE=2 SV=1 - [EI2BB_RAT] Cathepsin D OS=Rattus norvegicus GN=Ctsd PE=1 SV=1 - P24268 1.277952633 0.000768561 [CATD_RAT] Ectonucleoside triphosphate diphosphohydrolase 5 OS=Rattus F1LPB8 1.211922712 0.000899361 norvegicus GN=Entpd5 PE=1 SV=2 - [F1LPB8_RAT] UDP-glucuronosyltransferase 2B1 OS=Rattus norvegicus P09875 1.410760147 0.000984948 GN=Ugt2b1 PE=2 SV=1 - [UD2B1_RAT] PDZ and LIM domain protein 1 OS=Rattus norvegicus P52944 1.338035136 0.000997626 GN=Pdlim1 PE=1 SV=4 - [PDLI1_RAT] Platelet glycoprotein 4 OS=Rattus norvegicus GN=Cd36 PE=1 A0A096MJ39 1.226873712 0.001019201 SV=1 - [A0A096MJ39_RAT] 3-ketoacyl-CoA thiolase B, peroxisomal OS=Rattus norvegicus P07871 1.728987207 0.001173721 GN=Acaa1b PE=1 SV=2 - [THIKB_RAT] Cysteine dioxygenase type 1 OS=Rattus norvegicus GN=Cdo1 P21816 1.438903572 0.001253103 PE=1 SV=1 - [CDO1_RAT] UDP-glucuronosyltransferase OS=Rattus norvegicus A0A0G2K727 1.209882937 0.001325651 GN=Ugt2b35 PE=1 SV=1 - [A0A0G2K727_RAT] Dimethylaniline monooxygenase [N-oxide-forming] 1 P36365 1.21035083 0.001344383 OS=Rattus norvegicus GN=Fmo1 PE=1 SV=2 - [FMO1_RAT] 2,4-dienoyl CoA reductase 1, mitochondrial, isoform CRA_a G3V734 OS=Rattus norvegicus GN=Decr1 PE=1 SV=1 - 1.20205063 0.001385445 [G3V734_RAT] Palmitoyl-protein thioesterase 1 OS=Rattus norvegicus P45479 1.283496091 0.001414815 GN=Ppt1 PE=1 SV=1 - [PPT1_RAT] Srxn1 protein (Fragment) OS=Rattus norvegicus GN=Srxn1 B3DM86 1.226049465 0.001620823 PE=2 SV=1 - [B3DM86_RAT] Carboxylic ester hydrolase OS=Rattus norvegicus GN=Ces1a D4AA05 1.330073999 0.001718485 PE=1 SV=1 - [D4AA05_RAT] UDP-glucuronosyltransferase OS=Rattus norvegicus P97886 1.290171117 0.001795007 GN=UGT1 PE=2 SV=1 - [P97886_RAT] Prospero homeobox 2 OS=Rattus norvegicus GN=Prox2 PE=4 D3ZHL7 1.558385759 0.001853077 SV=2 - [D3ZHL7_RAT] UDP-glucuronosyltransferase OS=Rattus norvegicus F1LM22 1.228549218 0.002271255 GN=Ugt2b PE=1 SV=2 - [F1LM22_RAT] Sulfotransferase OS=Rattus norvegicus GN=Sult1c2a PE=2 Q569D0 1.284200924 0.002281477 SV=1 - [Q569D0_RAT] Enoyl-CoA delta isomerase 1, mitochondrial OS=Rattus P23965 1.218036059 0.002456794 norvegicus GN=Eci1 PE=1 SV=1 - [ECI1_RAT] N-acetyltransferase 8 OS=Rattus norvegicus GN=Nat8 PE=1 Q9QXT3 1.260794763 0.002624452 SV=1 - [NAT8_RAT] Proteoglycan 4 OS=Rattus norvegicus GN=Prg4 PE=1 SV=2 - F1LRA5 1.275701953 0.002921552 [F1LRA5_RAT] Carboxylic ester hydrolase OS=Rattus norvegicus GN=Ces1d A0A0G2JY66 1.321744902 0.002988524 PE=1 SV=1 - [A0A0G2JY66_RAT] BRISC and BRCA1-A complex member 1 OS=Rattus Q5XIJ6 2.047810457 0.003061915 norvegicus GN=Babam1 PE=1 SV=1 - [BABA1_RAT] Transmembrane protein 116 OS=Rattus norvegicus F1LRF5 1.221267555 0.003105812 GN=Tmem116 PE=4 SV=2 - [F1LRF5_RAT] Immediate early response 3-interacting protein 1 OS=Rattus P85007 1.225574395 0.003189177 norvegicus GN=Ier3ip1 PE=3 SV=1 - [IR3IP_RAT] UDP-glucuronosyltransferase OS=Rattus norvegicus F1LTB8 1.22465606 0.003317991 GN=RGD1559459 PE=1 SV=2 - [F1LTB8_RAT] Carboxylesterase 1C OS=Rattus norvegicus GN=Ces1c PE=1 P10959 1.252466596 0.003546064 SV=3 - [EST1C_RAT] Cysteine-sulfinate decarboxylase OS=Rattus norvegicus B3VPA7 1.463542701 0.003795817 GN=Csad PE=2 SV=1 - [B3VPA7_RAT] Myotilin-like OS=Rattus norvegicus GN=LOC100909868 M0R5Y4 1.682931624 0.003932265 PE=4 SV=1 - [M0R5Y4_RAT] Vacuolar protein
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    Table S2. List of proteins detected in anterior and posterior intestine pooled samples. Data on protein expression are mean ± SEM of 4 pools fed the experimental diets. The number of the contig in the Sea Bream Database (http://nutrigroup-iats.org/seabreamdb) is indicated. Contig Protein Description Symbol Anterior Posterior Ratio Ant/Pos C2_6629 1,4-alpha-glucan-branching enzyme GBE1 0.88±0.1 0.91±0.03 0.98 C2_4764 116 kDa U5 small nuclear ribonucleoprotein component EFTUD2 0.74±0.09 0.71±0.05 1.03 C2_299 14-3-3 protein beta/alpha-1 YWHAB 1.45±0.23 2.18±0.09 0.67 C2_268 14-3-3 protein epsilon YWHAE 1.28±0.2 2.01±0.13 0.63 C2_2474 14-3-3 protein gamma-1 YWHAG 1.8±0.41 2.72±0.09 0.66 C2_1017 14-3-3 protein zeta YWHAZ 1.33±0.14 4.41±0.38 0.30 C2_34474 14-3-3-like protein 2 YWHAQ 1.3±0.11 1.85±0.13 0.70 C2_4902 17-beta-hydroxysteroid dehydrogenase 14 HSD17B14 0.93±0.05 2.33±0.09 0.40 C2_3100 1-acylglycerol-3-phosphate O-acyltransferase ABHD5 ABHD5 0.85±0.07 0.78±0.13 1.10 C2_15440 1-phosphatidylinositol phosphodiesterase PLCD1 0.65±0.12 0.4±0.06 1.65 C2_12986 1-phosphatidylinositol-4,5-bisphosphate phosphodiesterase delta-1 PLCD1 0.76±0.08 1.15±0.16 0.66 C2_4412 1-phosphatidylinositol-4,5-bisphosphate phosphodiesterase gamma-2 PLCG2 1.13±0.08 2.08±0.27 0.54 C2_3170 2,4-dienoyl-CoA reductase, mitochondrial DECR1 1.16±0.1 0.83±0.03 1.39 C2_1520 26S protease regulatory subunit 10B PSMC6 1.37±0.21 1.43±0.04 0.96 C2_4264 26S protease regulatory subunit 4 PSMC1 1.2±0.2 1.78±0.08 0.68 C2_1666 26S protease regulatory subunit 6A PSMC3 1.44±0.24 1.61±0.08
  • Dual Proteome-Scale Networks Reveal Cell-Specific Remodeling of the Human Interactome

    Dual Proteome-Scale Networks Reveal Cell-Specific Remodeling of the Human Interactome

    bioRxiv preprint doi: https://doi.org/10.1101/2020.01.19.905109; this version posted January 19, 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. Dual Proteome-scale Networks Reveal Cell-specific Remodeling of the Human Interactome Edward L. Huttlin1*, Raphael J. Bruckner1,3, Jose Navarrete-Perea1, Joe R. Cannon1,4, Kurt Baltier1,5, Fana Gebreab1, Melanie P. Gygi1, Alexandra Thornock1, Gabriela Zarraga1,6, Stanley Tam1,7, John Szpyt1, Alexandra Panov1, Hannah Parzen1,8, Sipei Fu1, Arvene Golbazi1, Eila Maenpaa1, Keegan Stricker1, Sanjukta Guha Thakurta1, Ramin Rad1, Joshua Pan2, David P. Nusinow1, Joao A. Paulo1, Devin K. Schweppe1, Laura Pontano Vaites1, J. Wade Harper1*, Steven P. Gygi1*# 1Department of Cell Biology, Harvard Medical School, Boston, MA, 02115, USA. 2Broad Institute, Cambridge, MA, 02142, USA. 3Present address: ICCB-Longwood Screening Facility, Harvard Medical School, Boston, MA, 02115, USA. 4Present address: Merck, West Point, PA, 19486, USA. 5Present address: IQ Proteomics, Cambridge, MA, 02139, USA. 6Present address: Vor Biopharma, Cambridge, MA, 02142, USA. 7Present address: Rubius Therapeutics, Cambridge, MA, 02139, USA. 8Present address: RPS North America, South Kingstown, RI, 02879, USA. *Correspondence: [email protected] (E.L.H.), [email protected] (J.W.H.), [email protected] (S.P.G.) #Lead Contact: [email protected] bioRxiv preprint doi: https://doi.org/10.1101/2020.01.19.905109; this version posted January 19, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder.
  • A Computational Approach for Defining a Signature of Β-Cell Golgi Stress in Diabetes Mellitus

    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.
  • Systems Analysis Implicates WAVE2&Nbsp

    Systems Analysis Implicates WAVE2&Nbsp

    JACC: BASIC TO TRANSLATIONAL SCIENCE VOL.5,NO.4,2020 ª 2020 THE AUTHORS. PUBLISHED BY ELSEVIER ON BEHALF OF THE AMERICAN COLLEGE OF CARDIOLOGY FOUNDATION. THIS IS AN OPEN ACCESS ARTICLE UNDER THE CC BY-NC-ND LICENSE (http://creativecommons.org/licenses/by-nc-nd/4.0/). PRECLINICAL RESEARCH Systems Analysis Implicates WAVE2 Complex in the Pathogenesis of Developmental Left-Sided Obstructive Heart Defects a b b b Jonathan J. Edwards, MD, Andrew D. Rouillard, PHD, Nicolas F. Fernandez, PHD, Zichen Wang, PHD, b c d d Alexander Lachmann, PHD, Sunita S. Shankaran, PHD, Brent W. Bisgrove, PHD, Bradley Demarest, MS, e f g h Nahid Turan, PHD, Deepak Srivastava, MD, Daniel Bernstein, MD, John Deanfield, MD, h i j k Alessandro Giardini, MD, PHD, George Porter, MD, PHD, Richard Kim, MD, Amy E. Roberts, MD, k l m m,n Jane W. Newburger, MD, MPH, Elizabeth Goldmuntz, MD, Martina Brueckner, MD, Richard P. Lifton, MD, PHD, o,p,q r,s t d Christine E. Seidman, MD, Wendy K. Chung, MD, PHD, Martin Tristani-Firouzi, MD, H. Joseph Yost, PHD, b u,v Avi Ma’ayan, PHD, Bruce D. Gelb, MD VISUAL ABSTRACT Edwards, J.J. et al. J Am Coll Cardiol Basic Trans Science. 2020;5(4):376–86. ISSN 2452-302X https://doi.org/10.1016/j.jacbts.2020.01.012 JACC: BASIC TO TRANSLATIONALSCIENCEVOL.5,NO.4,2020 Edwards et al. 377 APRIL 2020:376– 86 WAVE2 Complex in LVOTO HIGHLIGHTS ABBREVIATIONS AND ACRONYMS Combining CHD phenotype–driven gene set enrichment and CRISPR knockdown screening in zebrafish is an effective approach to identifying novel CHD genes.
  • Genome-Wide DNA Methylation Analysis of KRAS Mutant Cell Lines Ben Yi Tew1,5, Joel K

    Genome-Wide DNA Methylation Analysis of KRAS Mutant Cell Lines Ben Yi Tew1,5, Joel K

    www.nature.com/scientificreports OPEN Genome-wide DNA methylation analysis of KRAS mutant cell lines Ben Yi Tew1,5, Joel K. Durand2,5, Kirsten L. Bryant2, Tikvah K. Hayes2, Sen Peng3, Nhan L. Tran4, Gerald C. Gooden1, David N. Buckley1, Channing J. Der2, Albert S. Baldwin2 ✉ & Bodour Salhia1 ✉ Oncogenic RAS mutations are associated with DNA methylation changes that alter gene expression to drive cancer. Recent studies suggest that DNA methylation changes may be stochastic in nature, while other groups propose distinct signaling pathways responsible for aberrant methylation. Better understanding of DNA methylation events associated with oncogenic KRAS expression could enhance therapeutic approaches. Here we analyzed the basal CpG methylation of 11 KRAS-mutant and dependent pancreatic cancer cell lines and observed strikingly similar methylation patterns. KRAS knockdown resulted in unique methylation changes with limited overlap between each cell line. In KRAS-mutant Pa16C pancreatic cancer cells, while KRAS knockdown resulted in over 8,000 diferentially methylated (DM) CpGs, treatment with the ERK1/2-selective inhibitor SCH772984 showed less than 40 DM CpGs, suggesting that ERK is not a broadly active driver of KRAS-associated DNA methylation. KRAS G12V overexpression in an isogenic lung model reveals >50,600 DM CpGs compared to non-transformed controls. In lung and pancreatic cells, gene ontology analyses of DM promoters show an enrichment for genes involved in diferentiation and development. Taken all together, KRAS-mediated DNA methylation are stochastic and independent of canonical downstream efector signaling. These epigenetically altered genes associated with KRAS expression could represent potential therapeutic targets in KRAS-driven cancer. Activating KRAS mutations can be found in nearly 25 percent of all cancers1.
  • Análise Integrativa De Perfis Transcricionais De Pacientes Com

    Análise Integrativa De Perfis Transcricionais De Pacientes Com

    UNIVERSIDADE DE SÃO PAULO FACULDADE DE MEDICINA DE RIBEIRÃO PRETO PROGRAMA DE PÓS-GRADUAÇÃO EM GENÉTICA ADRIANE FEIJÓ EVANGELISTA Análise integrativa de perfis transcricionais de pacientes com diabetes mellitus tipo 1, tipo 2 e gestacional, comparando-os com manifestações demográficas, clínicas, laboratoriais, fisiopatológicas e terapêuticas Ribeirão Preto – 2012 ADRIANE FEIJÓ EVANGELISTA Análise integrativa de perfis transcricionais de pacientes com diabetes mellitus tipo 1, tipo 2 e gestacional, comparando-os com manifestações demográficas, clínicas, laboratoriais, fisiopatológicas e terapêuticas Tese apresentada à Faculdade de Medicina de Ribeirão Preto da Universidade de São Paulo para obtenção do título de Doutor em Ciências. Área de Concentração: Genética Orientador: Prof. Dr. Eduardo Antonio Donadi Co-orientador: Prof. Dr. Geraldo A. S. Passos Ribeirão Preto – 2012 AUTORIZO A REPRODUÇÃO E DIVULGAÇÃO TOTAL OU PARCIAL DESTE TRABALHO, POR QUALQUER MEIO CONVENCIONAL OU ELETRÔNICO, PARA FINS DE ESTUDO E PESQUISA, DESDE QUE CITADA A FONTE. FICHA CATALOGRÁFICA Evangelista, Adriane Feijó Análise integrativa de perfis transcricionais de pacientes com diabetes mellitus tipo 1, tipo 2 e gestacional, comparando-os com manifestações demográficas, clínicas, laboratoriais, fisiopatológicas e terapêuticas. Ribeirão Preto, 2012 192p. Tese de Doutorado apresentada à Faculdade de Medicina de Ribeirão Preto da Universidade de São Paulo. Área de Concentração: Genética. Orientador: Donadi, Eduardo Antonio Co-orientador: Passos, Geraldo A. 1. Expressão gênica – microarrays 2. Análise bioinformática por module maps 3. Diabetes mellitus tipo 1 4. Diabetes mellitus tipo 2 5. Diabetes mellitus gestacional FOLHA DE APROVAÇÃO ADRIANE FEIJÓ EVANGELISTA Análise integrativa de perfis transcricionais de pacientes com diabetes mellitus tipo 1, tipo 2 e gestacional, comparando-os com manifestações demográficas, clínicas, laboratoriais, fisiopatológicas e terapêuticas.