Teneurins: an Integrative Molecular, Functional, and Biomedical Overview of Their Role in Cancer
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(12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization International Bureau (10) International Publication Number (43) International Publication Date Χ 1 / A 1 27 October 2011 (27.10.2011) WO 2Ull/13162o Al (51) International Patent Classification: AO, AT, AU, AZ, BA, BB, BG, BH, BR, BW, BY, BZ, C12N 9/02 (2006.01) A61K 38/44 (2006.01) CA, CH, CL, CN, CO, CR, CU, CZ, DE, DK, DM, DO, A61K 38/17 (2006.01) DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, HN, HR, HU, ID, IL, IN, IS, JP, KE, KG, KM, KN, KP, (21) International Application Number: KR, KZ, LA, LC, LK, LR, LS, LT, LU, LY, MA, MD, PCT/EP20 11/056142 ME, MG, MK, MN, MW, MX, MY, MZ, NA, NG, NI, (22) International Filing Date: NO, NZ, OM, PE, PG, PH, PL, PT, RO, RS, RU, SC, SD, 18 April 201 1 (18.04.201 1) SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, TM, TN, TR, TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, ZW. (25) Filing Language: English (84) Designated States (unless otherwise indicated, for every (26) Publication Langi English kind of regional protection available): ARIPO (BW, GH, (30) Priority Data: GM, KE, LR, LS, MW, MZ, NA, SD, SL, SZ, TZ, UG, 10160368.6 19 April 2010 (19.04.2010) EP ZM, ZW), Eurasian (AM, AZ, BY, KG, KZ, MD, RU, TJ, TM), European (AL, AT, BE, BG, CH, CY, CZ, DE, DK, (71) Applicants (for all designated States except US): MEDI- EE, ES, FI, FR, GB, GR, HR, HU, IE, IS, FT, LT, LU, ZINISCHE UNIVERSITAT INNSBRUCK [AT/AT]; LV, MC, MK, MT, NL, NO, PL, PT, RO, RS, SE, SI, SK, Christoph-Probst-Platz, Innrain 52, A-6020 Innsbruck SM, TR), OAPI (BF, BJ, CF, CG, CI, CM, GA, GN, GQ, (AT). -
Tenascin C: a Candidate for Chronic Inflammation?
RESEARCH HIGHLIGHTS RHEUMATOID ARTHRITIS Tenascin C: a candidate for chronic inflammation? After more than a decade of studying joint destruction after induction of during signal transduction) to block tenascin C, Kim Midwood and erosive arthritis—inflammatory cell FBG induction of IL-6. FBG also failed to colleagues have discovered a role for infiltration and synovial thickening induce cytokine synthesis in fibroblasts this extracellular matrix protein as an occurred, but tissue destruction and cell from Myd88–/– mice. Neutralizing endogenous ligand for Toll-like receptor death did not ensue. antibodies to TLR4 inhibited the (TLR) 4 that mediates persistent synovial Exogenous tenascin C induced tumor FBG-induced synthesis of TNF, IL-6 inflammation in arthritic joint disease. necrosis factor (TNF), interleukin and IL-8, and FBG could not induce these Tenascin C is normally only (IL)-6 and IL-8 in primary human cytokines in fibroblasts or macrophages expressed—transiently—in adult macrophages, and IL-6 in human from Tlr4–/– mice; furthermore FBG tissues in response to injury. However, fibroblasts. Tenascin C comprises several could not induce joint inflammation in in chronic inflammatory diseases, domains; the researchers established Tlr4–/–mice, indicating that FBG signals such as rheumatoid arthritis (RA), that only the ‘fibrinogen-like globe’ via TLR4. expression persists, particularly in the (FBG) domain was active in human The researchers plan to “…identify ways synovia, synovial fluid and cartilage. macrophages, synovial fibroblasts and to inhibit the proinflammatory action of This expression, together with the high an ex vivo model system of RA (synovial tenascin C in the hope that this may be homology of domains within tenascin C membranes from RA patients). -
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. -
Supplementary Table 3 Complete List of RNA-Sequencing Analysis of Gene Expression Changed by ≥ Tenfold Between Xenograft and Cells Cultured in 10%O2
Supplementary Table 3 Complete list of RNA-Sequencing analysis of gene expression changed by ≥ tenfold between xenograft and cells cultured in 10%O2 Expr Log2 Ratio Symbol Entrez Gene Name (culture/xenograft) -7.182 PGM5 phosphoglucomutase 5 -6.883 GPBAR1 G protein-coupled bile acid receptor 1 -6.683 CPVL carboxypeptidase, vitellogenic like -6.398 MTMR9LP myotubularin related protein 9-like, pseudogene -6.131 SCN7A sodium voltage-gated channel alpha subunit 7 -6.115 POPDC2 popeye domain containing 2 -6.014 LGI1 leucine rich glioma inactivated 1 -5.86 SCN1A sodium voltage-gated channel alpha subunit 1 -5.713 C6 complement C6 -5.365 ANGPTL1 angiopoietin like 1 -5.327 TNN tenascin N -5.228 DHRS2 dehydrogenase/reductase 2 leucine rich repeat and fibronectin type III domain -5.115 LRFN2 containing 2 -5.076 FOXO6 forkhead box O6 -5.035 ETNPPL ethanolamine-phosphate phospho-lyase -4.993 MYO15A myosin XVA -4.972 IGF1 insulin like growth factor 1 -4.956 DLG2 discs large MAGUK scaffold protein 2 -4.86 SCML4 sex comb on midleg like 4 (Drosophila) Src homology 2 domain containing transforming -4.816 SHD protein D -4.764 PLP1 proteolipid protein 1 -4.764 TSPAN32 tetraspanin 32 -4.713 N4BP3 NEDD4 binding protein 3 -4.705 MYOC myocilin -4.646 CLEC3B C-type lectin domain family 3 member B -4.646 C7 complement C7 -4.62 TGM2 transglutaminase 2 -4.562 COL9A1 collagen type IX alpha 1 chain -4.55 SOSTDC1 sclerostin domain containing 1 -4.55 OGN osteoglycin -4.505 DAPL1 death associated protein like 1 -4.491 C10orf105 chromosome 10 open reading frame 105 -4.491 -
Reporterseq Reveals Genome-Wide Dynamic Modulators of the Heat
RESEARCH ARTICLE ReporterSeq reveals genome-wide dynamic modulators of the heat shock response across diverse stressors Brian D Alford1†, Eduardo Tassoni-Tsuchida1,2†, Danish Khan1, Jeremy J Work1, Gregory Valiant3, Onn Brandman1* 1Department of Biochemistry, Stanford University, Stanford, United States; 2Department of Biology, Stanford University, Stanford, United States; 3Department of Computer Science, Stanford University, Stanford, United States Abstract Understanding cellular stress response pathways is challenging because of the complexity of regulatory mechanisms and response dynamics, which can vary with both time and the type of stress. We developed a reverse genetic method called ReporterSeq to comprehensively identify genes regulating a stress-induced transcription factor under multiple conditions in a time- resolved manner. ReporterSeq links RNA-encoded barcode levels to pathway-specific output under genetic perturbations, allowing pooled pathway activity measurements via DNA sequencing alone and without cell enrichment or single-cell isolation. We used ReporterSeq to identify regulators of the heat shock response (HSR), a conserved, poorly understood transcriptional program that protects cells from proteotoxicity and is misregulated in disease. Genome-wide HSR regulation in budding yeast was assessed across 15 stress conditions, uncovering novel stress-specific, time- specific, and constitutive regulators. ReporterSeq can assess the genetic regulators of any transcriptional pathway with the scale of pooled genetic screens and the precision of pathway- specific readouts. *For correspondence: [email protected] †These authors contributed equally to this work Introduction Competing interests: The The heat shock response (HSR) is a conserved stress response that shields cells from cytoplasmic authors declare that no proteotoxicity by increasing the expression of protective proteins (Lindquist, 1986; Mori- competing interests exist. -
Identification of Potential Key Genes and Pathway Linked with Sporadic Creutzfeldt-Jakob Disease Based on Integrated Bioinformatics Analyses
medRxiv preprint doi: https://doi.org/10.1101/2020.12.21.20248688; this version posted December 24, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission. Identification of potential key genes and pathway linked with sporadic Creutzfeldt-Jakob disease based on integrated bioinformatics analyses Basavaraj Vastrad1, Chanabasayya Vastrad*2 , Iranna Kotturshetti 1. Department of Biochemistry, Basaveshwar College of Pharmacy, Gadag, Karnataka 582103, India. 2. Biostatistics and Bioinformatics, Chanabasava Nilaya, Bharthinagar, Dharwad 580001, Karanataka, India. 3. Department of Ayurveda, Rajiv Gandhi Education Society`s Ayurvedic Medical College, Ron, Karnataka 562209, India. * Chanabasayya Vastrad [email protected] Ph: +919480073398 Chanabasava Nilaya, Bharthinagar, Dharwad 580001 , Karanataka, India NOTE: This preprint reports new research that has not been certified by peer review and should not be used to guide clinical practice. medRxiv preprint doi: https://doi.org/10.1101/2020.12.21.20248688; this version posted December 24, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission. Abstract Sporadic Creutzfeldt-Jakob disease (sCJD) is neurodegenerative disease also called prion disease linked with poor prognosis. The aim of the current study was to illuminate the underlying molecular mechanisms of sCJD. The mRNA microarray dataset GSE124571 was downloaded from the Gene Expression Omnibus database. Differentially expressed genes (DEGs) were screened. -
Supplementary Materials
Supplementary materials Supplementary Table S1: MGNC compound library Ingredien Molecule Caco- Mol ID MW AlogP OB (%) BBB DL FASA- HL t Name Name 2 shengdi MOL012254 campesterol 400.8 7.63 37.58 1.34 0.98 0.7 0.21 20.2 shengdi MOL000519 coniferin 314.4 3.16 31.11 0.42 -0.2 0.3 0.27 74.6 beta- shengdi MOL000359 414.8 8.08 36.91 1.32 0.99 0.8 0.23 20.2 sitosterol pachymic shengdi MOL000289 528.9 6.54 33.63 0.1 -0.6 0.8 0 9.27 acid Poricoic acid shengdi MOL000291 484.7 5.64 30.52 -0.08 -0.9 0.8 0 8.67 B Chrysanthem shengdi MOL004492 585 8.24 38.72 0.51 -1 0.6 0.3 17.5 axanthin 20- shengdi MOL011455 Hexadecano 418.6 1.91 32.7 -0.24 -0.4 0.7 0.29 104 ylingenol huanglian MOL001454 berberine 336.4 3.45 36.86 1.24 0.57 0.8 0.19 6.57 huanglian MOL013352 Obacunone 454.6 2.68 43.29 0.01 -0.4 0.8 0.31 -13 huanglian MOL002894 berberrubine 322.4 3.2 35.74 1.07 0.17 0.7 0.24 6.46 huanglian MOL002897 epiberberine 336.4 3.45 43.09 1.17 0.4 0.8 0.19 6.1 huanglian MOL002903 (R)-Canadine 339.4 3.4 55.37 1.04 0.57 0.8 0.2 6.41 huanglian MOL002904 Berlambine 351.4 2.49 36.68 0.97 0.17 0.8 0.28 7.33 Corchorosid huanglian MOL002907 404.6 1.34 105 -0.91 -1.3 0.8 0.29 6.68 e A_qt Magnogrand huanglian MOL000622 266.4 1.18 63.71 0.02 -0.2 0.2 0.3 3.17 iolide huanglian MOL000762 Palmidin A 510.5 4.52 35.36 -0.38 -1.5 0.7 0.39 33.2 huanglian MOL000785 palmatine 352.4 3.65 64.6 1.33 0.37 0.7 0.13 2.25 huanglian MOL000098 quercetin 302.3 1.5 46.43 0.05 -0.8 0.3 0.38 14.4 huanglian MOL001458 coptisine 320.3 3.25 30.67 1.21 0.32 0.9 0.26 9.33 huanglian MOL002668 Worenine -
Nuclear Export of Ubiquitinated Proteins Via the UBIN-POST System
Nuclear export of ubiquitinated proteins via the PNAS PLUS UBIN-POST system Shoshiro Hirayamaa,1,2, Munechika Sugiharab,1, Daisuke Moritoc,d, Shun-ichiro Iemurae, Tohru Natsumee, Shigeo Murataa, and Kazuhiro Nagatab,c,d,2 aLaboratory of Protein Metabolism, Graduate School of Pharmaceutical Sciences, University of Tokyo, Tokyo, 113-0033, Japan; bFaculty of Life Sciences, Kyoto Sangyo University, Kyoto, 603-8555, Japan; cInstitute for Protein Dynamics, Kyoto Sangyo University, Kyoto, 603-8555, Japan; dCore Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency, Saitama, 332-0012, Japan; and eBiomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, Tokyo, 135-0064, Japan Edited by Brenda A. Schulman, Max Planck Institute of Biochemistry, Martinsried, Germany, and approved March 19, 2018 (received for review June 19, 2017) Although mechanisms for protein homeostasis in the cytosol have folding enzymes with a broad range of activities, two strong and been studied extensively, those in the nucleus remain largely flexible proteolytic machineries (namely, the UPS and autophagy), unknown. Here, we identified that a protein complex mediates and regulated protein deposition systems, such as the aggresome, export of polyubiquitinated proteins from the nucleus to the aggresome-like induced structure (ALIS), insoluble protein de- cytosol. UBIN, a ubiquitin-associated (UBA) domain-containing pro- posit (IPOD), and juxta nuclear quality control compartment tein, shuttled between the nucleus and the cytosol in a CRM1- (JUNQ), which sequester damaged proteins (9–11). Thus, the dependent manner, despite the lack of intrinsic nuclear export signal cytosol constitutes a robust system for maintaining protein ho- (NES). Instead, the UBIN binding protein polyubiquitinated substrate meostasis that extends to distinct organelles within the cytosol. -
Tenascin-C Induces Migration and Invasion Through JNK/C-Jun Signalling in Pancreatic Cancer
www.impactjournals.com/oncotarget/ Oncotarget, 2017, Vol. 8, (No. 43), pp: 74406-74422 Research Paper Tenascin-C induces migration and invasion through JNK/c-Jun signalling in pancreatic cancer Jun Cai1, Shaoxia Du1, Hui Wang1, Beibei Xin1, Juan Wang1, Wenyuan Shen1, Wei Wei2, Zhongkui Guo1 and Xiaohong Shen1 1School of Medicine, Nankai University, Tianjin 300071, China 2Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin 300060, China Correspondence to: Xiaohong Shen, email: [email protected] Keywords: TNC, JNK/c-Jun, EMT, pancreatic cancer Received: December 28, 2016 Accepted: June 20, 2017 Published: August 10, 2017 Copyright: Cai et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License 3.0 (CC BY 3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. ABSTRACT Tenascin-C (TNC), a large extracellular matrix glycoprotein, has been reported to be associated with metastasis and poor prognosis in pancreatic cancer. However, the effects and mechanisms of TNC in pancreatic cancer metastasis largely remain unclear. We performed Transwell assays to investigate the effects of TNC on Capan-2, AsPC-1 and PANC-1 cells. In addition, western blot and RT-qPCR assays were used to examine potential TNC metastasis-associated targets, such as JNK/ c-Jun, Paxillin/FAK, E-cadherin, N-cadherin, Vimentin, and MMP9/2. Lastly, we utilized a variety of methods, such as immunofluorescence, gelatin zymography and immunoprecipitation, to determine the molecular mechanisms of TNC in pancreatic cancer cell motility. The present study showed that TNC induced migration and invasion in pancreatic cancer cells and regulated a number of metastasis-associated proteins, including the EMT markers, MMP9 and Paxillin. -
Development and Validation of a Protein-Based Risk Score for Cardiovascular Outcomes Among Patients with Stable Coronary Heart Disease
Supplementary Online Content Ganz P, Heidecker B, Hveem K, et al. Development and validation of a protein-based risk score for cardiovascular outcomes among patients with stable coronary heart disease. JAMA. doi: 10.1001/jama.2016.5951 eTable 1. List of 1130 Proteins Measured by Somalogic’s Modified Aptamer-Based Proteomic Assay eTable 2. Coefficients for Weibull Recalibration Model Applied to 9-Protein Model eFigure 1. Median Protein Levels in Derivation and Validation Cohort eTable 3. Coefficients for the Recalibration Model Applied to Refit Framingham eFigure 2. Calibration Plots for the Refit Framingham Model eTable 4. List of 200 Proteins Associated With the Risk of MI, Stroke, Heart Failure, and Death eFigure 3. Hazard Ratios of Lasso Selected Proteins for Primary End Point of MI, Stroke, Heart Failure, and Death eFigure 4. 9-Protein Prognostic Model Hazard Ratios Adjusted for Framingham Variables eFigure 5. 9-Protein Risk Scores by Event Type This supplementary material has been provided by the authors to give readers additional information about their work. Downloaded From: https://jamanetwork.com/ on 10/02/2021 Supplemental Material Table of Contents 1 Study Design and Data Processing ......................................................................................................... 3 2 Table of 1130 Proteins Measured .......................................................................................................... 4 3 Variable Selection and Statistical Modeling ........................................................................................ -
Mouse Tmtc2 Conditional Knockout Project (CRISPR/Cas9)
https://www.alphaknockout.com Mouse Tmtc2 Conditional Knockout Project (CRISPR/Cas9) Objective: To create a Tmtc2 conditional knockout Mouse model (C57BL/6J) by CRISPR/Cas-mediated genome engineering. Strategy summary: The Tmtc2 gene (NCBI Reference Sequence: NM_177368 ; Ensembl: ENSMUSG00000036019 ) is located on Mouse chromosome 10. 12 exons are identified, with the ATG start codon in exon 1 and the TGA stop codon in exon 12 (Transcript: ENSMUST00000061506). Exon 2 will be selected as conditional knockout region (cKO region). Deletion of this region should result in the loss of function of the Mouse Tmtc2 gene. To engineer the targeting vector, homologous arms and cKO region will be generated by PCR using BAC clone RP23-34F6 as template. Cas9, gRNA and targeting vector will be co-injected into fertilized eggs for cKO Mouse production. The pups will be genotyped by PCR followed by sequencing analysis. Note: Exon 2 starts from about 3.35% of the coding region. The knockout of Exon 2 will result in frameshift of the gene. The size of intron 1 for 5'-loxP site insertion: 159879 bp, and the size of intron 2 for 3'-loxP site insertion: 42438 bp. The size of effective cKO region: ~1071 bp. The cKO region does not have any other known gene. Page 1 of 8 https://www.alphaknockout.com Overview of the Targeting Strategy Wildtype allele gRNA region 5' gRNA region 3' 1 2 12 Targeting vector Targeted allele Constitutive KO allele (After Cre recombination) Legends Exon of mouse Tmtc2 Homology arm cKO region loxP site Page 2 of 8 https://www.alphaknockout.com Overview of the Dot Plot Window size: 10 bp Forward Reverse Complement Sequence 12 Note: The sequence of homologous arms and cKO region is aligned with itself to determine if there are tandem repeats. -
Target of Rapamycin in Control of Autophagy: Puppet Master and Signal Integrator
International Journal of Molecular Sciences Review Target of Rapamycin in Control of Autophagy: Puppet Master and Signal Integrator Yosia Mugume y , Zakayo Kazibwe y and Diane C. Bassham * Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011, USA; [email protected] (Y.M.); [email protected] (Z.K.) * Correspondence: [email protected]; Tel.: +515-294-7461 These authors contributed equally to the manuscript. y Received: 9 October 2020; Accepted: 3 November 2020; Published: 4 November 2020 Abstract: The target of rapamycin (TOR) is an evolutionarily-conserved serine/threonine kinase that senses and integrates signals from the environment to coordinate developmental and metabolic processes. TOR senses nutrients, hormones, metabolites, and stress signals to promote cell and organ growth when conditions are favorable. However, TOR is inhibited when conditions are unfavorable, promoting catabolic processes such as autophagy. Autophagy is a macromolecular degradation pathway by which cells degrade and recycle cytoplasmic materials. TOR negatively regulates autophagy through phosphorylation of ATG13, preventing activation of the autophagy-initiating ATG1-ATG13 kinase complex. Here we review TOR complex composition and function in photosynthetic and non-photosynthetic organisms. We also review recent developments in the identification of upstream TOR activators and downstream effectors of TOR. Finally, we discuss recent developments in our understanding of the regulation of autophagy by TOR in photosynthetic