The Extracellular Matrix: an Accomplice in Gastric Cancer Development and Progression
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Predictive QSAR Tools to Aid in Early Process Development of Monoclonal Antibodies
Predictive QSAR tools to aid in early process development of monoclonal antibodies John Micael Andreas Karlberg Published work submitted to Newcastle University for the degree of Doctor of Philosophy in the School of Engineering November 2019 Abstract Monoclonal antibodies (mAbs) have become one of the fastest growing markets for diagnostic and therapeutic treatments over the last 30 years with a global sales revenue around $89 billion reported in 2017. A popular framework widely used in pharmaceutical industries for designing manufacturing processes for mAbs is Quality by Design (QbD) due to providing a structured and systematic approach in investigation and screening process parameters that might influence the product quality. However, due to the large number of product quality attributes (CQAs) and process parameters that exist in an mAb process platform, extensive investigation is needed to characterise their impact on the product quality which makes the process development costly and time consuming. There is thus an urgent need for methods and tools that can be used for early risk-based selection of critical product properties and process factors to reduce the number of potential factors that have to be investigated, thereby aiding in speeding up the process development and reduce costs. In this study, a framework for predictive model development based on Quantitative Structure- Activity Relationship (QSAR) modelling was developed to link structural features and properties of mAbs to Hydrophobic Interaction Chromatography (HIC) retention times and expressed mAb yield from HEK cells. Model development was based on a structured approach for incremental model refinement and evaluation that aided in increasing model performance until becoming acceptable in accordance to the OECD guidelines for QSAR models. -
Bruch's Membrane Abnormalities in PRDM5-Related Brittle Cornea
Porter et al. Orphanet Journal of Rare Diseases (2015) 10:145 DOI 10.1186/s13023-015-0360-4 RESEARCH Open Access Bruch’s membrane abnormalities in PRDM5-related brittle cornea syndrome Louise F. Porter1,2,3, Roberto Gallego-Pinazo4, Catherine L. Keeling5, Martyna Kamieniorz5, Nicoletta Zoppi6, Marina Colombi6, Cecilia Giunta7, Richard Bonshek2,8, Forbes D. Manson1 and Graeme C. Black1,9* Abstract Background: Brittle cornea syndrome (BCS) is a rare, generalized connective tissue disorder associated with extreme corneal thinning and a high risk of corneal rupture. Recessive mutations in transcription factors ZNF469 and PRDM5 cause BCS. Both transcription factors are suggested to act on a common pathway regulating extracellular matrix genes, particularly fibrillar collagens. We identified bilateral myopic choroidal neovascularization as the presenting feature of BCS in a 26-year-old-woman carrying a novel PRDM5 mutation (p.Glu134*). We performed immunohistochemistry of anterior and posterior segment ocular tissues, as expression of PRDM5 in the eye has not been described, or the effects of PRDM5-associated disease on the retina, particularly the extracellular matrix composition of Bruch’smembrane. Methods: Immunohistochemistry using antibodies against PRDM5, collagens type I, III, and IV was performed on the eyes of two unaffected controls and two patients (both with Δ9-14 PRDM5). Expression of collagens, integrins, tenascin and fibronectin in skin fibroblasts of a BCS patient with a novel p.Glu134* PRDM5 mutation was assessed using immunofluorescence. Results: PRDM5 is expressed in the corneal epithelium and retina. We observe reduced expression of major components of Bruch’s membrane in the eyes of two BCS patients with a PRDM5 Δ9-14 mutation. -
Tanibirumab (CUI C3490677) Add to Cart
5/17/2018 NCI Metathesaurus Contains Exact Match Begins With Name Code Property Relationship Source ALL Advanced Search NCIm Version: 201706 Version 2.8 (using LexEVS 6.5) Home | NCIt Hierarchy | Sources | Help Suggest changes to this concept Tanibirumab (CUI C3490677) Add to Cart Table of Contents Terms & Properties Synonym Details Relationships By Source Terms & Properties Concept Unique Identifier (CUI): C3490677 NCI Thesaurus Code: C102877 (see NCI Thesaurus info) Semantic Type: Immunologic Factor Semantic Type: Amino Acid, Peptide, or Protein Semantic Type: Pharmacologic Substance NCIt Definition: A fully human monoclonal antibody targeting the vascular endothelial growth factor receptor 2 (VEGFR2), with potential antiangiogenic activity. Upon administration, tanibirumab specifically binds to VEGFR2, thereby preventing the binding of its ligand VEGF. This may result in the inhibition of tumor angiogenesis and a decrease in tumor nutrient supply. VEGFR2 is a pro-angiogenic growth factor receptor tyrosine kinase expressed by endothelial cells, while VEGF is overexpressed in many tumors and is correlated to tumor progression. PDQ Definition: A fully human monoclonal antibody targeting the vascular endothelial growth factor receptor 2 (VEGFR2), with potential antiangiogenic activity. Upon administration, tanibirumab specifically binds to VEGFR2, thereby preventing the binding of its ligand VEGF. This may result in the inhibition of tumor angiogenesis and a decrease in tumor nutrient supply. VEGFR2 is a pro-angiogenic growth factor receptor -
Endothelial Cell-Derived Nidogen-1 Inhibits Migration of SK-BR-3 Breast Cancer Cells Daniela A
Ferraro et al. BMC Cancer (2019) 19:312 https://doi.org/10.1186/s12885-019-5521-8 RESEARCH ARTICLE Open Access Endothelial cell-derived nidogen-1 inhibits migration of SK-BR-3 breast cancer cells Daniela A. Ferraro1, Francesca Patella2, Sara Zanivan2, Cinzia Donato3, Nicola Aceto3, Monica Giannotta4, Elisabetta Dejana4, Maren Diepenbruck1, Gerhard Christofori1 and Martin Buess5* Abstract Background: The tumour microenvironment is a critical regulator of malignant cancer progression. While endothelial cells have been widely studied in the context of tumour angiogenesis, their role as modulators of cancer cell invasion and migration is poorly understood. Methods: We have investigated the influence of endothelial cells on the invasive and migratory behaviour of human cancer cells in vitro. Results: Upon exposure to culture supernatants of endothelial cells, distinct cancer cells, such as SK-BR-3 cells, showed significantly increased invasion and cell migration concomitant with changes in cell morphology and gene expression reminiscent of an epithelial-mesenchymal transition (EMT). Interestingly, the pro-migratory effect on SK- BR-3 cells was significantly enhanced by supernatants obtained from subconfluent, proliferative endothelial cells rather than from confluent, quiescent endothelial cells. Systematically comparing the supernatants of subconfluent and confluent endothelial cells by quantitative MS proteomics revealed eight candidate proteins that were secreted at significantly higher levels by confluent endothelial cells representing potential inhibitors of cancer cell migration. Among these proteins, nidogen-1 was exclusively expressed in confluent endothelial cells and was found to be necessary and sufficient for the inhibition of SK-BR-3 cell migration. Indeed, SK-BR-3 cells exposed to nidogen-1- depleted endothelial supernatants showed increased promigratory STAT3 phosphorylation along with increased cell migration. -
WES Gene Package Multiple Congenital Anomalie.Xlsx
Whole Exome Sequencing Gene package Multiple congenital anomalie, version 5, 1‐2‐2018 Technical information DNA was enriched using Agilent SureSelect Clinical Research Exome V2 capture and paired‐end sequenced on the Illumina platform (outsourced). The aim is to obtain 8.1 Giga base pairs per exome with a mapped fraction of 0.99. The average coverage of the exome is ~50x. Duplicate reads are excluded. Data are demultiplexed with bcl2fastq Conversion Software from Illumina. Reads are mapped to the genome using the BWA‐MEM algorithm (reference: http://bio‐bwa.sourceforge.net/). Variant detection is performed by the Genome Analysis Toolkit HaplotypeCaller (reference: http://www.broadinstitute.org/gatk/). The detected variants are filtered and annotated with Cartagenia software and classified with Alamut Visual. It is not excluded that pathogenic mutations are being missed using this technology. At this moment, there is not enough information about the sensitivity of this technique with respect to the detection of deletions and duplications of more than 5 nucleotides and of somatic mosaic mutations (all types of sequence changes). HGNC approved Phenotype description including OMIM phenotype ID(s) OMIM median depth % covered % covered % covered gene symbol gene ID >10x >20x >30x A4GALT [Blood group, P1Pk system, P(2) phenotype], 111400 607922 101 100 100 99 [Blood group, P1Pk system, p phenotype], 111400 NOR polyagglutination syndrome, 111400 AAAS Achalasia‐addisonianism‐alacrimia syndrome, 231550 605378 73 100 100 100 AAGAB Keratoderma, palmoplantar, -
The Two Tontti Tudiul Lui Hi Ha Unit
THETWO TONTTI USTUDIUL 20170267753A1 LUI HI HA UNIT ( 19) United States (12 ) Patent Application Publication (10 ) Pub. No. : US 2017 /0267753 A1 Ehrenpreis (43 ) Pub . Date : Sep . 21 , 2017 ( 54 ) COMBINATION THERAPY FOR (52 ) U .S . CI. CO - ADMINISTRATION OF MONOCLONAL CPC .. .. CO7K 16 / 241 ( 2013 .01 ) ; A61K 39 / 3955 ANTIBODIES ( 2013 .01 ) ; A61K 31 /4706 ( 2013 .01 ) ; A61K 31 / 165 ( 2013 .01 ) ; CO7K 2317 /21 (2013 . 01 ) ; (71 ) Applicant: Eli D Ehrenpreis , Skokie , IL (US ) CO7K 2317/ 24 ( 2013. 01 ) ; A61K 2039/ 505 ( 2013 .01 ) (72 ) Inventor : Eli D Ehrenpreis, Skokie , IL (US ) (57 ) ABSTRACT Disclosed are methods for enhancing the efficacy of mono (21 ) Appl. No. : 15 /605 ,212 clonal antibody therapy , which entails co - administering a therapeutic monoclonal antibody , or a functional fragment (22 ) Filed : May 25 , 2017 thereof, and an effective amount of colchicine or hydroxy chloroquine , or a combination thereof, to a patient in need Related U . S . Application Data thereof . Also disclosed are methods of prolonging or increasing the time a monoclonal antibody remains in the (63 ) Continuation - in - part of application No . 14 / 947 , 193 , circulation of a patient, which entails co - administering a filed on Nov. 20 , 2015 . therapeutic monoclonal antibody , or a functional fragment ( 60 ) Provisional application No . 62/ 082, 682 , filed on Nov . of the monoclonal antibody , and an effective amount of 21 , 2014 . colchicine or hydroxychloroquine , or a combination thereof, to a patient in need thereof, wherein the time themonoclonal antibody remains in the circulation ( e . g . , blood serum ) of the Publication Classification patient is increased relative to the same regimen of admin (51 ) Int . -
Characterization of Drosophila Nidogen/Entactin Reveals Roles In
bioRxiv preprint doi: https://doi.org/10.1101/348631; this version posted June 18, 2018. 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. 1 Characterization of Drosophila Nidogen/entactin reveals roles in 2 basement membrane stability, barrier function and nervous system 3 plasticity 4 1, 3 1, * 3, 5 Georg WolfstetterP P (ORCID: 44T0000-0001-8763-1419)44T, Ina DahlitzP P, Kathrin PfeiferP * 2 6 P (ORCID: 44T0000-0002-2680-8425)44T, Joscha Arne AltP P (ORCID: 44T0000-0002-9144- 1 1 7 1041)44T, Uwe TöpferP P, Daniel Christoph PfeiferP P (ORCID: 44T0000-0001-7163-9985),44T 2 4 8 Reinhard Lakes-HarlanP P, Stefan BaumgartnerP P (ORCID: 44T0000-0001-5320-8321)44T, 3 1, # 9 Ruth H. PalmerP P (ORCID: 44T0000-0002-2735-8470)44T, and Anne HolzP P(ORCID: 44T0000- 10 0002-7028-654844T) 11 1 12 P P Justus-Liebig-Universitaet Giessen, Institut für Allgemeine und Spezielle 13 Zoologie, Allgemeine Zoologie und Entwicklungsbiologie, Stephanstraße 24, 14 35390 Gießen, Germany. 2 15 P P Justus-Liebig-Universitaet Giessen, Institut für Tierphysiologie, Integrative 16 Sinnesphysiologie, Heinrich-Buff-Ring 26, 35392 Gießen, Germany. 3 17 P P The Sahlgrenska Academy at the University of Gothenburg, Institute of 18 Biomedicine, Department of Medical Biochemistry and Cell Biology, 19 Medicinaregatan 9A, 41390 Gothenburg, Sweden. 4 20 P P Lund University, Department of Experimental Medical Sciences, BMC D10, 21 22184 Lund, Sweden. 22 * Both authors contributed equally. 23 24 # Correspondence should be send to: [email protected] 25 26 Keywords: Laminin, Collagen, Perlecan, extracellular matrix, ECM, muscle, dorsal 27 median cells, axon guidance, morphogenesis, NMJ. -
Role of Mesenchymal Nidogen for Epithelial Morphogenesis in Vitro
Development 120, 2003-2014 (1994) 2003 Printed in Great Britain © The Company of Biologists Limited 1994 Role of mesenchymal nidogen for epithelial morphogenesis in vitro Peter Ekblom1,2,*, Marja Ekblom1,2, Lothar Fecker2, Gerd Klein2, Hong-Yan Zhang1, Yuichi Kadoya1, Mon-Li Chu3, Ulrike Mayer4 and Rupert Timpl4 1Department of Animal Physiology, Uppsala University, S-75124 Uppsala, Sweden 2Friedrich-Miescher-Laboratorium der Max-Planck-Gesellschaft Tübingen, Germany 3Departments of Biochemistry and Molecular Biology, Jefferson Institute of Molecular Medicine, Thomas Jefferson University, Philadelphia, PA, USA 4Max-Planck-Institut für Biochemie Martinsried, Germany *Author for correspondence SUMMARY Recent biochemical studies suggested that the extracellular lial laminin may thus be a key event during epithelial devel- matrix protein nidogen is a binding molecule linking opment. This is supported by antibody perturbation exper- together basement membrane components. We studied its iments. Antibodies against the nidogen binding site on expression and role during development. By immunofluo- laminin B2 chain perturbed epithelial development in vitro rescence and northern blotting, nidogen was found early in embryonic kidney and lung. Mesenchymal nidogen during epithelial cell development of kidney and lung. Yet, could be important for early stages of epithelial morpho- in situ hybridization revealed that nidogen was not genesis. produced by epithelium but by the adjacent mesenchyme in both organs. Binding of mesenchymal nidogen to epithe- Key words: epithelium, laminin, nidogen INTRODUCTION 1987). Nidogen and laminin can be extracted from mouse tissues in approximately equimolar amounts (Dziadek and Much has recently been learned about the expression and role Timpl, 1985), in agreement with findings that one laminin of laminin chains during embryonic development (Adams and complex binds one nidogen molecule (Paulsson et al., 1987). -
Arming Tumor-Associated Macrophages to Reverse Epithelial
Published OnlineFirst August 15, 2019; DOI: 10.1158/0008-5472.CAN-19-1246 Cancer Tumor Biology and Immunology Research Arming Tumor-Associated Macrophages to Reverse Epithelial Cancer Progression Hiromi I.Wettersten1,2,3, Sara M.Weis1,2,3, Paulina Pathria1,2,Tami Von Schalscha1,2,3, Toshiyuki Minami1,2,3, Judith A. Varner1,2, and David A. Cheresh1,2,3 Abstract Tumor-associated macrophages (TAM) are highly expressed it engaged macrophages but not natural killer (NK) cells to within the tumor microenvironment of a wide range of cancers, induce antibody-dependent cellular cytotoxicity (ADCC) of where they exert a protumor phenotype by promoting tumor avb3-expressing tumor cells despite their expression of the cell growth and suppressing antitumor immune function. CD47 "don't eat me" signal. In contrast to strategies designed Here, we show that TAM accumulation in human and mouse to eliminate TAMs, these findings suggest that anti-avb3 tumors correlates with tumor cell expression of integrin avb3, represents a promising immunotherapeutic approach to redi- a known driver of epithelial cancer progression and drug rect TAMs to serve as tumor killers for late-stage or drug- resistance. A monoclonal antibody targeting avb3 (LM609) resistant cancers. exploited the coenrichment of avb3 and TAMs to not only eradicate highly aggressive drug-resistant human lung and Significance: Therapeutic antibodies are commonly engi- pancreas cancers in mice, but also to prevent the emergence neered to optimize engagement of NK cells as effectors. In of circulating tumor cells. Importantly, this antitumor activity contrast, LM609 targets avb3 to suppress tumor progression in mice was eliminated following macrophage depletion. -
WO 2016/176089 Al 3 November 2016 (03.11.2016) P O P C T
(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 WO 2016/176089 Al 3 November 2016 (03.11.2016) P O P C T (51) International Patent Classification: BZ, CA, CH, CL, CN, CO, CR, CU, CZ, DE, DK, DM, A01N 43/00 (2006.01) A61K 31/33 (2006.01) DO, DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, HN, HR, HU, ID, IL, IN, IR, IS, JP, KE, KG, KN, KP, KR, (21) International Application Number: KZ, LA, LC, LK, LR, LS, LU, LY, MA, MD, ME, MG, PCT/US2016/028383 MK, MN, MW, MX, MY, MZ, NA, NG, NI, NO, NZ, OM, (22) International Filing Date: PA, PE, PG, PH, PL, PT, QA, RO, RS, RU, RW, SA, SC, 20 April 2016 (20.04.2016) SD, 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 Language: English kind of regional protection available): ARIPO (BW, GH, (30) Priority Data: GM, KE, LR, LS, MW, MZ, NA, RW, SD, SL, ST, SZ, 62/154,426 29 April 2015 (29.04.2015) US TZ, UG, ZM, ZW), Eurasian (AM, AZ, BY, KG, KZ, RU, TJ, TM), European (AL, AT, BE, BG, CH, CY, CZ, DE, (71) Applicant: KARDIATONOS, INC. [US/US]; 4909 DK, EE, ES, FI, FR, GB, GR, HR, HU, IE, IS, IT, LT, LU, Lapeer Road, Metamora, Michigan 48455 (US). -
Complex Between Nidogen and Laminin
letters to nature Thin-layer chromatography 12. Nikolov, D. B. et al. Crystal structure of a TFIIB–TBP–TATA-element ternary complex. Nature 377, TLC was done on silica gel plates as previously described17. Acetyl-CoA and CoA were 119–128 (1995). visualized by UV at 254 nm. 13. Yan, Y., Harper, S., Speicher, D. W. & Marmorstein, R. The catalytic mechanism of the ESA1 histone acetyltransferase involves a self-acetylated intermediate. Nature Struct. Biol. 9, 862–869 (2002). Deacetylation of acetyl-TFIIB 14. Usheva, A. & Shenk, T. YY1 transcriptional initiator: protein interactions and association with a DNA site containing unpaired strands. Proc. Natl Acad. Sci. USA 93, 13571–13576 (1996). 0.1 nmol of [14C]-acetyl-CoA was incubated with 20 pmol rhTFIIB for 40 min, allowing 15. Fang, S. M. & Burton, Z. F. RNA polymerase II-associated protein (RAP) 74 binds transcription factor full acetylation. A 50-fold excess of CoA over initial acetyl-CoA was added and the mixture (TF) IIB and blocks TFIIB-RAP30 binding. J. Biol. Chem. 271, 11703–11709 (1996). was incubated for the number of hours shown. The results were visualized by SDS–PAGE 16. Luger, K., Rechsteiner, T. J. & Richmond, T. J. Preparation of nucleosome core particle from and autoradiography. The integrity of rhTFIIB after incubation was verified by western recombinant histones. Methods Enzymol. 304, 3–19 (1999). blotting with anti-TFIIB antibodies. 17. Mayer, R. T., Holman, G. M. & Bridges, A. C. Phosphorescence detection method for purine- containing compounds on thin-layer chromatograms. J. Chromatogr. 90, 390–391 (1974). Proteolytic determination of acetylation sites 18. -
Vesicoureteral Reflux and the Extracellular Matrix Connection
Vesicoureteral reflux and the extracellular matrix connection Fatima Tokhmafshan, Patrick D. Brophy, Rasheed A. Gbadegesin & Indra R. Gupta Pediatric Nephrology Journal of the International Pediatric Nephrology Association ISSN 0931-041X Pediatr Nephrol DOI 10.1007/s00467-016-3386-5 1 23 Your article is protected by copyright and all rights are held exclusively by IPNA. This e- offprint is for personal use only and shall not be self-archived in electronic repositories. If you wish to self-archive your article, please use the accepted manuscript version for posting on your own website. You may further deposit the accepted manuscript version in any repository, provided it is only made publicly available 12 months after official publication or later and provided acknowledgement is given to the original source of publication and a link is inserted to the published article on Springer's website. The link must be accompanied by the following text: "The final publication is available at link.springer.com”. 1 23 Author's personal copy Pediatr Nephrol DOI 10.1007/s00467-016-3386-5 REVIEW Vesicoureteral reflux and the extracellular matrix connection Fatima Tokhmafshan1 & Patrick D. Brophy 2 & Rasheed A. Gbadegesin3,4 & Indra R. Gupta1,5 Received: 22 October 2015 /Revised: 18 March 2016 /Accepted: 21 March 2016 # IPNA 2016 Abstract Primary vesicoureteral reflux (VUR) is a common Introduction pediatric condition due to a developmental defect in the ureterovesical junction. The prevalence of VUR among indi- The ureterovesical junction (UVJ) is a critical structure in the viduals with connective tissue disorders, as well as the impor- urinary tract. It protects the low-pressure upper urinary tract from tance of the ureter and bladder wall musculature for the anti- the intermittent high pressure in the bladder.