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Agrawal N, Lehtonen SI, Uusi-Mäkelä M, Jain P, Viitala S, Määttä JAE, Kähkönen N, Azizi L, Riihimäki TA, Kulomaa MS, Johnson MS, Hytönen VP, Airenne TT. Molecular features of steroid-binding antidins and their use for assaying serum progesterone. PLoS One 2019; 14:e0212339. [PMID: 30785944 PMCID: PMC6382169 DOI: 10.1371/journal.pone.0212339] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 01/31/2019] [Indexed: 11/23/2022] Open
Abstract
Chicken avidin (Avd) and streptavidin from Streptomyces avidinii are extensively used in bionanotechnology due to their extremely tight binding to biotin (Kd ~ 10−15 M for chicken Avd). We previously reported engineered Avds known as antidins, which have micro- to nanomolar affinities for steroids, non-natural ligands of Avd. Here, we report the 2.8 Å X-ray structure of the sbAvd-2 (I117Y) antidin co-crystallized with progesterone. We describe the creation of new synthetic phage display libraries and report the experimental as well as computational binding analysis of progesterone-binding antidins. We introduce a next-generation antidin with 5 nM binding affinity for progesterone, and demonstrate the use of antidins for measuring progesterone in serum samples. Our data give insights on how to engineer and alter the binding preferences of Avds and to develop better molecular tools for modern bionanotechnological applications.
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Affiliation(s)
- Nitin Agrawal
- Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, Turku, Finland
| | - Soili I. Lehtonen
- BioMediTech Institute and Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Meri Uusi-Mäkelä
- BioMediTech Institute and Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Purvi Jain
- BioMediTech Institute and Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Sari Viitala
- University of Eastern Finland, School of Pharmacy, Kuopio, Finland
| | - Juha A. E. Määttä
- BioMediTech Institute and Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Niklas Kähkönen
- BioMediTech Institute and Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Latifeh Azizi
- BioMediTech Institute and Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Tiina A. Riihimäki
- BioMediTech Institute and Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Markku S. Kulomaa
- BioMediTech Institute and Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Mark S. Johnson
- Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, Turku, Finland
| | - Vesa P. Hytönen
- BioMediTech Institute and Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Fimlab Laboratories, Tampere, Finland
- * E-mail: (TTA); (VPH)
| | - Tomi T. Airenne
- Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, Turku, Finland
- * E-mail: (TTA); (VPH)
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Kuosmanen SM, Viitala S, Laitinen T, Peräkylä M, Pölönen P, Kansanen E, Leinonen H, Raju S, Wienecke-Baldacchino A, Närvänen A, Poso A, Heinäniemi M, Heikkinen S, Levonen AL. The Effects of Sequence Variation on Genome-wide NRF2 Binding--New Target Genes and Regulatory SNPs. Nucleic Acids Res 2016; 44:1760-75. [PMID: 26826707 PMCID: PMC4770247 DOI: 10.1093/nar/gkw052] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Accepted: 01/16/2016] [Indexed: 12/11/2022] Open
Abstract
Transcription factor binding specificity is crucial for proper target gene regulation. Motif discovery algorithms identify the main features of the binding patterns, but the accuracy on the lower affinity sites is often poor. Nuclear factor E2-related factor 2 (NRF2) is a ubiquitous redox-activated transcription factor having a key protective role against endogenous and exogenous oxidant and electrophile stress. Herein, we decipher the effects of sequence variation on the DNA binding sequence of NRF2, in order to identify both genome-wide binding sites for NRF2 and disease-associated regulatory SNPs (rSNPs) with drastic effects on NRF2 binding. Interactions between NRF2 and DNA were studied using molecular modelling, and NRF2 chromatin immunoprecipitation-sequence datasets together with protein binding microarray measurements were utilized to study binding sequence variation in detail. The binding model thus generated was used to identify genome-wide binding sites for NRF2, and genomic binding sites with rSNPs that have strong effects on NRF2 binding and reside on active regulatory elements in human cells. As a proof of concept, miR-126–3p and -5p were identified as NRF2 target microRNAs, and a rSNP (rs113067944) residing on NRF2 target gene (Ferritin, light polypeptide, FTL) promoter was experimentally verified to decrease NRF2 binding and result in decreased transcriptional activity.
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Affiliation(s)
- Suvi M Kuosmanen
- Department of Biotechnology and Molecular Medicine, A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, FIN-70211 Kuopio, Finland
| | - Sari Viitala
- School of Pharmacy, University of Eastern Finland, FIN-70211 Kuopio, Finland
| | - Tuomo Laitinen
- School of Pharmacy, University of Eastern Finland, FIN-70211 Kuopio, Finland
| | - Mikael Peräkylä
- School of Pharmacy, University of Eastern Finland, FIN-70211 Kuopio, Finland
| | - Petri Pölönen
- Department of Biotechnology and Molecular Medicine, A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, FIN-70211 Kuopio, Finland Institute of Biomedicine, School of Medicine, University of Eastern Finland, FIN-70211 Kuopio, Finland
| | - Emilia Kansanen
- Department of Biotechnology and Molecular Medicine, A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, FIN-70211 Kuopio, Finland
| | - Hanna Leinonen
- Department of Biotechnology and Molecular Medicine, A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, FIN-70211 Kuopio, Finland
| | - Suresh Raju
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, FIN-70211 Kuopio, Finland
| | | | - Ale Närvänen
- School of Pharmacy, University of Eastern Finland, FIN-70211 Kuopio, Finland
| | - Antti Poso
- School of Pharmacy, University of Eastern Finland, FIN-70211 Kuopio, Finland
| | - Merja Heinäniemi
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, FIN-70211 Kuopio, Finland
| | - Sami Heikkinen
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, FIN-70211 Kuopio, Finland
| | - Anna-Liisa Levonen
- Department of Biotechnology and Molecular Medicine, A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, FIN-70211 Kuopio, Finland
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Huhtala T, Kaikkonen MU, Lesch HP, Viitala S, Ylä-Herttuala S, Närvänen A. Biodistribution and antitumor effect of Cetuximab-targeted lentivirus. Nucl Med Biol 2013; 41:77-83. [PMID: 24267054 DOI: 10.1016/j.nucmedbio.2013.10.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2013] [Revised: 09/18/2013] [Accepted: 10/02/2013] [Indexed: 10/26/2022]
Abstract
Viral vectors are central tools for gene therapy. Targeting of the vector to desired tissues followed by expression of the therapeutic gene forms one of the most critical points in effective therapy. In this study we used streptavidin-displaying lentivirus conjugated to biotinylated anti-epidermal growth factor receptor (EGFR) antibody (Cetuximab) to target vector specifically to ovarian tumors. Biodistribution of the targeted virus was studied in nude mice with orthotropic SKOV-3m human ovarian carcinoma xenografts. Radiolabeled antibodies were conjugated to streptavidin-displaying lentiviruses and biodistribution of the virus after the intravenous delivery to tumor-bearing mice was monitored up to 6 days using combined SPECT/CT imaging modality. Organ samples were collected post mortem and specific organ activities were measured. The integration of lentivirus vectors in collected tissue samples was analyzed using qPCR and the expression of green fluorescent protein (GFP)-transgene was tested by enzyme-linked immunosorbent assay. Our results showed that lentiviruses conjugated to Cetuximab (Cet-LV) or control human IgG (IgG-LV) accumulated mainly to the liver and spleen of the mice and to lower extent to lung, kidneys and tumors. Strikingly, in 50% of the mice injected with cetuximab-targeted lentivirus no tumor tissue was found, whereas the remaining half showed a significant decrease in tumor size. We hypothesize/present data that lentivirus-mediated INF-αβ production together with tumor targeting could function as an effective antitumor treatment.
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Affiliation(s)
- Tuulia Huhtala
- University of Eastern Finland, A.I. Virtanen institute, Department of Biotechnology and Molecular Medicine, P.O.B. 1627, 70211 Kuopio, Finland; Biocenter Kuopio, P.O.B. 1627, 70211 Kuopio, Finland
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Varvio SL, Iso-Touru T, Kantanen J, Viitala S, Tapio I, Mäki-Tanila A, Zerabruk M, Vilkki J. Molecular anatomy of the cytoplasmic domain of bovine growth hormone receptor, a quantitative trait locus. Proc Biol Sci 2008; 275:1525-34. [PMID: 18381258 DOI: 10.1098/rspb.2008.0181] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Quantitative trait loci (QTL) studies have indicated growth hormone receptor (GHR) as a candidate gene affecting cattle milk yield and composition. In order to characterize genetic variation at GHR in cattle, we studied European and East African breeds with different histories of selection, and Bos grunniens, Ovis aries, Sus scrofa, Bison bison and Rangifer tarandus as references. We sequenced most of the cytoplasmic domain (900 bp of exon 10), 89 bp of exon 8, including the putative causative mutation for the QTL effect, and 390 bp of intron 8 for comparison. In the cytoplasmic domain, seven synonymous and seven non-synonymous single nucleotide polymorphisms (SNP) were identified in cattle. Three non-synonymous SNPs were found in sheep and one synonymous SNP in yak, while other studied species were monomorphic. Three major haplotypes were observed, one unique to African breeds, one unique to European breeds and one shared. Bison and yak haplotypes are derivatives of the European haplotype lineage. Most of the exon 10 non-synonymous cattle SNPs appear at phylogenetically highly conserved sites. The polymorphisms in exon 10 cluster around a ruminant-specific tyrosine residue, suggesting that this site may act as an additional signalling domain of GHR in ruminants. Alternative explanations for the persistent polymorphism include balancing selection, hitch-hiking, pleiotropic or sexually antagonistic fitness effects or relaxed functional constraints.
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Affiliation(s)
- S-L Varvio
- Department of Mathematics and Statistics, University of Helsinki, 00014 Helsinki, Finland
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Sahana G, Lund MS, Andersson-Eklund L, Hastings N, Fernandez A, Iso-Touru T, Thomsen B, Viitala S, Sørensen P, Williams JL, Vilkki J. Fine-mapping QTL for mastitis resistance on BTA9 in three Nordic red cattle breeds. Anim Genet 2008; 39:354-62. [PMID: 18462482 PMCID: PMC2655356 DOI: 10.1111/j.1365-2052.2008.01729.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
A QTL affecting clinical mastitis and/or somatic cell score (SCS) has been reported previously on chromosome 9 from studies in 16 families from the Swedish Red and White (SRB), Finnish Ayrshire (FA) and Danish Red (DR) breeds. In order to refine the QTL location, 67 markers were genotyped over the whole chromosome in the 16 original families and 18 additional half-sib families. This enabled linkage disequilibrium information to be used in the analysis. Data were analysed by an approach that combines information from linkage and linkage disequilibrium, which allowed the QTL affecting clinical mastitis to be mapped to a small interval (<1 cM) between the markers BM4208 and INRA084. This QTL showed a pleiotropic effect on SCS in the DR and SRB breeds. Haplotypes associated with variations in mastitis resistance were identified. The haplotypes were predictive in the general population and can be used in marker-assisted selection. Pleiotropic effects of the mastitis QTL were studied for three milk production traits and eight udder conformation traits. This QTL was also associated with yield traits in DR but not in FA or SRB. No QTL were found for udder conformation traits on chromosome 9.
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Affiliation(s)
- G Sahana
- Department of Genetics and Biotechnology, Faculty of Agricultural Sciences, Aarhus University, Research Centre Foulum, DK-8830 Tjele, Denmark.
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Lund M, Sahana G, Andersson-Eklund L, Hastings N, Fernandez A, Schulman N, Thomsen B, Viitala S, Williams J, Sabry A, Viinalass H, Vilkki J. Joint Analysis of Quantitative Trait Loci for Clinical Mastitis and Somatic Cell Score on Five Chromosomes in Three Nordic Dairy Cattle Breeds. J Dairy Sci 2007; 90:5282-90. [DOI: 10.3168/jds.2007-0177] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Palo J, Viitala S. [Diagnosis of brain death]. Duodecim 2002; 116:809-10. [PMID: 11787124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
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